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source: trunk/GSASIIplot.py @ 1649

Last change on this file since 1649 was 1646, checked in by vondreele, 10 years ago
allow search for negative density peaks in charge flip and Fourier maps plot negative density in neutron maps & negative peaks in red
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1	# -- coding: utf-8 --
2	'''
3	GSASIIplot: plotting routines
4	===============================
5
6	'''
7	########### SVN repository information ###################
8	# $Date: 2015-02-11 19:33:27 +0000 (Wed, 11 Feb 2015) $
9	# $Author: vondreele $
10	# $Revision: 1646 $
11	# $URL: trunk/GSASIIplot.py $
12	# $Id: GSASIIplot.py 1646 2015-02-11 19:33:27Z 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: 1646 $")
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	GkDelta = unichr(0x0394)
65
66	class G2PlotMpl(wx.Panel):
67	'needs a doc string'
68	def __init__(self,parent,id=-1,dpi=None,**kwargs):
69	wx.Panel.__init__(self,parent,id=id,**kwargs)
70	mpl.rcParams['legend.fontsize'] = 10
71	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6))
72	self.canvas = Canvas(self,-1,self.figure)
73	self.toolbar = GSASIItoolbar(self.canvas)
74
75	self.toolbar.Realize()
76
77	sizer=wx.BoxSizer(wx.VERTICAL)
78	sizer.Add(self.canvas,1,wx.EXPAND)
79	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
80	self.SetSizer(sizer)
81
82	class G2PlotOgl(wx.Panel):
83	'needs a doc string'
84	def __init__(self,parent,id=-1,dpi=None,**kwargs):
85	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
86	if 'win' in sys.platform: #Windows (& Mac) already double buffered
87	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
88	else: #fix from Jim Hester for X systems
89	attribs = (wx.glcanvas.WX_GL_DOUBLEBUFFER,)
90	self.canvas = wx.glcanvas.GLCanvas(self,-1,attribList=attribs,**kwargs)
91	# create GL context for wx > 2.8
92	i,j= wx.__version__.split('.')[0:2]
93	if int(i)+int(j)/10. > 2.8:
94	self.context = wx.glcanvas.GLContext(self.canvas)
95	self.canvas.SetCurrent(self.context)
96	else:
97	self.context = None
98	self.camera = {}
99	sizer=wx.BoxSizer(wx.VERTICAL)
100	sizer.Add(self.canvas,1,wx.EXPAND)
101	self.SetSizer(sizer)
102
103	class G2Plot3D(wx.Panel):
104	'needs a doc string'
105	def __init__(self,parent,id=-1,dpi=None,**kwargs):
106	wx.Panel.__init__(self,parent,id=id,**kwargs)
107	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
108	self.canvas = Canvas(self,-1,self.figure)
109	self.toolbar = GSASIItoolbar(self.canvas)
110
111	self.toolbar.Realize()
112
113	sizer=wx.BoxSizer(wx.VERTICAL)
114	sizer.Add(self.canvas,1,wx.EXPAND)
115	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
116	self.SetSizer(sizer)
117
118	class G2PlotNoteBook(wx.Panel):
119	'create a tabbed window for plotting'
120	def __init__(self,parent,id=-1):
121	wx.Panel.__init__(self,parent,id=id)
122	#so one can't delete a plot page!!
123	self.nb = wx.aui.AuiNotebook(self, \
124	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
125	sizer = wx.BoxSizer()
126	sizer.Add(self.nb,1,wx.EXPAND)
127	self.SetSizer(sizer)
128	self.status = parent.CreateStatusBar()
129	self.status.SetFieldsCount(2)
130	self.status.SetStatusWidths([150,-1])
131	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
132	self.nb.Bind(wx.EVT_KEY_UP,self.OnNotebookKey)
133
134	self.plotList = []
135
136	def OnNotebookKey(self,event):
137	'''Called when a keystroke event gets picked up by the notebook window
138	rather the child. This is not expected, but somehow it does sometimes
139	on the Mac and perhaps Linux.
140
141	Assume that the page associated with the currently displayed tab
142	has a child, .canvas; give that child the focus and pass it the event.
143	'''
144	try:
145	Page = self.nb.GetPage(self.nb.GetSelection())
146	except ValueError: # occurs with no plot tabs
147	return
148	try:
149	Page.canvas.SetFocus()
150	wx.PostEvent(Page.canvas,event)
151	except AttributeError:
152	pass
153
154	def addMpl(self,name=""):
155	'Add a tabbed page with a matplotlib plot'
156	page = G2PlotMpl(self.nb)
157	self.nb.AddPage(page,name)
158
159	self.plotList.append(name)
160
161	return page.figure
162
163	def add3D(self,name=""):
164	'Add a tabbed page with a 3D plot'
165	page = G2Plot3D(self.nb)
166	self.nb.AddPage(page,name)
167
168	self.plotList.append(name)
169
170	return page.figure
171
172	def addOgl(self,name=""):
173	'Add a tabbed page with an openGL plot'
174	page = G2PlotOgl(self.nb)
175	self.nb.AddPage(page,name)
176
177	self.plotList.append(name)
178
179	return page.figure
180
181	def Delete(self,name):
182	'delete a tabbed page'
183	try:
184	item = self.plotList.index(name)
185	del self.plotList[item]
186	self.nb.DeletePage(item)
187	except ValueError: #no plot of this name - do nothing
188	return
189
190	def clear(self):
191	'clear all pages from plot window'
192	while self.nb.GetPageCount():
193	self.nb.DeletePage(0)
194	self.plotList = []
195	self.status.DestroyChildren()
196
197	def Rename(self,oldName,newName):
198	'rename a tab'
199	try:
200	item = self.plotList.index(oldName)
201	self.plotList[item] = newName
202	self.nb.SetPageText(item,newName)
203	except ValueError: #no plot of this name - do nothing
204	return
205
206	def OnPageChanged(self,event):
207	'respond to someone pressing a tab on the plot window'
208	if self.plotList:
209	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
210	self.status.DestroyChildren() #get rid of special stuff on status bar
211
212	class GSASIItoolbar(Toolbar):
213	'Override the matplotlib toolbar so we can add more icons'
214	ON_MPL_HELP = wx.NewId()
215	ON_MPL_KEY = wx.NewId()
216	arrows = {}
217	for direc in ('left','right','up','down','Expand X',
218	'Shrink X','Expand Y','Shrink Y'):
219	arrows[direc] = wx.NewId()
220	def __init__(self,plotCanvas):
221	'''Adds additional icons to toolbar'''
222	Toolbar.__init__(self,plotCanvas)
223	self.plotCanvas = plotCanvas
224	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6 # remove one button, nos. start at 1!
225	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
226	self.parent = self.GetParent()
227	key = os.path.join(os.path.split(__file__)[0],'key.ico')
228	self.AddSimpleTool(self.ON_MPL_KEY,_load_bitmap(key),'Key press','Select key press')
229	wx.EVT_TOOL(self,self.ON_MPL_KEY,self.OnKey)
230	help = os.path.join(os.path.split(__file__)[0],'help.ico')
231	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
232	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
233	# add arrow keys to control zooming
234	for direc in ('left','right','up','down'):
235	wx.EVT_TOOL(self,self.arrows[direc],self.OnArrow)
236	icon = os.path.join(os.path.split(__file__)[0],direc[0]+'arrow.ico')
237	self.AddSimpleTool(self.arrows[direc],_load_bitmap(icon),
238	'Shift '+direc,'Shift plot '+direc)
239	for direc in ('Expand X','Shrink X','Expand Y','Shrink Y'):
240	fil = ''.join([i[0].lower() for i in direc.split()]+['arrow.ico'])
241	wx.EVT_TOOL(self,self.arrows[direc],self.OnArrow)
242	icon = os.path.join(os.path.split(__file__)[0],fil)
243	self.AddSimpleTool(self.arrows[direc],_load_bitmap(icon),
244	direc,'Zoom: '+direc)
245	def OnArrow(self,event):
246	'reposition limits to scan or zoom by button press'
247	ax = self.plotCanvas.figure.get_axes()[0]
248	xmin,xmax,ymin,ymax = ax.axis()
249	#print xmin,xmax,ymin,ymax
250	if event.Id == self.arrows['right']:
251	delta = (xmax-xmin)/10.
252	xmin -= delta
253	xmax -= delta
254	elif event.Id == self.arrows['left']:
255	delta = (xmax-xmin)/10.
256	xmin += delta
257	xmax += delta
258	elif event.Id == self.arrows['up']:
259	delta = (ymax-ymin)/10.
260	ymin -= delta
261	ymax -= delta
262	elif event.Id == self.arrows['down']:
263	delta = (ymax-ymin)/10.
264	ymin += delta
265	ymax += delta
266	elif event.Id == self.arrows['Expand X']:
267	delta = (xmax-xmin)/10.
268	xmin += delta
269	xmax -= delta
270	elif event.Id == self.arrows['Expand Y']:
271	delta = (ymax-ymin)/10.
272	ymin += delta
273	ymax -= delta
274	elif event.Id == self.arrows['Shrink X']:
275	delta = (xmax-xmin)/10.
276	xmin -= delta
277	xmax += delta
278	elif event.Id == self.arrows['Shrink Y']:
279	delta = (ymax-ymin)/10.
280	ymin -= delta
281	ymax += delta
282	else:
283	# should not happen!
284	GSASIIpath.IPyBreak()
285	self.parent.toolbar.push_current()
286	ax.axis((xmin,xmax,ymin,ymax))
287	#print xmin,xmax,ymin,ymax
288	self.plotCanvas.figure.canvas.draw()
289	self.parent.toolbar.draw()
290	# self.parent.toolbar.push_current()
291
292	def OnHelp(self,event):
293	'Respond to press of help button on plot toolbar'
294	Page = self.GetParent().GetParent()
295	pageNo = Page.GetSelection()
296	bookmark = Page.GetPageText(pageNo)
297	bookmark = bookmark.strip(')').replace('(','_')
298	G2gd.ShowHelp(bookmark,self.TopLevelParent)
299	def OnKey(self,event):
300	'''Provide user with list of keystrokes defined for plot as well as an
301	alternate way to access the same functionality
302	'''
303	parent = self.GetParent()
304	if parent.Choice:
305	dlg = wx.SingleChoiceDialog(parent,'Select','Key press',list(parent.Choice))
306	if dlg.ShowModal() == wx.ID_OK:
307	sel = dlg.GetSelection()
308	event.key = parent.Choice[sel][0]
309	parent.keyPress(event)
310	dlg.Destroy()
311
312	################################################################################
313	##### PlotSngl
314	################################################################################
315
316	def PlotSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=''):
317	'''Structure factor plotting package - displays zone of reflections as rings proportional
318	to F, F**2, etc. as requested
319	'''
320	from matplotlib.patches import Circle,CirclePolygon
321	global HKL,HKLF
322
323	def OnSCKeyPress(event):
324	i = zones.index(Data['Zone'])
325	newPlot = False
326	pwdrChoice = {'f':'Fo','s':'Fosq','u':'Unit Fc'}
327	hklfChoice = {'1':'\|DFsq\|>sig','3':'\|DFsq\|>3sig','w':'\|DFsq\|/sig','f':'Fo','s':'Fosq','i':'Unit Fc'}
328	if event.key == 'h':
329	Data['Zone'] = '100'
330	newPlot = True
331	elif event.key == 'k':
332	Data['Zone'] = '010'
333	newPlot = True
334	elif event.key == 'l':
335	Data['Zone'] = '001'
336	newPlot = True
337	elif event.key == 'i':
338	Data['Scale'] *= 1.1
339	elif event.key == 'd':
340	Data['Scale'] /= 1.1
341	elif event.key == '+':
342	Data['Layer'] = min(Data['Layer']+1,HKLmax[i])
343	elif event.key == '-':
344	Data['Layer'] = max(Data['Layer']-1,HKLmin[i])
345	elif event.key == '0':
346	Data['Layer'] = 0
347	Data['Scale'] = 1.0
348	elif event.key in hklfChoice and 'HKLF' in Name:
349	Data['Type'] = hklfChoice[event.key]
350	newPlot = True
351	elif event.key in pwdrChoice and 'PWDR' in Name:
352	Data['Type'] = pwdrChoice[event.key]
353	newPlot = True
354	PlotSngl(G2frame,newPlot,Data,hklRef,Title)
355
356	def OnSCMotion(event):
357	xpos = event.xdata
358	if xpos:
359	xpos = round(xpos) #avoid out of frame mouse position
360	ypos = round(event.ydata)
361	zpos = Data['Layer']
362	if '100' in Data['Zone']:
363	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
364	elif '010' in Data['Zone']:
365	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
366	elif '001' in Data['Zone']:
367	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
368	Page.canvas.SetToolTipString(HKLtxt)
369	G2frame.G2plotNB.status.SetStatusText('HKL = '+HKLtxt,0)
370	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
371
372	def OnSCPress(event):
373	zpos = Data['Layer']
374	xpos = event.xdata
375	if xpos:
376	pos = int(round(event.xdata)),int(round(event.ydata))
377	if '100' in Data['Zone']:
378	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
379	hkl = np.array([zpos,pos[0],pos[1]])
380	elif '010' in Data['Zone']:
381	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
382	hkl = np.array([pos[0],zpos,pos[1]])
383	elif '001' in Data['Zone']:
384	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
385	hkl = np.array([pos[0],pos[1],zpos])
386	h,k,l = hkl
387	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
388	if len(hklf):
389	Fosq,sig,Fcsq = hklf[0]
390	HKLtxt = '( %.2f %.3f %.2f %.2f)'%(Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
391	G2frame.G2plotNB.status.SetStatusText('Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt,1)
392
393	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
394	if not Title:
395	Title = Name
396	try:
397	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
398	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
399	if not newPlot:
400	Plot = Page.figure.gca() #get previous powder plot & get limits
401	xylim = Plot.get_xlim(),Plot.get_ylim()
402	Page.figure.clf()
403	Plot = Page.figure.gca() #get a fresh plot after clf()
404	except ValueError:
405	Plot = G2frame.G2plotNB.addMpl('Structure Factors').gca()
406	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
407	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
408	Page.canvas.mpl_connect('button_press_event', OnSCPress)
409	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
410	Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
411	Page.keyPress = OnSCKeyPress
412	Page.Choice = (' key press','i: increase scale','d: decrease scale',
413	'h: select 100 zone','k: select 010 zone','l: select 001 zone',
414	'f: select Fo','s: select Fosq','u: select unit Fc',
415	'+: increase index','-: decrease index','0: zero layer',)
416	if 'HKLF' in Name:
417	Page.Choice += ('w: select \|DFsq\|/sig','1: select \|DFsq\|>sig','3: select \|DFsq\|>3sig',)
418	Page.SetFocus()
419
420	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
421	Plot.set_aspect(aspect='equal')
422
423	Type = Data['Type']
424	scale = Data['Scale']
425	HKLmax = Data['HKLmax']
426	HKLmin = Data['HKLmin']
427	FosqMax = Data['FoMax']
428	Super = Data['Super']
429	SuperVec = []
430	if Super:
431	SuperVec = np.array(Data['SuperVec'][0])
432	FoMax = math.sqrt(FosqMax)
433	xlabel = ['k, h=','h, k=','h, l=']
434	ylabel = ['l','l','k']
435	zones = ['100','010','001']
436	pzone = [[1,2],[0,2],[0,1]]
437	izone = zones.index(Data['Zone'])
438	Plot.set_title(Data['Type']+' for '+Title)
439	HKL = []
440	HKLF = []
441	time0 = time.time()
442	for refl in hklRef:
443	H = refl[:3]
444	if 'HKLF' in Name:
445	Fosq,sig,Fcsq = refl[5+Super:8+Super]
446	else:
447	Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super]
448	if Super:
449	HKL.append(H+SuperVec*refl[3])
450	else:
451	HKL.append(H)
452	HKLF.append([Fosq,sig,Fcsq])
453	if H[izone] == Data['Layer']:
454	A = 0
455	B = 0
456	if Type == 'Fosq':
457	A = scale*Fosq/FosqMax
458	B = scale*Fcsq/FosqMax
459	C = abs(A-B)
460	elif Type == 'Fo':
461	A = scale*math.sqrt(max(0,Fosq))/FoMax
462	B = scale*math.sqrt(max(0,Fcsq))/FoMax
463	C = abs(A-B)
464	elif Type == 'Unit Fc':
465	A = scale/2
466	B = scale/2
467	C = 0.0
468	if Fcsq and Fosq > 0:
469	A *= min(1.0,Fosq/Fcsq)
470	C = abs(A-B)
471	elif Type == '\|DFsq\|/sig':
472	if sig > 0.:
473	A = (Fosq-Fcsq)/(3*sig)
474	B = 0
475	elif Type == '\|DFsq\|>sig':
476	if sig > 0.:
477	A = (Fosq-Fcsq)/(3*sig)
478	if abs(A) < 1.0: A = 0
479	B = 0
480	elif Type == '\|DFsq\|>3sig':
481	if sig > 0.:
482	A = (Fosq-Fcsq)/(3*sig)
483	if abs(A) < 3.0: A = 0
484	B = 0
485	if Super:
486	h = H+SuperVec*refl[3]
487	else:
488	h = H
489	xy = (h[pzone[izone][0]],h[pzone[izone][1]])
490	if Type in ['\|DFsq\|/sig','\|DFsq\|>sig','\|DFsq\|>3sig']:
491	if A > 0.0:
492	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
493	else:
494	Plot.add_artist(Circle(xy,radius=-A,ec='r',fc='w'))
495	else:
496	if A > 0.0 and A > B:
497	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
498	if B:
499	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
500	if A < B:
501	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
502	radius = C
503	if radius > 0:
504	if A > B:
505	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
506	else:
507	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
508	# print 'plot time: %.3f'%(time.time()-time0)
509	HKL = np.array(HKL)
510	HKLF = np.array(HKLF)
511	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
512	Plot.set_ylabel(ylabel[izone],fontsize=12)
513	if not newPlot:
514	Page.toolbar.push_current()
515	Plot.set_xlim(xylim[0])
516	Plot.set_ylim(xylim[1])
517	# xylim = []
518	Page.toolbar.push_current()
519	Page.toolbar.draw()
520	else:
521	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
522	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
523	Page.canvas.draw()
524
525	################################################################################
526	##### Plot3DSngl
527	################################################################################
528
529	def Plot3DSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=False):
530	'''3D Structure factor plotting package - displays reflections as rings proportional
531	to F, F**2, etc. as requested as 3D array
532	'''
533
534	global ifBox
535	ifBox = False
536	def OnKeyBox(event):
537	mode = cb.GetValue()
538	if mode in ['jpeg','bmp','tiff',]:
539	try:
540	import Image as Im
541	except ImportError:
542	try:
543	from PIL import Image as Im
544	except ImportError:
545	print "PIL/pillow Image module not present. Cannot save images without this"
546	raise Exception("PIL/pillow Image module not found")
547	try:
548	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
549	except NameError: #for when generalData doesn't exist!
550	Fname = os.path.join(Mydir,'unknown'+'.'+mode)
551	print Fname+' saved'
552	size = Page.canvas.GetSize()
553	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
554	if mode in ['jpeg',]:
555	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
556	im = Im.new("RGBA", (size[0],size[1]))
557	else:
558	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
559	im = Im.new("RGB", (size[0],size[1]))
560	im.fromstring(Pix)
561	im.save(Fname,mode)
562	cb.SetValue(' save as/key:')
563	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
564	else:
565	event.key = cb.GetValue()[0]
566	cb.SetValue(' save as/key:')
567	wx.CallAfter(OnKey,event)
568	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
569
570	def OnKey(event): #on key UP!!
571	global ifBox
572	Choice = {'F':'Fo','S':'Fosq','U':'Unit','D':'dFsq','W':'dFsq/sig'}
573	try:
574	keyCode = event.GetKeyCode()
575	if keyCode > 255:
576	keyCode = 0
577	key = chr(keyCode)
578	except AttributeError: #if from OnKeyBox above
579	key = str(event.key).upper()
580	if key in ['C']:
581	drawingData['viewPoint'][0] = drawingData['default']
582	drawingData['viewDir'] = [0,0,1]
583	drawingData['oldxy'] = []
584	V0 = np.array([0,0,1])
585	V = np.inner(Amat,V0)
586	V /= np.sqrt(np.sum(V**2))
587	A = np.arccos(np.sum(V*V0))
588	Q = G2mth.AV2Q(A,[0,1,0])
589	drawingData['Quaternion'] = Q
590	Q = drawingData['Quaternion']
591	elif key in 'B':
592	ifBox = not ifBox
593	elif key == '+':
594	Data['Scale'] *= 1.25
595	elif key == '-':
596	Data['Scale'] /= 1.25
597	elif key == '0':
598	Data['Scale'] = 1.0
599	elif key == 'I':
600	Data['Iscale'] = not Data['Iscale']
601	elif key in Choice:
602	Data['Type'] = Choice[key]
603	Draw('key')
604
605	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
606	if Title: #NB: save image as e.g. jpeg will fail if False; MyDir is unknown
607	generalData = G2frame.GetPhaseData()[Title]['General']
608	cell = generalData['Cell'][1:7]
609	Mydir = generalData['Mydir']
610	else:
611	cell = [10,10,10,90,90,90]
612	Mydir = G2frame.dirname
613	drawingData = Data['Drawing']
614	Super = Data['Super']
615	SuperVec = []
616	if Super:
617	SuperVec = np.array(Data['SuperVec'][0])
618	defaultViewPt = copy.copy(drawingData['viewPoint'])
619	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
620	Gmat,gmat = G2lat.cell2Gmat(cell)
621	invcell = G2lat.Gmat2cell(Gmat)
622	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
623	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
624	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Bmat,[0,0,1]))
625	Wt = np.array([255,255,255])
626	Rd = np.array([255,0,0])
627	Gr = np.array([0,255,0])
628	wxGreen = wx.Colour(0,255,0)
629	Bl = np.array([0,0,255])
630	Or = np.array([255,128,0])
631	wxOrange = wx.Colour(255,128,0)
632	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]])
633	uEdges = np.array([
634	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
635	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
636	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
637	uColors = [Rd,Gr,Bl, Wt,Wt,Wt, Wt,Wt,Wt, Wt,Wt,Wt]
638	def FillHKLRC():
639	R = np.zeros(len(hklRef))
640	C = []
641	HKL = []
642	RC = []
643	for i,refl in enumerate(hklRef):
644	H = refl[:3]
645	if 'HKLF' in Name:
646	Fosq,sig,Fcsq = refl[5+Super:8+Super]
647	else:
648	Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super]
649	if Super:
650	HKL.append(H+SuperVec*refl[3])
651	else:
652	HKL.append(H)
653	if Data['Type'] == 'Unit':
654	R[i] = 0.1
655	C.append(Gr)
656	elif Data['Type'] == 'Fosq':
657	if Fosq > 0:
658	R[i] = Fosq
659	C.append(Gr)
660	else:
661	R[i] = -Fosq
662	C.append(Rd)
663	elif Data['Type'] == 'Fo':
664	if Fosq > 0:
665	R[i] = np.sqrt(Fosq)
666	C.append(Gr)
667	else:
668	R[i] = np.sqrt(-Fosq)
669	C.append(Rd)
670	elif Data['Type'] == 'dFsq/sig':
671	dFsig = (Fosq-Fcsq)/sig
672	if dFsig > 0:
673	R[i] = dFsig
674	C.append(Gr)
675	else:
676	R[i] = -dFsig
677	C.append(Rd)
678	elif Data['Type'] == 'dFsq':
679	dF = Fosq-Fcsq
680	if dF > 0:
681	R[i] = dF
682	C.append(Gr)
683	else:
684	R[i] = -dF
685	C.append(Rd)
686	R /= np.max(R)
687	R *= Data['Scale']
688	R = np.where(R<1.e-5,1.e-5,R)
689	if Data['Iscale']:
690	R = np.where(R<=1.,R,1.)
691	C = np.array(C)
692	C = (C.T*R).T
693	R = np.ones_like(R)*0.05
694	return HKL,zip(list(R),C)
695
696	def SetTranslation(newxy):
697	#first get translation vector in screen coords.
698	oldxy = drawingData['oldxy']
699	if not len(oldxy): oldxy = list(newxy)
700	dxy = newxy-oldxy
701	drawingData['oldxy'] = list(newxy)
702	V = np.array([-dxy[0],dxy[1],0.])
703	#then transform to rotated crystal coordinates & apply to view point
704	Q = drawingData['Quaternion']
705	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
706	Tx,Ty,Tz = drawingData['viewPoint'][0]
707	Tx += V[0]*0.1
708	Ty += V[1]*0.1
709	Tz += V[2]*0.1
710	drawingData['viewPoint'][0] = Tx,Ty,Tz
711
712	def SetRotation(newxy):
713	'Perform a rotation in x-y space due to a left-mouse drag'
714	#first get rotation vector in screen coords. & angle increment
715	oldxy = drawingData['oldxy']
716	if not len(oldxy): oldxy = list(newxy)
717	dxy = newxy-oldxy
718	drawingData['oldxy'] = list(newxy)
719	V = np.array([dxy[1],dxy[0],0.])
720	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
721	if not A: return # nothing changed, nothing to do
722	# next transform vector back to xtal coordinates via inverse quaternion
723	# & make new quaternion
724	Q = drawingData['Quaternion']
725	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
726	DQ = G2mth.AVdeg2Q(A,V)
727	Q = G2mth.prodQQ(Q,DQ)
728	drawingData['Quaternion'] = Q
729	# finally get new view vector - last row of rotation matrix
730	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
731	VD /= np.sqrt(np.sum(VD**2))
732	drawingData['viewDir'] = VD
733
734	def SetRotationZ(newxy):
735	#first get rotation vector (= view vector) in screen coords. & angle increment
736	View = glGetIntegerv(GL_VIEWPORT)
737	cent = [View[2]/2,View[3]/2]
738	oldxy = drawingData['oldxy']
739	if not len(oldxy): oldxy = list(newxy)
740	dxy = newxy-oldxy
741	drawingData['oldxy'] = list(newxy)
742	V = drawingData['viewDir']
743	A = [0,0]
744	A[0] = dxy[1]*.25
745	A[1] = dxy[0]*.25
746	if newxy[0] > cent[0]:
747	A[0] *= -1
748	if newxy[1] < cent[1]:
749	A[1] *= -1
750	# next transform vector back to xtal coordinates & make new quaternion
751	Q = drawingData['Quaternion']
752	V = np.inner(Amat,V)
753	Qx = G2mth.AVdeg2Q(A[0],V)
754	Qy = G2mth.AVdeg2Q(A[1],V)
755	Q = G2mth.prodQQ(Q,Qx)
756	Q = G2mth.prodQQ(Q,Qy)
757	drawingData['Quaternion'] = Q
758
759	def OnMouseDown(event):
760	xy = event.GetPosition()
761	drawingData['oldxy'] = list(xy)
762
763	def OnMouseMove(event):
764	if event.ShiftDown(): #don't want any inadvertant moves when picking
765	return
766	newxy = event.GetPosition()
767
768	if event.Dragging():
769	if event.LeftIsDown():
770	SetRotation(newxy)
771	Q = drawingData['Quaternion']
772	elif event.RightIsDown():
773	SetTranslation(newxy)
774	Tx,Ty,Tz = drawingData['viewPoint'][0]
775	elif event.MiddleIsDown():
776	SetRotationZ(newxy)
777	Q = drawingData['Quaternion']
778	Draw('move')
779
780	def OnMouseWheel(event):
781	if event.ShiftDown():
782	return
783	drawingData['cameraPos'] += event.GetWheelRotation()/120.
784	drawingData['cameraPos'] = max(0.1,min(20.00,drawingData['cameraPos']))
785	Draw('wheel')
786
787	def SetBackground():
788	R,G,B,A = Page.camera['backColor']
789	glClearColor(R,G,B,A)
790	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
791
792	def SetLights():
793	glEnable(GL_DEPTH_TEST)
794	glShadeModel(GL_SMOOTH)
795	glEnable(GL_LIGHTING)
796	glEnable(GL_LIGHT0)
797	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
798	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
799	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
800
801	def RenderBox(x,y,z):
802	xyz = np.array([x,y,z])
803	glEnable(GL_COLOR_MATERIAL)
804	glLineWidth(1)
805	glPushMatrix()
806	glTranslate(x,y,z)
807	glColor4ubv([0,0,0,0])
808	glBegin(GL_LINES)
809	for line,color in zip(uEdges,uColors):
810	glColor3ubv(color)
811	glVertex3fv(line[0])
812	glVertex3fv(line[1])
813	glEnd()
814	glPopMatrix()
815	glColor4ubv([0,0,0,0])
816	glDisable(GL_COLOR_MATERIAL)
817
818	def RenderUnitVectors(x,y,z):
819	xyz = np.array([x,y,z])
820	glEnable(GL_COLOR_MATERIAL)
821	glLineWidth(1)
822	glPushMatrix()
823	glTranslate(x,y,z)
824	glBegin(GL_LINES)
825	for line,color in zip(uEdges,uColors)[:3]:
826	glColor3ubv(color)
827	glVertex3fv(-line[1])
828	glVertex3fv(line[1])
829	glEnd()
830	glPopMatrix()
831	glColor4ubv([0,0,0,0])
832	glDisable(GL_COLOR_MATERIAL)
833
834	def RenderDots(XYZ,RC):
835	glEnable(GL_COLOR_MATERIAL)
836	XYZ = np.array(XYZ)
837	glPushMatrix()
838	for xyz,rc in zip(XYZ,RC):
839	x,y,z = xyz
840	r,c = rc
841	glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,c)
842	glPointSize(r*50)
843	glBegin(GL_POINTS)
844	glVertex3fv(xyz)
845	glEnd()
846	glPopMatrix()
847	glColor4ubv([0,0,0,0])
848	glDisable(GL_COLOR_MATERIAL)
849
850	def Draw(caller=''):
851	#useful debug?
852	# if caller:
853	# print caller
854	# end of useful debug
855	G2frame.G2plotNB.status.SetStatusText('Plot type = %s for %s'%(Data['Type'],Name),1)
856	VS = np.array(Page.canvas.GetSize())
857	aspect = float(VS[0])/float(VS[1])
858	cPos = drawingData['cameraPos']
859	Zclip = drawingData['Zclip']*cPos/20.
860	Q = drawingData['Quaternion']
861	Tx,Ty,Tz = drawingData['viewPoint'][0]
862	G,g = G2lat.cell2Gmat(cell)
863	GS = G
864	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
865	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
866	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
867
868	HKL,RC = FillHKLRC()
869
870	SetBackground()
871	glInitNames()
872	glPushName(0)
873
874	glMatrixMode(GL_PROJECTION)
875	glLoadIdentity()
876	glViewport(0,0,VS[0],VS[1])
877	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
878	gluLookAt(0,0,cPos,0,0,0,0,1,0)
879	SetLights()
880
881	glMatrixMode(GL_MODELVIEW)
882	glLoadIdentity()
883	matRot = G2mth.Q2Mat(Q)
884	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
885	glMultMatrixf(matRot.T)
886	glMultMatrixf(B4mat.T)
887	glTranslate(-Tx,-Ty,-Tz)
888	x,y,z = drawingData['viewPoint'][0]
889	if ifBox:
890	RenderBox(x,y,z)
891	else:
892	RenderUnitVectors(x,y,z)
893	RenderUnitVectors(0,0,0)
894	RenderDots(HKL,RC)
895	time0 = time.time()
896	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
897	Page.canvas.SwapBuffers()
898
899	# PlotStructure execution starts here (N.B. initialization above)
900	try:
901	plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors')
902	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
903	except ValueError:
904	Plot = G2frame.G2plotNB.addOgl('3D Structure Factors')
905	plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors')
906	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
907	Page.views = False
908	view = False
909	altDown = False
910	Font = Page.GetFont()
911	Page.SetFocus()
912	Page.Choice = None
913	choice = [' save as/key:','jpeg','tiff','bmp','c: recenter to default','b: toggle box ','+: increase scale',
914	'-: decrease scale','f: Fobs','s: Fobs**2','u: unit','d: Fo-Fc','w: DF/sig','i: toggle intensity scaling']
915	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
916	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
917	cb.SetValue(' save as/key:')
918	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
919	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
920	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
921	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
922	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
923	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
924	# Page.canvas.Bind(wx.EVT_SIZE, OnSize)
925	Page.camera['position'] = drawingData['cameraPos']
926	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
927	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
928	try:
929	Page.canvas.SetCurrent()
930	except:
931	pass
932	Draw('main')
933	# if firstCall: Draw('main') # draw twice the first time that graphics are displayed
934
935
936	################################################################################
937	##### PlotPatterns
938	################################################################################
939
940	def PlotPatterns(G2frame,newPlot=False,plotType='PWDR'):
941	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
942	2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I
943	plotting available.
944	'''
945	global HKL
946	global exclLines
947	global DifLine
948	global Ymax
949	plottype = plotType
950
951	def OnPlotKeyPress(event):
952	try: #one way to check if key stroke will work on plot
953	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
954	except TypeError:
955	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1)
956	return
957	newPlot = False
958	if event.key == 'w':
959	G2frame.Weight = not G2frame.Weight
960	if not G2frame.Weight and 'PWDR' in plottype:
961	G2frame.SinglePlot = True
962	newPlot = True
963	elif event.key == 'e' and 'SASD' in plottype:
964	G2frame.ErrorBars = not G2frame.ErrorBars
965	elif event.key == 'b':
966	G2frame.SubBack = not G2frame.SubBack
967	if not G2frame.SubBack:
968	G2frame.SinglePlot = True
969	elif event.key == 'n':
970	if G2frame.Contour:
971	pass
972	else:
973	G2frame.logPlot = not G2frame.logPlot
974	if not G2frame.logPlot:
975	G2frame.Offset[0] = 0
976	newPlot = True
977	elif event.key == 's' and 'PWDR' in plottype:
978	if G2frame.Contour:
979	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
980	choice.sort()
981	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
982	if dlg.ShowModal() == wx.ID_OK:
983	sel = dlg.GetSelection()
984	G2frame.ContourColor = choice[sel]
985	else:
986	G2frame.ContourColor = 'Paired'
987	dlg.Destroy()
988	elif G2frame.SinglePlot:
989	G2frame.SqrtPlot = not G2frame.SqrtPlot
990	if G2frame.SqrtPlot:
991	G2frame.delOffset = .002
992	G2frame.refOffset = -1.0
993	G2frame.refDelt = .001
994	else:
995	G2frame.delOffset = .02
996	G2frame.refOffset = -1.0
997	G2frame.refDelt = .01
998	newPlot = True
999	elif event.key == 'u' and (G2frame.Contour or not G2frame.SinglePlot):
1000	if G2frame.Contour:
1001	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1002	elif G2frame.Offset[0] < 100.:
1003	G2frame.Offset[0] += 1.
1004	elif event.key == 'd' and (G2frame.Contour or not G2frame.SinglePlot):
1005	if G2frame.Contour:
1006	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1007	elif G2frame.Offset[0] > 0.:
1008	G2frame.Offset[0] -= 1.
1009	elif event.key == 'l' and not G2frame.SinglePlot:
1010	G2frame.Offset[1] -= 1.
1011	elif event.key == 'r' and not G2frame.SinglePlot:
1012	G2frame.Offset[1] += 1.
1013	elif event.key == 'o' and not G2frame.SinglePlot:
1014	G2frame.Cmax = 1.0
1015	G2frame.Offset = [0,0]
1016	elif event.key == 'c' and 'PWDR' in plottype:
1017	newPlot = True
1018	if not G2frame.Contour:
1019	G2frame.SinglePlot = False
1020	G2frame.Offset = [0.,0.]
1021	else:
1022	G2frame.SinglePlot = True
1023	G2frame.Contour = not G2frame.Contour
1024	elif event.key == 'q':
1025	if 'PWDR' in plottype:
1026	newPlot = True
1027	G2frame.qPlot = not G2frame.qPlot
1028	G2frame.dPlot = False
1029	elif 'SASD' in plottype:
1030	newPlot = True
1031	G2frame.sqPlot = not G2frame.sqPlot
1032	elif event.key == 't' and 'PWDR' in plottype:
1033	G2frame.dPlot = not G2frame.dPlot
1034	G2frame.qPlot = False
1035	newPlot = True
1036	elif event.key == 'm':
1037	G2frame.SqrtPlot = False
1038	G2frame.SinglePlot = not G2frame.SinglePlot
1039	newPlot = True
1040	elif event.key == '+':
1041	if G2frame.PickId:
1042	G2frame.PickId = False
1043	elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot
1044	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1045	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1046	'mitchell','sinc','lanczos']
1047	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1048	if dlg.ShowModal() == wx.ID_OK:
1049	sel = dlg.GetSelection()
1050	G2frame.Interpolate = choice[sel]
1051	else:
1052	G2frame.Interpolate = 'nearest'
1053	dlg.Destroy()
1054	else:
1055	print 'no binding for key',event.key
1056	#GSASIIpath.IPyBreak()
1057	return
1058	wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype)
1059
1060	def OnMotion(event):
1061	xpos = event.xdata
1062	if xpos: #avoid out of frame mouse position
1063	ypos = event.ydata
1064	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1065	try:
1066	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
1067	if G2frame.qPlot and 'PWDR' in plottype:
1068	q = xpos
1069	dsp = 2.*np.pi/q
1070	try:
1071	xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos)
1072	except ValueError: #avoid bad value in asin beyond upper limit
1073	pass
1074	elif 'SASD' in plottype:
1075	q = xpos
1076	dsp = 2.*np.pi/q
1077	elif G2frame.dPlot:
1078	dsp = xpos
1079	q = 2.*np.pi/dsp
1080	xpos = G2lat.Dsp2pos(Parms,xpos)
1081	elif G2frame.Contour and 'T' in Parms['Type'][0]:
1082	xpos = X[xpos]
1083	dsp = G2lat.Pos2dsp(Parms,xpos)
1084	q = 2.*np.pi/dsp
1085	else:
1086	dsp = G2lat.Pos2dsp(Parms,xpos)
1087	q = 2.*np.pi/dsp
1088	if G2frame.Contour: #PWDR only
1089	if 'C' in Parms['Type'][0]:
1090	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
1091	else:
1092	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
1093	else:
1094	if 'C' in Parms['Type'][0]:
1095	if 'PWDR' in plottype:
1096	if G2frame.SqrtPlot:
1097	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
1098	else:
1099	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
1100	elif 'SASD' in plottype:
1101	G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1)
1102	else:
1103	if G2frame.SqrtPlot:
1104	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
1105	else:
1106	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
1107	if G2frame.itemPicked:
1108	Page.canvas.SetToolTipString('%9.5f'%(xpos))
1109	if G2frame.PickId:
1110	found = []
1111	pickIdText = G2frame.PatternTree.GetItemText(G2frame.PickId)
1112	if pickIdText in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
1113	'PWDR' in pickIdText:
1114	indx = -1
1115	if pickIdText in ['Index Peak List','Unit Cells List',]:
1116	indx = -2
1117	if len(HKL):
1118	view = Page.toolbar._views.forward()[0][:2]
1119	wid = view[1]-view[0]
1120	found = HKL[np.where(np.fabs(HKL.T[indx]-xpos) < 0.002*wid)]
1121	if len(found):
1122	if len(found[0]) > 6: #SS reflections
1123	h,k,l,m = found[0][:4]
1124	Page.canvas.SetToolTipString('%d,%d,%d,%d'%(int(h),int(k),int(l),int(m)))
1125	else:
1126	h,k,l = found[0][:3]
1127	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1128	else:
1129	Page.canvas.SetToolTipString('')
1130
1131	except TypeError:
1132	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1)
1133
1134	def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots
1135	olderr = np.seterr(invalid='ignore')
1136
1137	def OnPick(event):
1138	if G2frame.itemPicked is not None: return
1139	PatternId = G2frame.PatternId
1140	try:
1141	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
1142	except TypeError:
1143	return
1144	PickId = G2frame.PickId
1145	pick = event.artist
1146	mouse = event.mouseevent
1147	xpos = pick.get_xdata()
1148	ypos = pick.get_ydata()
1149	ind = event.ind
1150	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
1151	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
1152	if ind.all() != [0] and ObsLine[0].get_label() in str(pick): #picked a data point
1153	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
1154	if G2frame.qPlot: #qplot - convert back to 2-theta
1155	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
1156	elif G2frame.dPlot: #dplot - convert back to 2-theta
1157	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
1158	XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
1159	data['peaks'].append(XY)
1160	data['sigDict'] = {} #now invalid
1161	G2pdG.UpdatePeakGrid(G2frame,data)
1162	PlotPatterns(G2frame,plotType=plottype)
1163	else: #picked a peak list line
1164	G2frame.itemPicked = pick
1165	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
1166	if ind.all() != [0]: #picked a data point
1167	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1168	data = G2frame.PatternTree.GetItemPyData(LimitId)
1169	if G2frame.qPlot: #qplot - convert back to 2-theta
1170	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
1171	elif G2frame.dPlot: #dplot - convert back to 2-theta
1172	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
1173	if G2frame.ifGetExclude:
1174	excl = [0,0]
1175	excl[0] = max(data[1][0],min(xy[0],data[1][1]))
1176	excl[1] = excl[0]+0.1
1177	data.append(excl)
1178	G2frame.ifGetExclude = False
1179	else:
1180	if mouse.button==1:
1181	data[1][0] = min(xy[0],data[1][1])
1182	if mouse.button==3:
1183	data[1][1] = max(xy[0],data[1][0])
1184	G2frame.PatternTree.SetItemPyData(LimitId,data)
1185	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
1186	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
1187	else: #picked a limit line
1188	G2frame.itemPicked = pick
1189	elif G2frame.PatternTree.GetItemText(PickId) == 'Models':
1190	if ind.all() != [0]: #picked a data point
1191	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1192	data = G2frame.PatternTree.GetItemPyData(LimitId)
1193	if mouse.button==1:
1194	data[1][0] = min(xy[0],data[1][1])
1195	if mouse.button==3:
1196	data[1][1] = max(xy[0],data[1][0])
1197	G2frame.PatternTree.SetItemPyData(LimitId,data)
1198	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
1199	else: #picked a limit line
1200	G2frame.itemPicked = pick
1201	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
1202	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1203	G2frame.itemPicked = pick
1204	pick = str(pick)
1205
1206	def OnRelease(event):
1207	if G2frame.itemPicked is None: return
1208	if str(DifLine[0]) == str(G2frame.itemPicked):
1209	ypos = event.ydata
1210	G2frame.delOffset = -ypos/Ymax
1211	G2frame.itemPicked = None
1212	PlotPatterns(G2frame,plotType=plottype)
1213	return
1214	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
1215	xpos = event.xdata
1216	PickId = G2frame.PickId
1217	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
1218	lines = []
1219	for line in G2frame.Lines:
1220	lines.append(line.get_xdata()[0])
1221	try:
1222	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
1223	except ValueError:
1224	lineNo = -1
1225	if lineNo in [0,1] or lineNo in exclLines:
1226	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
1227	data = G2frame.PatternTree.GetItemPyData(LimitId)
1228	id = lineNo/2+1
1229	id2 = lineNo%2
1230	if G2frame.qPlot and 'PWDR' in plottype:
1231	data[id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
1232	elif G2frame.dPlot and 'PWDR' in plottype:
1233	data[id][id2] = G2lat.Dsp2pos(Parms,xpos)
1234	else:
1235	data[id][id2] = xpos
1236	if id > 1 and data[id][0] > data[id][1]:
1237	data[id].reverse()
1238	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
1239	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
1240	G2frame.PatternTree.SetItemPyData(LimitId,data)
1241	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
1242	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
1243	elif lineNo > 1:
1244	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
1245	data = G2frame.PatternTree.GetItemPyData(PeakId)
1246	if event.button == 3:
1247	del data['peaks'][lineNo-2]
1248	else:
1249	if G2frame.qPlot:
1250	data['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
1251	elif G2frame.dPlot:
1252	data['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,xpos)
1253	else:
1254	data['peaks'][lineNo-2][0] = xpos
1255	data['sigDict'] = {} #no longer valid
1256	G2frame.PatternTree.SetItemPyData(PeakId,data)
1257	G2pdG.UpdatePeakGrid(G2frame,data)
1258	elif G2frame.PatternTree.GetItemText(PickId) in ['Models',] and xpos:
1259	lines = []
1260	for line in G2frame.Lines:
1261	lines.append(line.get_xdata()[0])
1262	try:
1263	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
1264	except ValueError:
1265	lineNo = -1
1266	if lineNo in [0,1]:
1267	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
1268	data = G2frame.PatternTree.GetItemPyData(LimitId)
1269	data[1][lineNo] = xpos
1270	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
1271	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
1272	G2frame.PatternTree.SetItemPyData(LimitId,data)
1273	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
1274	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
1275	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1276	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
1277	if 'line' not in pick: #avoid data points, etc.
1278	num = Phases.keys().index(pick)
1279	if num:
1280	G2frame.refDelt = -(event.ydata-G2frame.refOffset)/(num*Ymax)
1281	else: #1st row of refl ticks
1282	G2frame.refOffset = event.ydata
1283	PlotPatterns(G2frame,plotType=plottype)
1284	G2frame.itemPicked = None
1285
1286	try:
1287	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
1288	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1289	if not newPlot:
1290	Plot = Page.figure.gca() #get previous powder plot & get limits
1291	xylim = Plot.get_xlim(),Plot.get_ylim()
1292	Page.figure.clf()
1293	Plot = Page.figure.gca() #get a fresh plot after clf()
1294	except ValueError:
1295	if plottype == 'SASD':
1296	G2frame.logPlot = True
1297	G2frame.ErrorBars = True
1298	newPlot = True
1299	G2frame.Cmax = 1.0
1300	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
1301	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
1302	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1303	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1304	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1305	Page.canvas.mpl_connect('pick_event', OnPick)
1306	Page.canvas.mpl_connect('button_release_event', OnRelease)
1307	Page.canvas.mpl_connect('button_press_event',OnPress)
1308	if plottype == 'PWDR': # avoids a very nasty clash with KILL_FOCUS in SASD TextCtrl?
1309	Page.SetFocus()
1310	G2frame.G2plotNB.status.DestroyChildren()
1311	if G2frame.Contour:
1312	Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
1313	'i: interpolation method','s: color scheme','c: contour off')
1314	else:
1315	if G2frame.logPlot:
1316	if 'PWDR' in plottype:
1317	if G2frame.SinglePlot:
1318	Page.Choice = (' key press','n: log(I) off',
1319	'c: contour on','q: toggle q plot','t: toggle d-spacing plot',
1320	'm: toggle multidata plot','w: toggle divide by sig','+: no selection')
1321	else:
1322	Page.Choice = (' key press','n: log(I) off',
1323	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
1324	'c: contour on','q: toggle q plot','t: toggle d-spacing plot',
1325	'm: toggle multidata plot','w: toggle divide by sig','+: no selection')
1326	elif 'SASD' in plottype:
1327	if G2frame.SinglePlot:
1328	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
1329	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1330	else:
1331	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
1332	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
1333	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1334	else:
1335	if 'PWDR' in plottype:
1336	if G2frame.SinglePlot:
1337	Page.Choice = (' key press',
1338	'b: toggle subtract background','n: log(I) on','s: toggle sqrt plot','c: contour on',
1339	'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot',
1340	'w: toggle divide by sig','+: no selection')
1341	else:
1342	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down',
1343	'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on',
1344	'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot',
1345	'w: toggle divide by sig','+: no selection')
1346	elif 'SASD' in plottype:
1347	if G2frame.SinglePlot:
1348	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
1349	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1350	else:
1351	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
1352	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
1353	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1354
1355	Page.keyPress = OnPlotKeyPress
1356	PickId = G2frame.PickId
1357	PatternId = G2frame.PatternId
1358	colors=['b','g','r','c','m','k']
1359	Lines = []
1360	exclLines = []
1361	if G2frame.SinglePlot and PatternId:
1362	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1363	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1364	PlotList = [Pattern,]
1365	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
1366	G2frame.PatternId, 'Instrument Parameters'))
1367	Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
1368	ParmList = [Parms,]
1369	SampleList = [Sample,]
1370	Title = Pattern[-1]
1371	else:
1372	Title = os.path.split(G2frame.GSASprojectfile)[1]
1373	PlotList = []
1374	ParmList = []
1375	SampleList = []
1376	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1377	while item:
1378	if plottype in G2frame.PatternTree.GetItemText(item):
1379	Pattern = G2frame.PatternTree.GetItemPyData(item)
1380	if len(Pattern) < 3: # put name on end if needed
1381	Pattern.append(G2frame.PatternTree.GetItemText(item))
1382	PlotList.append(Pattern)
1383	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
1384	item,'Instrument Parameters'))[0])
1385	SampleList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
1386	item, 'Sample Parameters')))
1387	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1388	lenX = 0
1389	if PickId:
1390	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
1391	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1392	HKL = []
1393	if Phases:
1394	try:
1395	for peak in Phases[G2frame.RefList]['RefList']:
1396	if len(peak) > 15:
1397	HKL.append(peak[:7]) #SS reflection list - need peak[:7]
1398	else:
1399	HKL.append(peak[:6])
1400	except TypeError: #old style patch
1401	for peak in Phases[G2frame.RefList]:
1402	HKL.append(peak[:6])
1403	HKL = np.array(HKL)
1404	else:
1405	HKL = np.array(G2frame.HKL)
1406	Ymax = None
1407	for Pattern in PlotList:
1408	xye = Pattern[1]
1409	if xye[1] is None: continue
1410	if Ymax is None: Ymax = max(xye[1])
1411	Ymax = max(Ymax,max(xye[1]))
1412	if Ymax is None: return # nothing to plot
1413	offset = G2frame.Offset[0]*Ymax/100.0
1414	if G2frame.logPlot:
1415	Title = 'log('+Title+')'
1416	Plot.set_title(Title)
1417	if G2frame.qPlot or 'SASD' in plottype and not G2frame.Contour:
1418	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=16)
1419	elif G2frame.dPlot and 'PWDR' in plottype and not G2frame.Contour:
1420	Plot.set_xlabel(r'$d, \AA$',fontsize=16)
1421	else:
1422	if 'C' in ParmList[0]['Type'][0]:
1423	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=16)
1424	else:
1425	if G2frame.Contour:
1426	Plot.set_xlabel(r'Channel no.',fontsize=16)
1427	else:
1428	Plot.set_xlabel(r'$TOF, \mathsf{\mu}$s',fontsize=16)
1429	if G2frame.Weight:
1430	if 'PWDR' in plottype:
1431	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=16)
1432	elif 'SASD' in plottype:
1433	Plot.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16)
1434	else:
1435	if 'C' in ParmList[0]['Type'][0]:
1436	if 'PWDR' in plottype:
1437	if G2frame.SqrtPlot:
1438	Plot.set_ylabel(r'$\sqrt{Intensity}$',fontsize=16)
1439	else:
1440	Plot.set_ylabel(r'$Intensity$',fontsize=16)
1441	elif 'SASD' in plottype:
1442	if G2frame.sqPlot:
1443	Plot.set_ylabel(r'$S(Q)=I*Q^{4}$',fontsize=16)
1444	else:
1445	Plot.set_ylabel(r'$Intensity, cm^{-1}$',fontsize=16)
1446	else:
1447	if G2frame.SqrtPlot:
1448	Plot.set_ylabel(r'$\sqrt{Normalized\ intensity}$',fontsize=16)
1449	else:
1450	Plot.set_ylabel(r'$Normalized\ intensity$',fontsize=16)
1451	if G2frame.Contour:
1452	ContourZ = []
1453	ContourY = []
1454	Nseq = 0
1455	for N,Pattern in enumerate(PlotList):
1456	Parms = ParmList[N]
1457	Sample = SampleList[N]
1458	if 'C' in Parms['Type'][0]:
1459	wave = G2mth.getWave(Parms)
1460	else:
1461	difC = Parms['difC'][1]
1462	ifpicked = False
1463	LimitId = 0
1464	if Pattern[1] is None: continue # skip over uncomputed simulations
1465	xye = ma.array(ma.getdata(Pattern[1]))
1466	Zero = Parms.get('Zero',[0.,0.])[1]
1467	if PickId:
1468	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1469	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1470	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
1471	excls = limits[2:]
1472	for excl in excls:
1473	xye[0] = ma.masked_inside(xye[0],excl[0],excl[1])
1474	if G2frame.qPlot and 'PWDR' in plottype:
1475	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
1476	X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye[0])
1477	elif G2frame.dPlot and 'PWDR' in plottype:
1478	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
1479	X = G2lat.Pos2dsp(Parms,xye[0])
1480	else:
1481	X = xye[0]
1482	if not lenX:
1483	lenX = len(X)
1484	if 'PWDR' in plottype:
1485	if G2frame.SqrtPlot:
1486	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
1487	Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1]))
1488	np.seterr(invalid=olderr['invalid'])
1489	else:
1490	Y = xye[1]+offset*N
1491	elif 'SASD' in plottype:
1492	B = xye[5]
1493	if G2frame.sqPlot:
1494	Y = xye[1]Sample['Scale'][0](1.05)*(G2frame.Offset[0]N)X*4
1495	else:
1496	Y = xye[1]Sample['Scale'][0](1.05)*(G2frame.Offset[0]N)
1497	if LimitId and ifpicked:
1498	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
1499	lims = limits[1]
1500	if G2frame.qPlot and 'PWDR' in plottype:
1501	lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims)
1502	elif G2frame.dPlot and 'PWDR' in plottype:
1503	lims = G2lat.Pos2dsp(Parms,lims)
1504	Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.))
1505	Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.))
1506	for i,item in enumerate(limits[2:]):
1507	Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))
1508	Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.))
1509	exclLines += [2i+2,2i+3]
1510	if G2frame.Contour:
1511	if lenX == len(X):
1512	ContourY.append(N)
1513	ContourZ.append(Y)
1514	if 'C' in ParmList[0]['Type'][0]:
1515	ContourX = X
1516	else: #'T'OF
1517	ContourX = range(lenX)
1518	Nseq += 1
1519	Plot.set_ylabel('Data sequence',fontsize=12)
1520	else:
1521	if 'SASD' in plottype and G2frame.logPlot:
1522	X = (1.01)(G2frame.Offset[1]N)
1523	else:
1524	X += G2frame.Offset[1].005N
1525	Xum = ma.getdata(X)
1526	DifLine = ['']
1527	if ifpicked:
1528	if G2frame.SqrtPlot:
1529	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
1530	Z = np.where(xye[3]>=0.,np.sqrt(xye[3]),-np.sqrt(-xye[3]))
1531	np.seterr(invalid=olderr['invalid'])
1532	else:
1533	Z = xye[3]+offset*N
1534	if 'PWDR' in plottype:
1535	if G2frame.SqrtPlot:
1536	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
1537	W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4]))
1538	np.seterr(invalid=olderr['invalid'])
1539	D = np.where(xye[5],(Y-Z),0.)-Ymax*G2frame.delOffset
1540	else:
1541	W = xye[4]+offset*N
1542	D = xye[5]-Ymax*G2frame.delOffset #powder background
1543	elif 'SASD' in plottype:
1544	if G2frame.sqPlot:
1545	W = xye[4]X*4
1546	Z = xye[3]X*4
1547	B = BX*4
1548	else:
1549	W = xye[4]
1550	if G2frame.SubBack:
1551	YB = Y-B
1552	ZB = Z
1553	else:
1554	YB = Y
1555	ZB = Z+B
1556	Plot.set_yscale("log",nonposy='mask')
1557	if np.any(W>0.):
1558	Plot.set_ylim(bottom=np.min(np.trim_zeros(W))/2.,top=np.max(Y)*2.)
1559	else:
1560	Plot.set_ylim(bottom=np.min(np.trim_zeros(YB))/2.,top=np.max(Y)*2.)
1561	if G2frame.logPlot:
1562	if 'PWDR' in plottype:
1563	Plot.set_yscale("log",nonposy='mask')
1564	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1565	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
1566	Plot.plot(X,W,colors[(N+2)%6],picker=False) #background
1567	elif 'SASD' in plottype:
1568	Plot.set_xscale("log",nonposx='mask')
1569	Ibeg = np.searchsorted(X,limits[1][0])
1570	Ifin = np.searchsorted(X,limits[1][1])
1571	if G2frame.Weight:
1572	Plot.set_yscale("linear")
1573	DS = (YB-ZB)*np.sqrt(xye[2])
1574	Plot.plot(X[Ibeg:Ifin],DS[Ibeg:Ifin],colors[(N+3)%6],picker=False)
1575	Plot.axhline(0.,color=wx.BLACK)
1576	Plot.set_ylim(bottom=np.min(DS[Ibeg:Ifin])1.2,top=np.max(DS[Ibeg:Ifin])1.2)
1577	else:
1578	Plot.set_yscale("log",nonposy='mask')
1579	if G2frame.ErrorBars:
1580	if G2frame.sqPlot:
1581	Plot.errorbar(X,YB,yerr=X*4Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
1582	ecolor=colors[N%6],picker=3.,clip_on=False)
1583	else:
1584	Plot.errorbar(X,YB,yerr=Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
1585	ecolor=colors[N%6],picker=3.,clip_on=False)
1586	else:
1587	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1588	Plot.plot(X,W,colors[(N+2)%6],picker=False) #const. background
1589	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1590	elif G2frame.Weight and 'PWDR' in plottype:
1591	DY = xye[1]*np.sqrt(xye[2])
1592	Ymax = max(DY)
1593	DZ = xye[3]*np.sqrt(xye[2])
1594	DS = xye[5]np.sqrt(xye[2])-YmaxG2frame.delOffset
1595	ObsLine = Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False) #Io/sig(Io)
1596	Plot.plot(X,DZ,colors[(N+1)%6],picker=False) #Ic/sig(Io)
1597	DifLine = Plot.plot(X,DS,colors[(N+3)%6],picker=1.) #(Io-Ic)/sig(Io)
1598	Plot.axhline(0.,color=wx.BLACK)
1599	else:
1600	if G2frame.SubBack:
1601	if 'PWDR' in plottype:
1602	Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=False,clip_on=False) #Io-Ib
1603	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False) #Ic-Ib
1604	else:
1605	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1606	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1607	else:
1608	if 'PWDR' in plottype:
1609	ObsLine = Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False) #Io
1610	Plot.plot(X,Z,colors[(N+1)%6],picker=False) #Ic
1611	else:
1612	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1613	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1614	if 'PWDR' in plottype:
1615	Plot.plot(X,W,colors[(N+2)%6],picker=False) #Ib
1616	DifLine = Plot.plot(X,D,colors[(N+3)%6],picker=1.) #Io-Ic
1617	Plot.axhline(0.,color=wx.BLACK)
1618	Page.canvas.SetToolTipString('')
1619	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
1620	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
1621	Page.canvas.SetToolTipString(tip)
1622	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
1623	for item in data['peaks']:
1624	if G2frame.qPlot:
1625	Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
1626	elif G2frame.dPlot:
1627	Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
1628	else:
1629	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
1630	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
1631	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
1632	Page.canvas.SetToolTipString(tip)
1633	data = G2frame.LimitsTable.GetData()
1634
1635	else: #not picked
1636	if G2frame.logPlot:
1637	if 'PWDR' in plottype:
1638	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1639	elif 'SASD' in plottype:
1640	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1641	else:
1642	if 'PWDR' in plottype:
1643	Plot.plot(X,Y,colors[N%6],picker=False)
1644	elif 'SASD' in plottype:
1645	Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask')
1646	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1647
1648	if G2frame.logPlot and 'PWDR' in plottype:
1649	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1650	if PickId and not G2frame.Contour:
1651	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1652	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
1653	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
1654	if not len(peaks): return # are there any peaks?
1655	for peak in peaks[0]:
1656	if peak[2]:
1657	if G2frame.qPlot:
1658	Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b')
1659	if G2frame.dPlot:
1660	Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b')
1661	else:
1662	Plot.axvline(peak[0],color='b')
1663	for hkl in G2frame.HKL:
1664	clr = 'r'
1665	if len(hkl) > 6 and hkl[3]:
1666	clr = 'g'
1667	if G2frame.qPlot:
1668	Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5))
1669	if G2frame.dPlot:
1670	Plot.axvline(G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5))
1671	else:
1672	Plot.axvline(hkl[-2],color=clr,dashes=(5,5))
1673	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
1674	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1675	refColors=['b','r','c','g','m','k']
1676	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1677	for pId,phase in enumerate(Phases):
1678	try: #patch for old style reflection lists
1679	peaks = Phases[phase]['RefList']
1680	except TypeError:
1681	peaks = Phases[phase]
1682	if not len(peaks):
1683	continue
1684	if len(peaks[0]) > 15: #is there a way to plot ss lines differnt color than main ones?
1685	peak = np.array([[peak[5],peak[6]] for peak in peaks])
1686	else:
1687	peak = np.array([[peak[4],peak[5]] for peak in peaks])
1688	pos = G2frame.refOffset-pIdYmaxG2frame.refDelt*np.ones_like(peak)
1689	if G2frame.qPlot:
1690	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1691	elif G2frame.dPlot:
1692	Plot.plot(peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1693	else:
1694	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1695	if len(Phases):
1696	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
1697	if handles:
1698	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
1699
1700	if G2frame.Contour:
1701	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1702	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1703	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1704	Page.figure.colorbar(Img)
1705	else:
1706	G2frame.Lines = Lines
1707	if not newPlot:
1708	Page.toolbar.push_current()
1709	Plot.set_xlim(xylim[0])
1710	Plot.set_ylim(xylim[1])
1711	# xylim = []
1712	Page.toolbar.push_current()
1713	Page.toolbar.draw()
1714	else:
1715	Page.canvas.draw()
1716	olderr = np.seterr(invalid='ignore') #ugh - this removes a matplotlib error for mouse clicks in log plots
1717	# and sqrt(-ve) in np.where usage
1718	# G2frame.Pwdr = True
1719
1720	################################################################################
1721	##### PlotDeltSig
1722	################################################################################
1723
1724	def PlotDeltSig(G2frame,kind):
1725	'needs a doc string'
1726	try:
1727	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1728	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1729	Page.figure.clf()
1730	Plot = Page.figure.gca() #get a fresh plot after clf()
1731	except ValueError:
1732	newPlot = True
1733	G2frame.Cmax = 1.0
1734	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
1735	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1736	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1737	Page.Choice = None
1738	PatternId = G2frame.PatternId
1739	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1740	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1741	wtFactor = Pattern[0]['wtFactor']
1742	if kind == 'PWDR':
1743	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
1744	xye = np.array(Pattern[1])
1745	xmin = np.searchsorted(xye[0],limits[0])
1746	xmax = np.searchsorted(xye[0],limits[1])
1747	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
1748	elif kind == 'HKLF':
1749	refl = Pattern[1]
1750	DS = []
1751	for ref in refl:
1752	if ref[6] > 0.:
1753	DS.append((ref[5]-ref[7])/ref[6])
1754	Page.SetFocus()
1755	G2frame.G2plotNB.status.DestroyChildren()
1756	DS.sort()
1757	EDS = np.zeros_like(DS)
1758	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
1759	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
1760	T = np.sqrt(np.log(1.0/DX**2))
1761	top = 2.515517+0.802853T+0.010328T**2
1762	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
1763	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
1764	low1 = np.searchsorted(EDS,-1.)
1765	hi1 = np.searchsorted(EDS,1.)
1766	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
1767	frac = 100.*(hi1-low1)/len(DS)
1768	G2frame.G2plotNB.status.SetStatusText( \
1769	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
1770	Plot.set_title('Normal probability for '+Pattern[-1])
1771	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
1772	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
1773	Plot.plot(EDS,DS,'r+',label='result')
1774	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
1775	Plot.legend(loc='upper left')
1776	np.seterr(invalid='warn')
1777	Page.canvas.draw()
1778
1779	################################################################################
1780	##### PlotISFG
1781	################################################################################
1782
1783	def PlotISFG(G2frame,newPlot=False,type=''):
1784	''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
1785	or multiple plots with waterfall and contour plots as options
1786	'''
1787	if not type:
1788	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
1789	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
1790	return
1791	superMinusOne = unichr(0xaf)+unichr(0xb9)
1792
1793	def OnPlotKeyPress(event):
1794	newPlot = False
1795	if event.key == 'u':
1796	if G2frame.Contour:
1797	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1798	elif G2frame.Offset[0] < 100.:
1799	G2frame.Offset[0] += 1.
1800	elif event.key == 'd':
1801	if G2frame.Contour:
1802	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1803	elif G2frame.Offset[0] > 0.:
1804	G2frame.Offset[0] -= 1.
1805	elif event.key == 'l':
1806	G2frame.Offset[1] -= 1.
1807	elif event.key == 'r':
1808	G2frame.Offset[1] += 1.
1809	elif event.key == 'o':
1810	G2frame.Offset = [0,0]
1811	elif event.key == 'c':
1812	newPlot = True
1813	G2frame.Contour = not G2frame.Contour
1814	if not G2frame.Contour:
1815	G2frame.SinglePlot = False
1816	G2frame.Offset = [0.,0.]
1817	elif event.key == 's':
1818	if G2frame.Contour:
1819	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1820	choice.sort()
1821	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1822	if dlg.ShowModal() == wx.ID_OK:
1823	sel = dlg.GetSelection()
1824	G2frame.ContourColor = choice[sel]
1825	else:
1826	G2frame.ContourColor = 'Paired'
1827	dlg.Destroy()
1828	else:
1829	G2frame.SinglePlot = not G2frame.SinglePlot
1830	elif event.key == 'i': #for smoothing contour plot
1831	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1832	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1833	'mitchell','sinc','lanczos']
1834	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1835	if dlg.ShowModal() == wx.ID_OK:
1836	sel = dlg.GetSelection()
1837	G2frame.Interpolate = choice[sel]
1838	else:
1839	G2frame.Interpolate = 'nearest'
1840	dlg.Destroy()
1841	elif event.key == 't' and not G2frame.Contour:
1842	G2frame.Legend = not G2frame.Legend
1843	PlotISFG(G2frame,newPlot=newPlot,type=type)
1844
1845	def OnKeyBox(event):
1846	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
1847	event.key = cb.GetValue()[0]
1848	cb.SetValue(' key press')
1849	wx.CallAfter(OnPlotKeyPress,event)
1850	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
1851
1852	def OnMotion(event):
1853	xpos = event.xdata
1854	if xpos: #avoid out of frame mouse position
1855	ypos = event.ydata
1856	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1857	try:
1858	if G2frame.Contour:
1859	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
1860	else:
1861	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
1862	except TypeError:
1863	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1864
1865	xylim = []
1866	try:
1867	plotNum = G2frame.G2plotNB.plotList.index(type)
1868	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1869	if not newPlot:
1870	Plot = Page.figure.gca() #get previous plot & get limits
1871	xylim = Plot.get_xlim(),Plot.get_ylim()
1872	Page.figure.clf()
1873	Plot = Page.figure.gca()
1874	except ValueError:
1875	newPlot = True
1876	G2frame.Cmax = 1.0
1877	Plot = G2frame.G2plotNB.addMpl(type).gca()
1878	plotNum = G2frame.G2plotNB.plotList.index(type)
1879	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1880	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1881	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1882
1883	Page.SetFocus()
1884	G2frame.G2plotNB.status.DestroyChildren()
1885	if G2frame.Contour:
1886	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
1887	'i: interpolation method','s: color scheme','c: contour off')
1888	else:
1889	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
1890	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
1891	Page.keyPress = OnPlotKeyPress
1892	PatternId = G2frame.PatternId
1893	PickId = G2frame.PickId
1894	Plot.set_title(type)
1895	if type == 'G(R)':
1896	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
1897	else:
1898	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
1899	Plot.set_ylabel(r''+type,fontsize=14)
1900	colors=['b','g','r','c','m','k']
1901	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
1902	Pattern = []
1903	if G2frame.SinglePlot:
1904	name = G2frame.PatternTree.GetItemText(PatternId)
1905	name = type+name[4:]
1906	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
1907	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1908	if Pattern:
1909	Pattern.append(name)
1910	PlotList = [Pattern,]
1911	else:
1912	PlotList = []
1913	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1914	while item:
1915	if 'PDF' in G2frame.PatternTree.GetItemText(item):
1916	name = type+G2frame.PatternTree.GetItemText(item)[4:]
1917	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
1918	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1919	if Pattern:
1920	Pattern.append(name)
1921	PlotList.append(Pattern)
1922	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1923	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1924	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1925	Xb = [0.,10.]
1926	Yb = [0.,-40.np.pinumbDen]
1927	Ymax = 1.0
1928	lenX = 0
1929	for Pattern in PlotList:
1930	try:
1931	xye = Pattern[1]
1932	except IndexError:
1933	return
1934	Ymax = max(Ymax,max(xye[1]))
1935	offset = G2frame.Offset[0]*Ymax/100.0
1936	if G2frame.Contour:
1937	ContourZ = []
1938	ContourY = []
1939	Nseq = 0
1940	for N,Pattern in enumerate(PlotList):
1941	xye = Pattern[1]
1942	if PickId:
1943	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1944	X = xye[0]
1945	if not lenX:
1946	lenX = len(X)
1947	Y = xye[1]+offset*N
1948	if G2frame.Contour:
1949	if lenX == len(X):
1950	ContourY.append(N)
1951	ContourZ.append(Y)
1952	ContourX = X
1953	Nseq += 1
1954	Plot.set_ylabel('Data sequence',fontsize=12)
1955	else:
1956	X = xye[0]+G2frame.Offset[1].005N
1957	if ifpicked:
1958	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1959	Page.canvas.SetToolTipString('')
1960	else:
1961	if G2frame.Legend:
1962	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1963	else:
1964	Plot.plot(X,Y,colors[N%6],picker=False)
1965	if type == 'G(R)':
1966	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1967	elif type == 'F(Q)':
1968	Plot.axhline(0.,color=wx.BLACK)
1969	elif type == 'S(Q)':
1970	Plot.axhline(1.,color=wx.BLACK)
1971	if G2frame.Contour:
1972	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1973	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1974	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1975	Page.figure.colorbar(Img)
1976	elif G2frame.Legend:
1977	Plot.legend(loc='best')
1978	if not newPlot:
1979	Page.toolbar.push_current()
1980	Plot.set_xlim(xylim[0])
1981	Plot.set_ylim(xylim[1])
1982	xylim = []
1983	Page.toolbar.push_current()
1984	Page.toolbar.draw()
1985	else:
1986	Page.canvas.draw()
1987
1988	################################################################################
1989	##### PlotCalib
1990	################################################################################
1991
1992	def PlotCalib(G2frame,Inst,XY,Sigs,newPlot=False):
1993	'''plot of CW or TOF peak calibration
1994	'''
1995	def OnMotion(event):
1996	xpos = event.xdata
1997	if xpos: #avoid out of frame mouse position
1998	ypos = event.ydata
1999	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2000	try:
2001	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3g'%(xpos,Title,ypos),1)
2002	except TypeError:
2003	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
2004	found = []
2005	wid = 1
2006	view = Page.toolbar._views.forward()
2007	if view:
2008	view = view[0][:2]
2009	wid = view[1]-view[0]
2010	found = XY[np.where(np.fabs(XY.T[0]-xpos) < 0.005*wid)]
2011	if len(found):
2012	pos = found[0][1]
2013	if 'C' in Inst['Type'][0]:
2014	Page.canvas.SetToolTipString('position=%.4f'%(pos))
2015	else:
2016	Page.canvas.SetToolTipString('position=%.2f'%(pos))
2017	else:
2018	Page.canvas.SetToolTipString('')
2019
2020	Title = 'Position calibration'
2021	try:
2022	plotNum = G2frame.G2plotNB.plotList.index(Title)
2023	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2024	if not newPlot:
2025	Plot = Page.figure.gca()
2026	xylim = Plot.get_xlim(),Plot.get_ylim()
2027	Page.figure.clf()
2028	Plot = Page.figure.gca()
2029	except ValueError:
2030	newPlot = True
2031	Plot = G2frame.G2plotNB.addMpl(Title).gca()
2032	plotNum = G2frame.G2plotNB.plotList.index(Title)
2033	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2034	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2035
2036	Page.Choice = None
2037	Page.SetFocus()
2038	G2frame.G2plotNB.status.DestroyChildren()
2039	Plot.set_title(Title)
2040	Plot.set_xlabel(r'd-spacing',fontsize=14)
2041	if 'C' in Inst['Type'][0]:
2042	Plot.set_ylabel(r'$\mathsf{\Delta(2\theta)}$',fontsize=14)
2043	else:
2044	Plot.set_ylabel(r'$\mathsf{\Delta}T/T$',fontsize=14)
2045	for ixy,xyw in enumerate(XY):
2046	if len(xyw) > 2:
2047	X,Y,W = xyw
2048	else:
2049	X,Y = xyw
2050	W = 0.
2051	Yc = G2lat.Dsp2pos(Inst,X)
2052	if 'C' in Inst['Type'][0]:
2053	Y = Y-Yc
2054	E = Sigs[ixy]
2055	bin = W/2.
2056	else:
2057	Y = (Y-Yc)/Yc
2058	E = Sigs[ixy]/Yc
2059	bin = W/(2.*Yc)
2060	if E:
2061	Plot.errorbar(X,Y,ecolor='k',yerr=E)
2062	if ixy:
2063	Plot.plot(X,Y,'kx',picker=3)
2064	else:
2065	Plot.plot(X,Y,'kx',label='peak')
2066	if W:
2067	if ixy:
2068	Plot.plot(X,bin,'b+')
2069	else:
2070	Plot.plot(X,bin,'b+',label='bin width')
2071	Plot.plot(X,-bin,'b+')
2072	Plot.axhline(0.,color='r',linestyle='--')
2073	Plot.legend(loc='best')
2074	if not newPlot:
2075	Page.toolbar.push_current()
2076	Plot.set_xlim(xylim[0])
2077	Plot.set_ylim(xylim[1])
2078	# xylim = []
2079	Page.toolbar.push_current()
2080	Page.toolbar.draw()
2081	else:
2082	Page.canvas.draw()
2083
2084	################################################################################
2085	##### PlotXY
2086	################################################################################
2087
2088	def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,Title=''):
2089	'''simple plot of xy data, used for diagnostic purposes
2090	'''
2091	def OnMotion(event):
2092	xpos = event.xdata
2093	if xpos: #avoid out of frame mouse position
2094	ypos = event.ydata
2095	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2096	try:
2097	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,Title,ypos),1)
2098	except TypeError:
2099	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
2100
2101	try:
2102	plotNum = G2frame.G2plotNB.plotList.index(Title)
2103	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2104	if not newPlot:
2105	Plot = Page.figure.gca()
2106	xylim = Plot.get_xlim(),Plot.get_ylim()
2107	Page.figure.clf()
2108	Plot = Page.figure.gca()
2109	except ValueError:
2110	newPlot = True
2111	Plot = G2frame.G2plotNB.addMpl(Title).gca()
2112	plotNum = G2frame.G2plotNB.plotList.index(Title)
2113	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2114	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2115
2116	Page.Choice = None
2117	Page.SetFocus()
2118	G2frame.G2plotNB.status.DestroyChildren()
2119	Plot.set_title(Title)
2120	if labelX:
2121	Plot.set_xlabel(r''+labelX,fontsize=14)
2122	else:
2123	Plot.set_xlabel(r'X',fontsize=14)
2124	if labelY:
2125	Plot.set_ylabel(r''+labelY,fontsize=14)
2126	else:
2127	Plot.set_ylabel(r'Y',fontsize=14)
2128	colors=['b','g','r','c','m','k']
2129	for ixy,xy in enumerate(XY):
2130	X,Y = xy
2131	Plot.plot(X,Y,colors[ixy%6]+'+',picker=False)
2132	if len(XY2):
2133	for ixy,xy in enumerate(XY2):
2134	X,Y = xy
2135	Plot.plot(X,Y,colors[ixy%6],picker=False)
2136	if not newPlot:
2137	Page.toolbar.push_current()
2138	Plot.set_xlim(xylim[0])
2139	Plot.set_ylim(xylim[1])
2140	xylim = []
2141	Page.toolbar.push_current()
2142	Page.toolbar.draw()
2143	else:
2144	Page.canvas.draw()
2145
2146	################################################################################
2147	##### PlotStrain
2148	################################################################################
2149
2150	def PlotStrain(G2frame,data,newPlot=False):
2151	'''plot of strain data, used for diagnostic purposes
2152	'''
2153	def OnMotion(event):
2154	xpos = event.xdata
2155	if xpos: #avoid out of frame mouse position
2156	ypos = event.ydata
2157	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2158	try:
2159	G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1)
2160	except TypeError:
2161	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
2162
2163	try:
2164	plotNum = G2frame.G2plotNB.plotList.index('Strain')
2165	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2166	if not newPlot:
2167	Plot = Page.figure.gca()
2168	xylim = Plot.get_xlim(),Plot.get_ylim()
2169	Page.figure.clf()
2170	Plot = Page.figure.gca()
2171	except ValueError:
2172	newPlot = True
2173	Plot = G2frame.G2plotNB.addMpl('Strain').gca()
2174	plotNum = G2frame.G2plotNB.plotList.index('Strain')
2175	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2176	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2177
2178	Page.Choice = None
2179	Page.SetFocus()
2180	G2frame.G2plotNB.status.DestroyChildren()
2181	Plot.set_title('Strain')
2182	Plot.set_ylabel(r'd-spacing',fontsize=14)
2183	Plot.set_xlabel(r'Azimuth',fontsize=14)
2184	colors=['b','g','r','c','m','k']
2185	for N,item in enumerate(data['d-zero']):
2186	Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y
2187	Plot.plot(X,Y,colors[N%6]+'+',picker=False)
2188	Y,X = np.array(item['ImtaCalc'])
2189	Plot.plot(X,Y,colors[N%6],picker=False)
2190	if not newPlot:
2191	Page.toolbar.push_current()
2192	Plot.set_xlim(xylim[0])
2193	Plot.set_ylim(xylim[1])
2194	xylim = []
2195	Page.toolbar.push_current()
2196	Page.toolbar.draw()
2197	else:
2198	Page.canvas.draw()
2199
2200	################################################################################
2201	##### PlotSASDSizeDist
2202	################################################################################
2203
2204	def PlotSASDSizeDist(G2frame):
2205
2206	def OnPageChanged(event):
2207	PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
2208	if 'Powder' in PlotText:
2209	PlotPatterns(G2frame,plotType='SASD',newPlot=True)
2210	elif 'Size' in PlotText:
2211	PlotSASDSizeDist(G2frame)
2212
2213	def OnMotion(event):
2214	xpos = event.xdata
2215	if xpos: #avoid out of frame mouse position
2216	ypos = event.ydata
2217	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2218	try:
2219	G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1)
2220	except TypeError:
2221	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
2222
2223	try:
2224	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
2225	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2226	Page.figure.clf()
2227	Plot = Page.figure.gca() #get a fresh plot after clf()
2228	except ValueError:
2229	newPlot = True
2230	Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca()
2231	G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged)
2232	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
2233	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2234	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2235	Page.Choice = None
2236	Page.SetFocus()
2237	PatternId = G2frame.PatternId
2238	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models'))
2239	Bins,Dbins,BinMag = data['Size']['Distribution']
2240	Plot.set_title('Size Distribution')
2241	Plot.set_xlabel(r'$D, \AA$',fontsize=14)
2242	Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
2243	if data['Size']['logBins']:
2244	Plot.set_xscale("log",nonposy='mask')
2245	Plot.set_xlim([np.min(2.Bins)/2.,np.max(2.Bins)*2.])
2246	Plot.bar(2.Bins-Dbins,BinMag,2.Dbins,facecolor='white') #plot diameters
2247	if 'Size Calc' in data:
2248	Rbins,Dist = data['Size Calc']
2249	for i in range(len(Rbins)):
2250	if len(Rbins[i]):
2251	Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters
2252	Page.canvas.draw()
2253
2254	################################################################################
2255	##### PlotPowderLines
2256	################################################################################
2257
2258	def PlotPowderLines(G2frame):
2259	''' plotting of powder lines (i.e. no powder pattern) as sticks
2260	'''
2261	global HKL
2262
2263	def OnMotion(event):
2264	xpos = event.xdata
2265	if xpos: #avoid out of frame mouse position
2266	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2267	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
2268	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
2269	found = []
2270	if len(HKL):
2271	view = Page.toolbar._views.forward()[0][:2]
2272	wid = view[1]-view[0]
2273	found = HKL[np.where(np.fabs(HKL.T[-1]-xpos) < 0.002*wid)]
2274	if len(found):
2275	h,k,l = found[0][:3]
2276	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
2277	else:
2278	Page.canvas.SetToolTipString('')
2279
2280	try:
2281	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
2282	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2283	Page.figure.clf()
2284	Plot = Page.figure.gca()
2285	except ValueError:
2286	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
2287	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
2288	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2289	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2290
2291	Page.Choice = None
2292	Page.SetFocus()
2293	Plot.set_title('Powder Pattern Lines')
2294	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
2295	PickId = G2frame.PickId
2296	PatternId = G2frame.PatternId
2297	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))[0]
2298	for peak in peaks:
2299	Plot.axvline(peak[0],color='b')
2300	HKL = np.array(G2frame.HKL)
2301	for hkl in G2frame.HKL:
2302	Plot.axvline(hkl[-1],color='r',dashes=(5,5))
2303	xmin = peaks[0][0]
2304	xmax = peaks[-1][0]
2305	delt = xmax-xmin
2306	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
2307	Plot.set_xlim(xlim)
2308	Page.canvas.draw()
2309	Page.toolbar.push_current()
2310
2311	################################################################################
2312	##### PlotPeakWidths
2313	################################################################################
2314
2315	def PlotPeakWidths(G2frame):
2316	''' Plotting of instrument broadening terms as function of 2-theta
2317	Seen when "Instrument Parameters" chosen from powder pattern data tree
2318	'''
2319	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
2320	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
2321	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.)
2322	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
2323	PatternId = G2frame.PatternId
2324	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
2325	if limitID:
2326	limits = G2frame.PatternTree.GetItemPyData(limitID)[:2]
2327	else:
2328	return
2329	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
2330	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
2331	if 'C' in Parms['Type'][0]:
2332	lam = G2mth.getWave(Parms)
2333	else:
2334	difC = Parms['difC'][0]
2335	try: # PATCH: deal with older peak lists, before changed to dict to implement TOF
2336	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))['peaks']
2337	except TypeError:
2338	print "Your peak list needs reformatting...",
2339	item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
2340	G2frame.PatternTree.SelectItem(item)
2341	item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters')
2342	G2frame.PatternTree.SelectItem(item)
2343	print "done"
2344	return
2345	try:
2346	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
2347	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2348	Page.figure.clf()
2349	Plot = Page.figure.gca()
2350	except ValueError:
2351	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
2352	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
2353	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2354	Page.Choice = None
2355	Page.SetFocus()
2356
2357	Page.canvas.SetToolTipString('')
2358	colors=['b','g','r','c','m','k']
2359	X = []
2360	Y = []
2361	Z = []
2362	W = []
2363	if 'C' in Parms['Type'][0]:
2364	Plot.set_title('Instrument and sample peak widths')
2365	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
2366	Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14)
2367	try:
2368	Xmin,Xmax = limits[1]
2369	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
2370	Q = 4.np.pinpsind(X/2.)/lam
2371	Z = np.ones_like(X)
2372	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
2373	s = 1.17741np.sqrt(data[4])np.pi/18000.
2374	g = data[6]*np.pi/18000.
2375	G = G2pwd.getgamFW(g,s)
2376	Y = s/nptand(X/2.)
2377	Z = g/nptand(X/2.)
2378	W = G/nptand(X/2.)
2379	Plot.plot(Q,Y,color='r',label='Gaussian')
2380	Plot.plot(Q,Z,color='g',label='Lorentzian')
2381	Plot.plot(Q,W,color='b',label='G+L')
2382
2383	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
2384	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
2385	gf = fit[6]*np.pi/18000.
2386	Gf = G2pwd.getgamFW(gf,sf)
2387	Yf = sf/nptand(X/2.)
2388	Zf = gf/nptand(X/2.)
2389	Wf = Gf/nptand(X/2.)
2390	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
2391	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
2392	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
2393
2394	X = []
2395	Y = []
2396	Z = []
2397	W = []
2398	V = []
2399	for peak in peaks:
2400	X.append(4.0math.pisind(peak[0]/2.0)/lam)
2401	try:
2402	s = 1.17741math.sqrt(peak[4])math.pi/18000.
2403	except ValueError:
2404	s = 0.01
2405	g = peak[6]*math.pi/18000.
2406	G = G2pwd.getgamFW(g,s)
2407	Y.append(s/tand(peak[0]/2.))
2408	Z.append(g/tand(peak[0]/2.))
2409	W.append(G/tand(peak[0]/2.))
2410	if len(peaks):
2411	Plot.plot(X,Y,'+',color='r',label='G peak')
2412	Plot.plot(X,Z,'+',color='g',label='L peak')
2413	Plot.plot(X,W,'+',color='b',label='G+L peak')
2414	Plot.legend(loc='best')
2415	Page.canvas.draw()
2416	except ValueError:
2417	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
2418	'%.3f'%(2*theta)
2419	G2frame.G2plotNB.Delete('Peak Widths')
2420	else: #'T'OF
2421	Plot.set_title('Instrument and sample peak coefficients')
2422	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
2423	Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14)
2424	Xmin,Xmax = limits[1]
2425	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
2426	Z = np.ones_like(T)
2427	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
2428	ds = T/difC
2429	Q = 2.*np.pi/ds
2430	A = data[4]
2431	B = data[6]
2432	S = 1.17741*np.sqrt(data[8])/T
2433	G = data[10]/T
2434	Plot.plot(Q,A,color='r',label='Alpha')
2435	Plot.plot(Q,B,color='g',label='Beta')
2436	Plot.plot(Q,S,color='b',label='Gaussian')
2437	Plot.plot(Q,G,color='m',label='Lorentzian')
2438
2439	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
2440	ds = T/difC
2441	Q = 2.*np.pi/ds
2442	Af = fit[4]
2443	Bf = fit[6]
2444	Sf = 1.17741*np.sqrt(fit[8])/T
2445	Gf = fit[10]/T
2446	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
2447	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
2448	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
2449	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
2450
2451	T = []
2452	A = []
2453	B = []
2454	S = []
2455	G = []
2456	W = []
2457	Q = []
2458	V = []
2459	for peak in peaks:
2460	T.append(peak[0])
2461	A.append(peak[4])
2462	B.append(peak[6])
2463	Q.append(2.np.pidifC/peak[0])
2464	S.append(1.17741*np.sqrt(peak[8])/peak[0])
2465	G.append(peak[10]/peak[0])
2466
2467
2468	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
2469	Plot.plot(Q,B,'+',color='g',label='Beta peak')
2470	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
2471	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
2472	Plot.legend(loc='best')
2473	Page.canvas.draw()
2474
2475
2476	################################################################################
2477	##### PlotSizeStrainPO
2478	################################################################################
2479
2480	def PlotSizeStrainPO(G2frame,data,Start=False):
2481	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
2482	'''
2483
2484	PatternId = G2frame.PatternId
2485	generalData = data['General']
2486	SGData = generalData['SGData']
2487	SGLaue = SGData['SGLaue']
2488	if Start: #initialize the spherical harmonics qlmn arrays
2489	ptx.pyqlmninit()
2490	Start = False
2491	# MuStrKeys = G2spc.MustrainNames(SGData)
2492	cell = generalData['Cell'][1:]
2493	A,B = G2lat.cell2AB(cell[:6])
2494	Vol = cell[6]
2495	useList = data['Histograms']
2496	phase = generalData['Name']
2497	plotType = generalData['Data plot type']
2498	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
2499	for ptype in plotDict:
2500	G2frame.G2plotNB.Delete(ptype)
2501	if plotType in ['None']:
2502	return
2503
2504	for item in useList:
2505	if useList[item]['Show']:
2506	break
2507	else:
2508	return #nothing to show!!
2509
2510	numPlots = len(useList)
2511
2512	if plotType in ['Mustrain','Size']:
2513	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
2514	else:
2515	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
2516	plotNum = G2frame.G2plotNB.plotList.index(plotType)
2517	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2518	Page.Choice = None
2519	Page.SetFocus()
2520	G2frame.G2plotNB.status.SetStatusText('',1)
2521	if not Page.IsShown():
2522	Page.Show()
2523
2524	for item in useList:
2525	if useList[item]['Show']:
2526	PHI = np.linspace(0.,360.,30,True)
2527	PSI = np.linspace(0.,180.,30,True)
2528	X = np.outer(npsind(PHI),npsind(PSI))
2529	Y = np.outer(npcosd(PHI),npsind(PSI))
2530	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
2531	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
2532	coeff = useList[item][plotDict[plotType]]
2533	except KeyError:
2534	break
2535	if plotType in ['Mustrain','Size']:
2536	if coeff[0] == 'isotropic':
2537	X *= coeff[1][0]
2538	Y *= coeff[1][0]
2539	Z *= coeff[1][0]
2540	elif coeff[0] == 'uniaxial':
2541
2542	def uniaxCalc(xyz,iso,aniso,axes):
2543	Z = np.array(axes)
2544	cp = abs(np.dot(xyz,Z))
2545	sp = np.sqrt(1.-cp**2)
2546	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
2547	return R*xyz
2548
2549	iso,aniso = coeff[1][:2]
2550	axes = np.inner(A,np.array(coeff[3]))
2551	axes /= nl.norm(axes)
2552	Shkl = np.array(coeff[1])
2553	XYZ = np.dstack((X,Y,Z))
2554	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
2555	X,Y,Z = np.dsplit(XYZ,3)
2556	X = X[:,:,0]
2557	Y = Y[:,:,0]
2558	Z = Z[:,:,0]
2559
2560	elif coeff[0] == 'ellipsoidal':
2561
2562	def ellipseCalc(xyz,E,R):
2563	XYZ = xyz*E.T
2564	return np.inner(XYZ.T,R)
2565
2566	S6 = coeff[4]
2567	Sij = G2lat.U6toUij(S6)
2568	E,R = nl.eigh(Sij)
2569	XYZ = np.dstack((X,Y,Z))
2570	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
2571	X,Y,Z = np.dsplit(XYZ,3)
2572	X = X[:,:,0]
2573	Y = Y[:,:,0]
2574	Z = Z[:,:,0]
2575
2576	elif coeff[0] == 'generalized':
2577
2578	def genMustrain(xyz,SGData,A,Shkl):
2579	uvw = np.inner(A.T,xyz)
2580	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
2581	Sum = np.sum(np.multiply(Shkl,Strm))
2582	Sum = np.where(Sum > 0.01,Sum,0.01)
2583	Sum = np.sqrt(Sum)
2584	return Sum*xyz
2585
2586	Shkl = np.array(coeff[4])
2587	if np.any(Shkl):
2588	XYZ = np.dstack((X,Y,Z))
2589	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
2590	X,Y,Z = np.dsplit(XYZ,3)
2591	X = X[:,:,0]
2592	Y = Y[:,:,0]
2593	Z = Z[:,:,0]
2594
2595	if np.any(X) and np.any(Y) and np.any(Z):
2596	errFlags = np.seterr(all='ignore')
2597	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
2598	np.seterr(all='ignore')
2599	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
2600	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
2601	Plot.set_xlim3d(XYZlim)
2602	Plot.set_ylim3d(XYZlim)
2603	Plot.set_zlim3d(XYZlim)
2604	Plot.set_aspect('equal')
2605	if plotType == 'Size':
2606	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
2607	Plot.set_xlabel(r'X, $\mu$m')
2608	Plot.set_ylabel(r'Y, $\mu$m')
2609	Plot.set_zlabel(r'Z, $\mu$m')
2610	else:
2611	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
2612	Plot.set_xlabel(r'X, $\mu$strain')
2613	Plot.set_ylabel(r'Y, $\mu$strain')
2614	Plot.set_zlabel(r'Z, $\mu$strain')
2615	else:
2616	h,k,l = generalData['POhkl']
2617	if coeff[0] == 'MD':
2618	print 'March-Dollase preferred orientation plot'
2619
2620	else:
2621	PH = np.array(generalData['POhkl'])
2622	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
2623	SHCoef = {}
2624	for item in coeff[5]:
2625	L,N = eval(item.strip('C'))
2626	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
2627	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
2628	X = np.linspace(0,90.0,26)
2629	Y = G2lat.polfcal(ODFln,'0',X,0.0)
2630	Plot.plot(X,Y,color='k',label=str(PH))
2631	Plot.legend(loc='best')
2632	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
2633	Plot.set_xlabel(r'$\psi$',fontsize=16)
2634	Plot.set_ylabel('MRD',fontsize=14)
2635	Page.canvas.draw()
2636
2637	################################################################################
2638	##### PlotTexture
2639	################################################################################
2640
2641	def PlotTexture(G2frame,data,Start=False):
2642	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
2643	plotting.
2644	dict generalData contains all phase info needed which is in data
2645	'''
2646
2647	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2648	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2649	PatternId = G2frame.PatternId
2650	generalData = data['General']
2651	SGData = generalData['SGData']
2652	textureData = generalData['SH Texture']
2653	G2frame.G2plotNB.Delete('Texture')
2654	if not textureData['Order']:
2655	return #no plot!!
2656	SHData = generalData['SH Texture']
2657	SHCoef = SHData['SH Coeff'][1]
2658	cell = generalData['Cell'][1:7]
2659	Amat,Bmat = G2lat.cell2AB(cell)
2660	sq2 = 1.0/math.sqrt(2.0)
2661
2662	def rp2xyz(r,p):
2663	z = npcosd(r)
2664	xy = np.sqrt(1.-z**2)
2665	return xynpsind(p),xynpcosd(p),z
2666
2667	def OnMotion(event):
2668	SHData = data['General']['SH Texture']
2669	if event.xdata and event.ydata: #avoid out of frame errors
2670	xpos = event.xdata
2671	ypos = event.ydata
2672	if 'Inverse' in SHData['PlotType']:
2673	r = xpos2+ypos2
2674	if r <= 1.0:
2675	if 'equal' in G2frame.Projection:
2676	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
2677	else:
2678	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
2679	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
2680	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
2681	y,x,z = list(xyz/np.max(np.abs(xyz)))
2682
2683	G2frame.G2plotNB.status.SetFields(['',
2684	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
2685
2686	elif 'Axial' in SHData['PlotType']:
2687	pass
2688
2689	else: #ordinary pole figure
2690	z = xpos2+ypos2
2691	if z <= 1.0:
2692	z = np.sqrt(z)
2693	if 'equal' in G2frame.Projection:
2694	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
2695	else:
2696	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
2697	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
2698	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
2699
2700	try:
2701	plotNum = G2frame.G2plotNB.plotList.index('Texture')
2702	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2703	Page.figure.clf()
2704	Plot = Page.figure.gca()
2705	if not Page.IsShown():
2706	Page.Show()
2707	except ValueError:
2708	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
2709	plotNum = G2frame.G2plotNB.plotList.index('Texture')
2710	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2711	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2712
2713	Page.Choice = None
2714	Page.SetFocus()
2715	G2frame.G2plotNB.status.SetFields(['',''])
2716	PH = np.array(SHData['PFhkl'])
2717	phi,beta = G2lat.CrsAng(PH,cell,SGData)
2718	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
2719	PX = np.array(SHData['PFxyz'])
2720	gam = atan2d(PX[0],PX[1])
2721	xy = math.sqrt(PX[0]2+PX[1]2)
2722	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
2723	psi = asind(xy/xyz)
2724	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
2725	if 'Axial' in SHData['PlotType']:
2726	X = np.linspace(0,90.0,26)
2727	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
2728	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
2729	Plot.legend(loc='best')
2730	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
2731	Plot.set_xlabel(r'$\psi$',fontsize=16)
2732	Plot.set_ylabel('MRD',fontsize=14)
2733
2734	else:
2735	npts = 201
2736	if 'Inverse' in SHData['PlotType']:
2737	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2738	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2739	if 'equal' in G2frame.Projection:
2740	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2741	else:
2742	R = np.where(R <= 1.,2.*npatand(R),0.0)
2743	Z = np.zeros_like(R)
2744	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
2745	Z = np.reshape(Z,(npts,npts))
2746	CS = Plot.contour(Y,X,Z,aspect='equal')
2747	Plot.clabel(CS,fontsize=9,inline=1)
2748	try:
2749	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2750	except ValueError:
2751	pass
2752	Page.figure.colorbar(Img)
2753	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
2754	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2755
2756	else:
2757	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2758	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2759	if 'equal' in G2frame.Projection:
2760	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2761	else:
2762	R = np.where(R <= 1.,2.*npatand(R),0.0)
2763	Z = np.zeros_like(R)
2764	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
2765	Z = np.reshape(Z,(npts,npts))
2766	try:
2767	CS = Plot.contour(Y,X,Z,aspect='equal')
2768	Plot.clabel(CS,fontsize=9,inline=1)
2769	except ValueError:
2770	pass
2771	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2772	Page.figure.colorbar(Img)
2773	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
2774	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2775	Page.canvas.draw()
2776
2777	################################################################################
2778	##### Plot Modulation
2779	################################################################################
2780
2781	def ModulationPlot(G2frame,data,atom,ax,off=0):
2782	global Off,Atom,Ax
2783	Off = off
2784	Atom = atom
2785	Ax = ax
2786	def OnMotion(event):
2787	xpos = event.xdata
2788	if xpos: #avoid out of frame mouse position
2789	ypos = event.ydata
2790	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2791	try:
2792	G2frame.G2plotNB.status.SetStatusText('t =%9.3f %s =%9.3f'%(xpos,GkDelta+Ax,ypos),1)
2793	except TypeError:
2794	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
2795
2796	def OnPlotKeyPress(event):
2797	global Off,Atom,Ax
2798	newPlot = False
2799	if event.key == '0':
2800	Off = 0
2801	elif event.key == '+':
2802	Off += 1
2803	elif event.key == '-':
2804	Off -= 1
2805	elif event.key in ['l','r',] and mapData['Flip']:
2806	roll = 1
2807	if event.key == 'l':
2808	roll = -1
2809	rho = Map['rho']
2810	Map['rho'] = np.roll(rho,roll,axis=3)
2811	wx.CallAfter(ModulationPlot,G2frame,data,Atom,Ax,Off)
2812
2813	try:
2814	plotNum = G2frame.G2plotNB.plotList.index('Modulation')
2815	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2816	Page.figure.clf()
2817	Plot = Page.figure.gca()
2818	if not Page.IsShown():
2819	Page.Show()
2820	except ValueError:
2821	Plot = G2frame.G2plotNB.addMpl('Modulation').gca()
2822	plotNum = G2frame.G2plotNB.plotList.index('Modulation')
2823	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2824	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2825	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2826
2827	Page.SetFocus()
2828	General = data['General']
2829	cx,ct,cs,cia = General['AtomPtrs']
2830	mapData = General['Map']
2831	if mapData['Flip']:
2832	Page.Choice = ['+: shift up','-: shift down','0: reset shift','l: move left','r: move right']
2833	else:
2834	Page.Choice = ['+: shift up','-: shift down','0: reset shift']
2835	Page.keyPress = OnPlotKeyPress
2836	Map = General['4DmapData']
2837	MapType = Map['MapType']
2838	rhoSize = np.array(Map['rho'].shape)
2839	atxyz = np.array(atom[cx:cx+3])
2840	waveType = atom[-1]['SS1']['waveType']
2841	Spos = atom[-1]['SS1']['Spos']
2842	tau = np.linspace(0.,2.,101)
2843	wave = np.zeros((3,101))
2844	if len(Spos):
2845	scof = []
2846	ccof = []
2847	for i,spos in enumerate(Spos):
2848	if waveType in ['Sawtooth','ZigZag'] and not i:
2849	Toff = spos[0][0]
2850	slopes = np.array(spos[0][1:])
2851	if waveType == 'Sawtooth':
2852	wave = G2mth.posSawtooth(tau,Toff,slopes)
2853	elif waveType == 'ZigZag':
2854	wave = G2mth.posZigZag(tau,Toff,slopes)
2855	else:
2856	scof.append(spos[0][:3])
2857	ccof.append(spos[0][3:])
2858	wave += G2mth.posFourier(tau,np.array(scof),np.array(ccof))
2859	if mapData['Flip']:
2860	Title = 'Charge flip'
2861	else:
2862	Title = MapType
2863	Title += ' map for atom '+atom[0]+ \
2864	' at %.4f %.4f %.4f'%(atxyz[0],atxyz[1],atxyz[2])
2865	ix = -np.array(np.rint(rhoSize[:3]*atxyz),dtype='i')
2866	ix += (rhoSize[:3]/2)
2867	ix = ix%rhoSize[:3]
2868	rho = np.roll(np.roll(np.roll(Map['rho'],ix[0],axis=0),ix[1],axis=1),ix[2],axis=2)
2869	ix = rhoSize[:3]/2
2870	ib = 4
2871	if Ax == 'x':
2872	slab = np.sum(np.sum(rho[:,ix[1]-ib:ix[1]+ib,ix[2]-ib:ix[2]+ib,:],axis=2),axis=1)
2873	Plot.plot(tau,wave[0])
2874	elif Ax == 'y':
2875	slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,:,ix[2]-ib:ix[2]+ib,:],axis=2),axis=0)
2876	Plot.plot(tau,wave[1])
2877	elif Ax == 'z':
2878	slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,ix[1]-ib:ix[1]+ib,:,:],axis=1),axis=0)
2879	Plot.plot(tau,wave[2])
2880	Plot.set_title(Title)
2881	Plot.set_xlabel('t')
2882	Plot.set_ylabel(r'$\mathsf{\Delta}$%s'%(Ax))
2883	Slab = np.hstack((slab,slab,slab))
2884	Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Off.005,.5+Off.005))
2885	Page.canvas.draw()
2886
2887	################################################################################
2888	##### PlotCovariance
2889	################################################################################
2890
2891	def PlotCovariance(G2frame,Data):
2892	'needs a doc string'
2893	if not Data:
2894	print 'No covariance matrix available'
2895	return
2896	varyList = Data['varyList']
2897	values = Data['variables']
2898	Xmax = len(varyList)
2899	covMatrix = Data['covMatrix']
2900	sig = np.sqrt(np.diag(covMatrix))
2901	xvar = np.outer(sig,np.ones_like(sig))
2902	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
2903	title = ' for\n'+Data['title']
2904	newAtomDict = Data.get('newAtomDict',{})
2905
2906
2907	def OnPlotKeyPress(event):
2908	newPlot = False
2909	if event.key == 's':
2910	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2911	choice.sort()
2912	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2913	if dlg.ShowModal() == wx.ID_OK:
2914	sel = dlg.GetSelection()
2915	G2frame.VcovColor = choice[sel]
2916	else:
2917	G2frame.VcovColor = 'RdYlGn'
2918	dlg.Destroy()
2919	PlotCovariance(G2frame,Data)
2920
2921	def OnMotion(event):
2922	#there is a problem here - reports wrong values
2923	if event.button:
2924	ytics = imgAx.get_yticks()
2925	ytics = np.where(ytics<len(varyList),ytics,-1)
2926	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
2927	imgAx.set_yticklabels(ylabs)
2928	if event.xdata and event.ydata: #avoid out of frame errors
2929	xpos = int(event.xdata+.5)
2930	ypos = int(event.ydata+.5)
2931	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
2932	if xpos == ypos:
2933	value = values[xpos]
2934	name = varyList[xpos]
2935	if varyList[xpos] in newAtomDict:
2936	name,value = newAtomDict[name]
2937	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
2938	else:
2939	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
2940	Page.canvas.SetToolTipString(msg)
2941	G2frame.G2plotNB.status.SetFields(['',msg])
2942
2943	try:
2944	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2945	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2946	Page.figure.clf()
2947	Plot = Page.figure.gca()
2948	if not Page.IsShown():
2949	Page.Show()
2950	except ValueError:
2951	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
2952	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2953	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2954	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2955	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2956	Page.Choice = ['s: to change colors']
2957	Page.keyPress = OnPlotKeyPress
2958	Page.SetFocus()
2959	G2frame.G2plotNB.status.SetFields(['',''])
2960	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
2961	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower',
2962	vmin=-1.,vmax=1.)
2963	imgAx = Img.get_axes()
2964	ytics = imgAx.get_yticks()
2965	ylabs = [varyList[int(i)] for i in ytics[:-1]]
2966	imgAx.set_yticklabels(ylabs)
2967	colorBar = Page.figure.colorbar(Img)
2968	Plot.set_title('V-Cov matrix'+title)
2969	Plot.set_xlabel('Variable number')
2970	Plot.set_ylabel('Variable name')
2971	Page.canvas.draw()
2972
2973	################################################################################
2974	##### PlotTorsion
2975	################################################################################
2976
2977	def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]):
2978	'needs a doc string'
2979
2980	global names
2981	names = Names
2982	sum = np.sum(Torsion)
2983	torsion = np.log(2*Torsion+1.)/sum
2984	tMin = np.min(torsion)
2985	tMax = np.max(torsion)
2986	torsion = 3.*(torsion-tMin)/(tMax-tMin)
2987	X = np.linspace(0.,360.,num=45)
2988
2989	def OnPick(event):
2990	ind = event.ind[0]
2991	msg = 'atoms:'+names[ind]
2992	Page.canvas.SetToolTipString(msg)
2993	try:
2994	page = G2frame.dataDisplay.GetSelection()
2995	except:
2996	return
2997	if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints':
2998	torGrid = G2frame.dataDisplay.GetPage(page).Torsions
2999	torGrid.ClearSelection()
3000	for row in range(torGrid.GetNumberRows()):
3001	if names[ind] in torGrid.GetCellValue(row,0):
3002	torGrid.SelectRow(row)
3003	torGrid.ForceRefresh()
3004
3005	def OnMotion(event):
3006	if event.xdata and event.ydata: #avoid out of frame errors
3007	xpos = event.xdata
3008	ypos = event.ydata
3009	msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos)
3010	Page.canvas.SetToolTipString(msg)
3011
3012	try:
3013	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
3014	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3015	Page.figure.clf()
3016	Plot = Page.figure.gca()
3017	if not Page.IsShown():
3018	Page.Show()
3019	except ValueError:
3020	Plot = G2frame.G2plotNB.addMpl('Torsion').gca()
3021	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
3022	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3023	Page.canvas.mpl_connect('pick_event', OnPick)
3024	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3025
3026	Page.SetFocus()
3027	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms'])
3028	Plot.plot(X,torsion,'b+')
3029	if len(Coeff):
3030	X2 = np.linspace(0.,360.,45)
3031	Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2])
3032	Plot.plot(X2,Y2,'r')
3033	if len(Angles):
3034	Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles])
3035	Plot.plot(Angles,Eval,'ro',picker=5)
3036	Plot.set_xlim((0.,360.))
3037	Plot.set_title('Torsion angles for '+TorName+' in '+phaseName)
3038	Plot.set_xlabel('angle',fontsize=16)
3039	Plot.set_ylabel('Energy',fontsize=16)
3040	Page.canvas.draw()
3041
3042	################################################################################
3043	##### PlotRama
3044	################################################################################
3045
3046	def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]):
3047	'needs a doc string'
3048
3049	global names
3050	names = Names
3051	rama = np.log(2*Rama+1.)
3052	ramaMax = np.max(rama)
3053	rama = np.reshape(rama,(45,45))
3054	global Phi,Psi
3055	Phi = []
3056	Psi = []
3057
3058	def OnPlotKeyPress(event):
3059	newPlot = False
3060	if event.key == 's':
3061	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3062	choice.sort()
3063	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
3064	if dlg.ShowModal() == wx.ID_OK:
3065	sel = dlg.GetSelection()
3066	G2frame.RamaColor = choice[sel]
3067	else:
3068	G2frame.RamaColor = 'RdYlGn'
3069	dlg.Destroy()
3070	PlotRama(G2frame,phaseName,Rama)
3071
3072	def OnPick(event):
3073	ind = event.ind[0]
3074	msg = 'atoms:'+names[ind]
3075	Page.canvas.SetToolTipString(msg)
3076	try:
3077	page = G2frame.dataDisplay.GetSelection()
3078	except:
3079	return
3080	if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints':
3081	ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas
3082	ramaGrid.ClearSelection()
3083	for row in range(ramaGrid.GetNumberRows()):
3084	if names[ind] in ramaGrid.GetCellValue(row,0):
3085	ramaGrid.SelectRow(row)
3086	ramaGrid.ForceRefresh()
3087
3088	def OnMotion(event):
3089	if event.xdata and event.ydata: #avoid out of frame errors
3090	xpos = event.xdata
3091	ypos = event.ydata
3092	msg = 'phi/psi: %5.3f %5.3f'%(xpos,ypos)
3093	Page.canvas.SetToolTipString(msg)
3094
3095	try:
3096	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
3097	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3098	Page.figure.clf()
3099	Plot = Page.figure.gca()
3100	if not Page.IsShown():
3101	Page.Show()
3102	except ValueError:
3103	Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca()
3104	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
3105	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3106	Page.canvas.mpl_connect('pick_event', OnPick)
3107	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3108	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
3109
3110	Page.Choice = ['s: to change colors']
3111	Page.keyPress = OnPlotKeyPress
3112	Page.SetFocus()
3113	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms'])
3114	acolor = mpl.cm.get_cmap(G2frame.RamaColor)
3115	if RamaName == 'All' or '-1' in RamaName:
3116	if len(Coeff):
3117	X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45))
3118	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
3119	Plot.contour(X,Y,np.reshape(Z,(45,45)))
3120	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
3121	extent=[-180,180,-180,180],origin='lower')
3122	if len(PhiPsi):
3123	Phi,Psi = PhiPsi.T
3124	Phi = np.where(Phi>180.,Phi-360.,Phi)
3125	Psi = np.where(Psi>180.,Psi-360.,Psi)
3126	Plot.plot(Phi,Psi,'ro',picker=5)
3127	Plot.set_xlim((-180.,180.))
3128	Plot.set_ylim((-180.,180.))
3129	else:
3130	if len(Coeff):
3131	X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45))
3132	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
3133	Plot.contour(X,Y,np.reshape(Z,(45,45)))
3134	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
3135	extent=[0,360,0,360],origin='lower')
3136	if len(PhiPsi):
3137	Phi,Psi = PhiPsi.T
3138	Plot.plot(Phi,Psi,'ro',picker=5)
3139	Plot.set_xlim((0.,360.))
3140	Plot.set_ylim((0.,360.))
3141	Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName)
3142	Plot.set_xlabel(r'$\phi$',fontsize=16)
3143	Plot.set_ylabel(r'$\psi$',fontsize=16)
3144	colorBar = Page.figure.colorbar(Img)
3145	Page.canvas.draw()
3146
3147
3148	################################################################################
3149	##### PlotSeq
3150	################################################################################
3151	def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX,fitnum=None,fitvals=None):
3152	'''Plot a result from a sequential refinement
3153
3154	:param wx.Frame G2frame: The main GSAS-II tree "window"
3155	:param list ColumnList: list of int values corresponding to columns
3156	selected as y values
3157	:param function TableGet: a function that takes a column number
3158	as argument and returns the column label, the values and there ESDs (or None)
3159	:param function SelectX: a function that returns a selected column
3160	number (or None) as the X-axis selection
3161	'''
3162	global Title,xLabel,yLabel
3163	xLabel = yLabel = Title = ''
3164	def OnMotion(event):
3165	if event.xdata and event.ydata: #avoid out of frame errors
3166	xpos = event.xdata
3167	ypos = event.ydata
3168	msg = '%5.3f %.6g'%(xpos,ypos)
3169	Page.canvas.SetToolTipString(msg)
3170
3171	def OnKeyPress(event):
3172	global Title,xLabel,yLabel
3173	if event.key == 's':
3174	G2frame.seqXaxis = G2frame.seqXselect()
3175	Draw()
3176	elif event.key == 't':
3177	dlg = G2gd.MultiStringDialog(G2frame,'Set titles & labels',[' Title ',' x-Label ',' y-Label '],
3178	[Title,xLabel,yLabel])
3179	if dlg.Show():
3180	Title,xLabel,yLabel = dlg.GetValues()
3181	dlg.Destroy()
3182	Draw()
3183
3184	def Draw():
3185	global Title,xLabel,yLabel
3186	Page.SetFocus()
3187	G2frame.G2plotNB.status.SetStatusText('press s to select X axis, t to change titles',1)
3188	Plot.clear()
3189	if G2frame.seqXaxis is not None:
3190	xName,X,Xsig = Page.seqTableGet(G2frame.seqXaxis)
3191	else:
3192	X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1)
3193	xName = 'Data sequence number'
3194	for col in Page.seqYaxisList:
3195	name,Y,sig = Page.seqTableGet(col)
3196	# deal with missing (None) values
3197	Xnew = []
3198	Ynew = []
3199	Ysnew = []
3200	for i in range(len(X)):
3201	if X[i] is None or Y[i] is None: continue
3202	Xnew.append(X[i])
3203	Ynew.append(Y[i])
3204	if sig: Ysnew.append(sig[i])
3205	if Ysnew:
3206	if G2frame.seqReverse and not G2frame.seqXaxis:
3207	Ynew = Ynew[::-1]
3208	Ysnew = Ysnew[::-1]
3209	Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name)
3210	else:
3211	if G2frame.seqReverse and not G2frame.seqXaxis:
3212	Ynew = Ynew[::-1]
3213	Plot.plot(Xnew,Ynew)
3214	Plot.plot(Xnew,Ynew,'o',label=name)
3215	if Page.fitvals: # TODO: deal with fitting of None values
3216	if G2frame.seqReverse and not G2frame.seqXaxis:
3217	Page.fitvals = Page.fitvals[::-1]
3218	Plot.plot(X,Page.fitvals,label='Fit')
3219
3220	Plot.legend(loc='best')
3221	print Title,xLabel,yLabel
3222	if Title:
3223	Plot.set_title(Title)
3224	else:
3225	Plot.set_title('')
3226	if xLabel:
3227	Plot.set_xlabel(xLabel)
3228	else:
3229	Plot.set_xlabel(xName)
3230	if yLabel:
3231	Plot.set_ylabel(yLabel)
3232	else:
3233	Plot.set_ylabel('Parameter values')
3234	Page.canvas.draw()
3235
3236	G2frame.seqXselect = SelectX
3237	try:
3238	G2frame.seqXaxis
3239	except:
3240	G2frame.seqXaxis = None
3241
3242	if fitnum is None:
3243	label = 'Sequential refinement'
3244	else:
3245	label = 'Parametric fit #'+str(fitnum+1)
3246	try:
3247	plotNum = G2frame.G2plotNB.plotList.index(label)
3248	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3249	Page.figure.clf()
3250	Plot = Page.figure.gca()
3251	if not Page.IsShown():
3252	Page.Show()
3253	except ValueError:
3254	Plot = G2frame.G2plotNB.addMpl(label).gca()
3255	plotNum = G2frame.G2plotNB.plotList.index(label)
3256	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3257	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
3258	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3259	Page.Choice = ['s - select x-axis','t - change titles',]
3260	Page.keyPress = OnKeyPress
3261	Page.seqYaxisList = ColumnList
3262	Page.seqTableGet = TableGet
3263	Page.fitvals = fitvals
3264
3265	Draw()
3266	G2frame.G2plotNB.nb.SetSelection(plotNum) # raises plot tab
3267
3268	################################################################################
3269	##### PlotExposedImage & PlotImage
3270	################################################################################
3271
3272	def PlotExposedImage(G2frame,newPlot=False,event=None):
3273	'''General access module for 2D image plotting
3274	'''
3275	plotNo = G2frame.G2plotNB.nb.GetSelection()
3276	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
3277	PlotImage(G2frame,newPlot,event,newImage=True)
3278	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
3279	PlotIntegration(G2frame,newPlot,event)
3280
3281	def OnStartMask(G2frame):
3282	'''Initiate the start of a Frame or Polygon map
3283
3284	:param wx.Frame G2frame: The main GSAS-II tree "window"
3285	:param str eventkey: a single letter ('f' or 'p') that
3286	determines what type of mask is created.
3287	'''
3288	Masks = G2frame.PatternTree.GetItemPyData(
3289	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3290	if G2frame.MaskKey == 'f':
3291	Masks['Frames'] = []
3292	elif G2frame.MaskKey == 'p':
3293	Masks['Polygons'].append([])
3294	elif G2frame.MaskKey == 's':
3295	Masks['Points'].append([])
3296	elif G2frame.MaskKey == 'a':
3297	Masks['Arcs'].append([])
3298	elif G2frame.MaskKey == 'r':
3299	Masks['Rings'].append([])
3300	G2imG.UpdateMasks(G2frame,Masks)
3301	PlotImage(G2frame,newImage=True)
3302
3303	def OnStartNewDzero(G2frame):
3304	'''Initiate the start of adding a new d-zero to a strain data set
3305
3306	:param wx.Frame G2frame: The main GSAS-II tree "window"
3307	:param str eventkey: a single letter ('a') that
3308	triggers the addition of a d-zero.
3309	'''
3310	G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',0)
3311	G2frame.PickId = G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain')
3312	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
3313	return data
3314
3315	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
3316	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
3317	masks, etc.
3318	'''
3319	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
3320	import numpy.ma as ma
3321	Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.))
3322	global Data,Masks,StrSta
3323	colors=['b','g','r','c','m','k']
3324	Data = G2frame.PatternTree.GetItemPyData(
3325	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3326	# patch
3327	if 'invert_x' not in Data:
3328	Data['invert_x'] = False
3329	Data['invert_y'] = True
3330	# end patch
3331	Masks = G2frame.PatternTree.GetItemPyData(
3332	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3333	try: #may be absent
3334	StrSta = G2frame.PatternTree.GetItemPyData(
3335	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
3336	except TypeError: #is missing
3337	StrSta = {}
3338
3339	def OnImMotion(event):
3340	Page.canvas.SetToolTipString('')
3341	sizexy = Data['size']
3342	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
3343	Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata))
3344	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3345	item = G2frame.itemPicked
3346	pixelSize = Data['pixelSize']
3347	scalex = 1000./pixelSize[0]
3348	scaley = 1000./pixelSize[1]
3349	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
3350	if 'Text' in str(item):
3351	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
3352	else:
3353	xcent,ycent = Data['center']
3354	xpos = event.xdata-xcent
3355	ypos = event.ydata-ycent
3356	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
3357	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
3358	Page.canvas.SetToolTipString('%6d deg'%(azm))
3359	elif 'line1' in str(item) or 'line2' in str(item):
3360	Page.canvas.SetToolTipString('%8.3f deg'%(tth))
3361	else:
3362	xpos = event.xdata
3363	ypos = event.ydata
3364	xpix = xpos*scalex
3365	ypix = ypos*scaley
3366	Int = 0
3367	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
3368	Int = G2frame.ImageZ[ypix][xpix]
3369	tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
3370	Q = 2.*math.pi/dsp
3371	fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)]
3372	if G2frame.MaskKey in ['p','f']:
3373	fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon'
3374	elif G2frame.StrainKey:
3375	fields[0] = 'd-zero pick active'
3376	G2frame.G2plotNB.status.SetFields(fields)
3377
3378	def OnImPlotKeyPress(event):
3379	try:
3380	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
3381	except TypeError:
3382	return
3383	if PickName == 'Masks':
3384	if event.key in ['l','p','f','s','a','r']:
3385	G2frame.MaskKey = event.key
3386	OnStartMask(G2frame)
3387	PlotImage(G2frame,newPlot=False)
3388
3389	elif PickName == 'Stress/Strain':
3390	if event.key in ['a',]:
3391	G2frame.StrainKey = event.key
3392	StrSta = OnStartNewDzero(G2frame)
3393	PlotImage(G2frame,newPlot=False)
3394
3395	elif PickName == 'Image Controls':
3396	if event.key in ['c',]:
3397	Xpos = event.xdata
3398	if not Xpos: #got point out of frame
3399	return
3400	Ypos = event.ydata
3401	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
3402	'Center change',style=wx.OK\|wx.CANCEL)
3403	try:
3404	if dlg.ShowModal() == wx.ID_OK:
3405	print 'move center to: ',Xpos,Ypos
3406	Data['center'] = [Xpos,Ypos]
3407	G2imG.UpdateImageControls(G2frame,Data,Masks)
3408	PlotImage(G2frame,newPlot=False)
3409	finally:
3410	dlg.Destroy()
3411	return
3412	elif event.key == 'l':
3413	G2frame.logPlot = not G2frame.logPlot
3414	elif event.key in ['x',]:
3415	Data['invert_x'] = not Data['invert_x']
3416	elif event.key in ['y',]:
3417	Data['invert_y'] = not Data['invert_y']
3418	PlotImage(G2frame,newPlot=True)
3419
3420	def OnKeyBox(event):
3421	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
3422	event.key = cb.GetValue()[0]
3423	cb.SetValue(' key press')
3424	if event.key in ['l','s','a','r','p','x','y']:
3425	wx.CallAfter(OnImPlotKeyPress,event)
3426	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
3427
3428	def OnImPick(event):
3429	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
3430	return
3431	if G2frame.itemPicked is not None: return
3432	G2frame.itemPicked = event.artist
3433	G2frame.mousePicked = event.mouseevent
3434
3435	def OnImRelease(event):
3436	try:
3437	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
3438	except TypeError:
3439	return
3440	if PickName not in ['Image Controls','Masks','Stress/Strain']:
3441	return
3442	pixelSize = Data['pixelSize']
3443	scalex = 1000./pixelSize[0]
3444	scaley = 1000./pixelSize[1]
3445	# pixLimit = Data['pixLimit'] #can be too tight
3446	pixLimit = 20 #this makes the search box 40x40 pixels
3447	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
3448	Xpos = event.xdata
3449	if not (Xpos and G2frame.ifGetRing): #got point out of frame
3450	return
3451	Ypos = event.ydata
3452	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
3453	if event.button == 1:
3454	Xpix = Xpos*scalex
3455	Ypix = Ypos*scaley
3456	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix)
3457	if I and J:
3458	xpos += .5 #shift to pixel center
3459	ypos += .5
3460	xpos /= scalex #convert to mm
3461	ypos /= scaley
3462	Data['ring'].append([xpos,ypos])
3463	elif event.button == 3:
3464	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...',0)
3465	if G2img.ImageCalibrate(G2frame,Data):
3466	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check',0)
3467	print 'Calibration successful'
3468	else:
3469	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose',0)
3470	print 'Calibration failed'
3471	G2frame.ifGetRing = False
3472	G2imG.UpdateImageControls(G2frame,Data,Masks)
3473	return
3474	PlotImage(G2frame,newImage=False)
3475	return
3476	elif G2frame.MaskKey and PickName == 'Masks':
3477	Xpos,Ypos = [event.xdata,event.ydata]
3478	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
3479	return
3480	if G2frame.MaskKey == 's' and event.button == 1:
3481	Masks['Points'][-1] = [Xpos,Ypos,1.]
3482	G2frame.MaskKey = ''
3483	elif G2frame.MaskKey == 'r' and event.button == 1:
3484	tth = G2img.GetTth(Xpos,Ypos,Data)
3485	Masks['Rings'][-1] = [tth,0.1]
3486	G2frame.MaskKey = ''
3487	elif G2frame.MaskKey == 'a' and event.button == 1:
3488	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
3489	azm = int(azm)
3490	Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1]
3491	G2frame.MaskKey = ''
3492	elif G2frame.MaskKey =='p':
3493	polygon = Masks['Polygons'][-1]
3494	if len(polygon) > 2 and event.button == 3:
3495	x0,y0 = polygon[0]
3496	polygon.append([x0,y0])
3497	G2frame.MaskKey = ''
3498	G2frame.G2plotNB.status.SetFields(['','Polygon closed'])
3499	else:
3500	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)])
3501	polygon.append([Xpos,Ypos])
3502	elif G2frame.MaskKey =='f':
3503	frame = Masks['Frames']
3504	if len(frame) > 2 and event.button == 3:
3505	x0,y0 = frame[0]
3506	frame.append([x0,y0])
3507	G2frame.MaskKey = ''
3508	G2frame.G2plotNB.status.SetFields(['','Frame closed'])
3509	else:
3510	G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)])
3511	frame.append([Xpos,Ypos])
3512	G2imG.UpdateMasks(G2frame,Masks)
3513	PlotImage(G2frame,newImage=False)
3514	elif PickName == 'Stress/Strain' and G2frame.StrainKey:
3515	Xpos,Ypos = [event.xdata,event.ydata]
3516	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
3517	return
3518	dsp = G2img.GetDsp(Xpos,Ypos,Data)
3519	StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':1.0,
3520	'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]})
3521	R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ,Data)
3522	if not len(R):
3523	del StrSta['d-zero'][-1]
3524	G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection')
3525	StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True)
3526	G2frame.StrainKey = ''
3527	G2imG.UpdateStressStrain(G2frame,StrSta)
3528	PlotStrain(G2frame,StrSta)
3529	PlotImage(G2frame,newPlot=False)
3530	else:
3531	Xpos,Ypos = [event.xdata,event.ydata]
3532	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
3533	return
3534	if G2frame.ifGetRing: #delete a calibration ring pick
3535	xypos = [Xpos,Ypos]
3536	rings = Data['ring']
3537	for ring in rings:
3538	if np.allclose(ring,xypos,.01,0):
3539	rings.remove(ring)
3540	else:
3541	tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3]
3542	itemPicked = str(G2frame.itemPicked)
3543	if 'Line2D' in itemPicked and PickName == 'Image Controls':
3544	if 'line1' in itemPicked:
3545	Data['IOtth'][0] = max(tth,0.001)
3546	elif 'line2' in itemPicked:
3547	Data['IOtth'][1] = tth
3548	elif 'line3' in itemPicked:
3549	Data['LRazimuth'][0] = int(azm)
3550	elif 'line4' in itemPicked and not Data['fullIntegrate']:
3551	Data['LRazimuth'][1] = int(azm)
3552
3553	Data['LRazimuth'][0] %= 360
3554	Data['LRazimuth'][1] %= 360
3555	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
3556	Data['LRazimuth'][1] += 360
3557	if Data['fullIntegrate']:
3558	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
3559
3560	if Data['IOtth'][0] > Data['IOtth'][1]:
3561	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
3562
3563	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
3564	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
3565	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
3566	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
3567	elif 'Circle' in itemPicked and PickName == 'Masks':
3568	spots = Masks['Points']
3569	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
3570	newPos = np.array([float(newPos[0]),float(newPos[1])])
3571	for spot in spots:
3572	if spot and np.allclose(np.array([spot[:2]]),newPos):
3573	spot[:2] = Xpos,Ypos
3574	G2imG.UpdateMasks(G2frame,Masks)
3575	elif 'Line2D' in itemPicked and PickName == 'Masks':
3576	Obj = G2frame.itemPicked.findobj()
3577	rings = Masks['Rings']
3578	arcs = Masks['Arcs']
3579	polygons = Masks['Polygons']
3580	frame = Masks['Frames']
3581	for ring in G2frame.ringList:
3582	if Obj == ring[0]:
3583	rN = ring[1]
3584	if ring[2] == 'o':
3585	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2.
3586	else:
3587	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2.
3588	for arc in G2frame.arcList:
3589	if Obj == arc[0]:
3590	aN = arc[1]
3591	if arc[2] == 'o':
3592	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2
3593	elif arc[2] == 'i':
3594	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2
3595	elif arc[2] == 'l':
3596	arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data))
3597	else:
3598	arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data))
3599	for poly in G2frame.polyList: #merging points problem here?
3600	if Obj == poly[0]:
3601	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
3602	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
3603	pN = poly[1]
3604	for i,xy in enumerate(polygons[pN]):
3605	if np.allclose(np.array([xy]),oldPos,atol=1.0):
3606	if event.button == 1:
3607	polygons[pN][i] = Xpos,Ypos
3608	elif event.button == 3:
3609	polygons[pN].insert(i,[Xpos,Ypos])
3610	break
3611	if frame:
3612	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
3613	for i,xy in enumerate(frame):
3614	if np.allclose(np.array([xy]),oldPos,atol=1.0):
3615	if event.button == 1:
3616	frame[i] = Xpos,Ypos
3617	elif event.button == 3:
3618	frame.insert(i,[Xpos,Ypos])
3619	break
3620	G2imG.UpdateMasks(G2frame,Masks)
3621	# else: #keep for future debugging
3622	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
3623	PlotImage(G2frame,newImage=True)
3624	G2frame.itemPicked = None
3625
3626	try:
3627	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
3628	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3629	if not newPlot:
3630	Plot = Page.figure.gca() #get previous powder plot & get limits
3631	xylim = Plot.get_xlim(),Plot.get_ylim()
3632	if newImage:
3633	Page.figure.clf()
3634	Plot = Page.figure.gca() #get a fresh plot after clf()
3635	except ValueError:
3636	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
3637	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
3638	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3639	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
3640	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
3641	Page.canvas.mpl_connect('pick_event', OnImPick)
3642	Page.canvas.mpl_connect('button_release_event', OnImRelease)
3643	xylim = []
3644	Page.Choice = None
3645	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
3646	Page.SetFocus()
3647	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
3648	G2frame.G2plotNB.status.DestroyChildren()
3649	if G2frame.logPlot:
3650	Title = 'log('+Title+')'
3651	Plot.set_title(Title)
3652	try:
3653	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
3654	Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',)
3655	if G2frame.logPlot:
3656	Page.Choice[1] = 'l: log(I) off'
3657	Page.keyPress = OnImPlotKeyPress
3658	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]:
3659	Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask',
3660	'p: polygon mask','f: frame mask',)
3661	if G2frame.logPlot:
3662	Page.Choice[1] = 'l: log(I) off'
3663	Page.keyPress = OnImPlotKeyPress
3664	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]:
3665	Page.Choice = (' key press','a: add new ring',)
3666	Page.keyPress = OnImPlotKeyPress
3667	except TypeError:
3668	pass
3669	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
3670	dark = Data.get('dark image',[0,''])
3671	if dark[0]:
3672	darkfile = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
3673	G2frame.root,dark[0]))[1]
3674	if imagefile != G2frame.oldImagefile:
3675	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
3676	if not imagefile:
3677	G2frame.G2plotNB.Delete('2D Powder Image')
3678	return
3679	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
3680	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
3681	if dark[0]:
3682	darkImg = G2IO.GetImageData(G2frame,darkfile,imageOnly=True)
3683	G2frame.ImageZ += dark[1]*darkImg
3684	G2frame.oldImagefile = imagefile
3685
3686	imScale = 1
3687	if len(G2frame.ImageZ) > 1024:
3688	imScale = len(G2frame.ImageZ)/1024
3689	sizexy = Data['size']
3690	pixelSize = Data['pixelSize']
3691	scalex = 1000./pixelSize[0]
3692	scaley = 1000./pixelSize[1]
3693	Xmax = sizexy[0]*pixelSize[0]/1000.
3694	Ymax = sizexy[1]*pixelSize[1]/1000.
3695	xlim = (0,Xmax)
3696	ylim = (Ymax,0)
3697	Imin,Imax = Data['range'][1]
3698	acolor = mpl.cm.get_cmap(Data['color'])
3699	xcent,ycent = Data['center']
3700	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
3701	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
3702	#do threshold mask - "real" mask - others are just bondaries
3703	Zlim = Masks['Thresholds'][1]
3704	wx.BeginBusyCursor()
3705	try:
3706
3707	if newImage:
3708	Imin,Imax = Data['range'][1]
3709	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]),Zlim[1])
3710	MaskA = ma.getmaskarray(MA)
3711	A = G2img.ImageCompress(MA,imScale)
3712	AM = G2img.ImageCompress(MaskA,imScale)
3713	if G2frame.logPlot:
3714	A = np.where(A>Imin,np.where(A<Imax,A,0),0)
3715	A = np.where(A>0,np.log(A),0)
3716	AM = np.where(AM>0,np.log(AM),0)
3717	Imin,Imax = [np.amin(A),np.amax(A)]
3718	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
3719	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
3720	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
3721	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
3722
3723	Plot.plot(xcent,ycent,'x')
3724	#G2frame.PatternTree.GetItemText(item)
3725	if Data['showLines']:
3726	LRAzim = Data['LRazimuth'] #NB: integers
3727	Nazm = Data['outAzimuths']
3728	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
3729	AzmthOff = Data['azmthOff']
3730	IOtth = Data['IOtth']
3731	wave = Data['wavelength']
3732	dspI = wave/(2.0*sind(IOtth[0]/2.0))
3733	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
3734	dspO = wave/(2.0*sind(IOtth[1]/2.0))
3735	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
3736	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
3737	if ellI:
3738	xyI = []
3739	for azm in Azm:
3740	xy = G2img.GetDetectorXY(dspI,azm,Data)
3741	if np.any(xy):
3742	xyI.append(xy)
3743	if len(xyI):
3744	xyI = np.array(xyI)
3745	arcxI,arcyI = xyI.T
3746	Plot.plot(arcxI,arcyI,picker=3)
3747	if ellO:
3748	xyO = []
3749	for azm in Azm:
3750	xy = G2img.GetDetectorXY(dspO,azm,Data)
3751	if np.any(xy):
3752	xyO.append(xy)
3753	if len(xyO):
3754	xyO = np.array(xyO)
3755	arcxO,arcyO = xyO.T
3756	Plot.plot(arcxO,arcyO,picker=3)
3757	if ellO and ellI:
3758	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
3759	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
3760	for i in range(Nazm):
3761	cake = LRAzim[0]+i*delAzm-AzmthOff
3762	if Data['centerAzm']:
3763	cake += delAzm/2.
3764	ind = np.searchsorted(Azm,cake)
3765	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
3766
3767	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
3768	for xring,yring in Data['ring']:
3769	Plot.plot(xring,yring,'r+',picker=3)
3770	if Data['setRings']:
3771	N = 0
3772	for ring in Data['rings']:
3773	xring,yring = np.array(ring).T[:2]
3774	Plot.plot(xring,yring,'.',color=colors[N%6])
3775	N += 1
3776	for ellipse in Data['ellipses']: #what about hyperbola?
3777	cent,phi,[width,height],col = ellipse
3778	if width > 0: #ellipses
3779	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
3780	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
3781	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
3782	for N,ring in enumerate(StrSta['d-zero']):
3783	xring,yring = ring['ImxyObs']
3784	Plot.plot(xring,yring,colors[N%6]+'.')
3785	#masks - mask lines numbered after integration limit lines
3786	spots = Masks['Points']
3787	rings = Masks['Rings']
3788	arcs = Masks['Arcs']
3789	polygons = Masks['Polygons']
3790	if 'Frames' not in Masks:
3791	Masks['Frames'] = []
3792	frame = Masks['Frames']
3793	for spot in spots:
3794	if spot:
3795	x,y,d = spot
3796	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
3797	G2frame.ringList = []
3798	for iring,ring in enumerate(rings):
3799	if ring:
3800	tth,thick = ring
3801	wave = Data['wavelength']
3802	xy1 = []
3803	xy2 = []
3804	Azm = np.linspace(0,362,181)
3805	for azm in Azm:
3806	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
3807	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
3808	x1,y1 = np.array(xy1).T
3809	x2,y2 = np.array(xy2).T
3810	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
3811	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
3812	G2frame.arcList = []
3813	for iarc,arc in enumerate(arcs):
3814	if arc:
3815	tth,azm,thick = arc
3816	wave = Data['wavelength']
3817	xy1 = []
3818	xy2 = []
3819	aR = azm[0],azm[1],azm[1]-azm[0]
3820	if azm[1]-azm[0] > 180:
3821	aR[2] /= 2
3822	Azm = np.linspace(aR[0],aR[1],aR[2])
3823	for azm in Azm:
3824	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
3825	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
3826	x1,y1 = np.array(xy1).T
3827	x2,y2 = np.array(xy2).T
3828	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
3829	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
3830	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
3831	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
3832	G2frame.polyList = []
3833	for ipoly,polygon in enumerate(polygons):
3834	if polygon:
3835	x,y = np.hsplit(np.array(polygon),2)
3836	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
3837	Plot.plot(x,y,'r')
3838	G2frame.frameList = []
3839	if frame:
3840	x,y = np.hsplit(np.array(frame),2)
3841	G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0])
3842	Plot.plot(x,y,'g')
3843	if newImage:
3844	colorBar = Page.figure.colorbar(Img)
3845	Plot.set_xlim(xlim)
3846	Plot.set_ylim(ylim)
3847	if Data['invert_x']:
3848	Plot.invert_xaxis()
3849	if Data['invert_y']:
3850	Plot.invert_yaxis()
3851	if not newPlot and xylim:
3852	Page.toolbar.push_current()
3853	Plot.set_xlim(xylim[0])
3854	Plot.set_ylim(xylim[1])
3855	xylim = []
3856	Page.toolbar.push_current()
3857	Page.toolbar.draw()
3858	# patch for wx 2.9 on Mac, to force a redraw
3859	i,j= wx.__version__.split('.')[0:2]
3860	if int(i)+int(j)/10. > 2.8 and 'wxOSX' in wx.PlatformInfo:
3861	Page.canvas.draw()
3862	else:
3863	Page.canvas.draw()
3864	finally:
3865	wx.EndBusyCursor()
3866
3867	################################################################################
3868	##### PlotIntegration
3869	################################################################################
3870
3871	def PlotIntegration(G2frame,newPlot=False,event=None):
3872	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
3873	'''
3874
3875	def OnMotion(event):
3876	Page.canvas.SetToolTipString('')
3877	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3878	azm = event.ydata
3879	tth = event.xdata
3880	if azm and tth:
3881	G2frame.G2plotNB.status.SetFields(\
3882	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3883
3884	try:
3885	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
3886	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3887	if not newPlot:
3888	Plot = Page.figure.gca() #get previous plot & get limits
3889	xylim = Plot.get_xlim(),Plot.get_ylim()
3890	Page.figure.clf()
3891	Plot = Page.figure.gca() #get a fresh plot after clf()
3892
3893	except ValueError:
3894	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
3895	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
3896	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3897	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3898	Page.views = False
3899	view = False
3900	Page.Choice = None
3901	if not event:
3902	Page.SetFocus()
3903
3904	Data = G2frame.PatternTree.GetItemPyData(
3905	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3906	image = G2frame.Integrate[0]
3907	xsc = G2frame.Integrate[1]
3908	ysc = G2frame.Integrate[2]
3909	Imin,Imax = Data['range'][1]
3910	acolor = mpl.cm.get_cmap(Data['color'])
3911	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3912	Plot.set_ylabel('azimuth',fontsize=12)
3913	Plot.set_xlabel('2-theta',fontsize=12)
3914	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
3915	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
3916	colorBar = Page.figure.colorbar(Img)
3917	# if Data['ellipses']:
3918	# for ellipse in Data['ellipses']:
3919	# x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3920	# tth,azm = G2img.GetTthAzm(x,y,Data)
3921	## azm = np.where(azm < 0.,azm+360,azm)
3922	# Plot.plot(tth,azm,'b,')
3923	if not newPlot:
3924	Page.toolbar.push_current()
3925	Plot.set_xlim(xylim[0])
3926	Plot.set_ylim(xylim[1])
3927	xylim = []
3928	Page.toolbar.push_current()
3929	Page.toolbar.draw()
3930	else:
3931	Page.canvas.draw()
3932
3933	################################################################################
3934	##### PlotTRImage
3935	################################################################################
3936
3937	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
3938	'''a test plot routine - not normally used
3939	'''
3940
3941	def OnMotion(event):
3942	Page.canvas.SetToolTipString('')
3943	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3944	azm = event.xdata
3945	tth = event.ydata
3946	if azm and tth:
3947	G2frame.G2plotNB.status.SetFields(\
3948	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3949
3950	try:
3951	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3952	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3953	if not newPlot:
3954	Plot = Page.figure.gca() #get previous plot & get limits
3955	xylim = Plot.get_xlim(),Plot.get_ylim()
3956	Page.figure.clf()
3957	Plot = Page.figure.gca() #get a fresh plot after clf()
3958
3959	except ValueError:
3960	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
3961	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3962	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3963	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3964	Page.views = False
3965	view = False
3966	Page.Choice = None
3967	Page.SetFocus()
3968
3969	Data = G2frame.PatternTree.GetItemPyData(
3970	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3971	Imin,Imax = Data['range'][1]
3972	step = (Imax-Imin)/5.
3973	V = np.arange(Imin,Imax,step)
3974	acolor = mpl.cm.get_cmap(Data['color'])
3975	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3976	Plot.set_xlabel('azimuth',fontsize=12)
3977	Plot.set_ylabel('2-theta',fontsize=12)
3978	Plot.contour(tax,tay,taz,V,cmap=acolor)
3979	if Data['showLines']:
3980	IOtth = Data['IOtth']
3981	if Data['fullIntegrate']:
3982	LRAzim = [-180,180]
3983	else:
3984	LRAzim = Data['LRazimuth'] #NB: integers
3985	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
3986	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
3987	if not Data['fullIntegrate']:
3988	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
3989	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
3990	if Data['setRings']:
3991	rings = np.concatenate((Data['rings']),axis=0)
3992	for xring,yring,dsp in rings:
3993	x,y = G2img.GetTthAzm(xring,yring,Data)
3994	Plot.plot(y,x,'r+')
3995	if Data['ellipses']:
3996	for ellipse in Data['ellipses']:
3997	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3998	x,y = np.hsplit(ring,2)
3999	tth,azm = G2img.GetTthAzm(x,y,Data)
4000	Plot.plot(azm,tth,'b,')
4001	if not newPlot:
4002	Page.toolbar.push_current()
4003	Plot.set_xlim(xylim[0])
4004	Plot.set_ylim(xylim[1])
4005	xylim = []
4006	Page.toolbar.push_current()
4007	Page.toolbar.draw()
4008	else:
4009	Page.canvas.draw()
4010
4011	################################################################################
4012	##### PlotStructure
4013	################################################################################
4014
4015	def PlotStructure(G2frame,data,firstCall=False):
4016	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
4017	thermal motion ellipsoids and polyhedra
4018	'''
4019
4020	def FindPeaksBonds(XYZ):
4021	rFact = data['Drawing'].get('radiusFactor',0.85) #data['Drawing'] could be empty!
4022	Bonds = [[] for x in XYZ]
4023	for i,xyz in enumerate(XYZ):
4024	Dx = XYZ-xyz
4025	dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
4026	IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2))
4027	for j in IndB[0]:
4028	Bonds[i].append(Dx[j]/2.)
4029	Bonds[j].append(-Dx[j]/2.)
4030	return Bonds
4031
4032	# PlotStructure initialization here
4033	ForthirdPI = 4.0*math.pi/3.0
4034	generalData = data['General']
4035	cell = generalData['Cell'][1:7]
4036	Vol = generalData['Cell'][7:8][0]
4037	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
4038	Gmat,gmat = G2lat.cell2Gmat(cell)
4039	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4040	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4041	SGData = generalData['SGData']
4042	if generalData['Type'] in ['modulated','magnetic']:
4043	SSGData = generalData['SSGData']
4044	Mydir = generalData['Mydir']
4045	atomData = data['Atoms']
4046	mapPeaks = []
4047	drawingData = data['Drawing']
4048	if not drawingData:
4049	return #nothing setup, nothing to draw
4050	if 'Map Peaks' in data:
4051	mapPeaks = np.array(data['Map Peaks'])
4052	peakMax = 100.
4053	if len(mapPeaks):
4054	peakMax = np.max(mapPeaks.T[0])
4055	resRBData = data['RBModels'].get('Residue',[])
4056	vecRBData = data['RBModels'].get('Vector',[])
4057	rbAtmDict = {}
4058	for rbObj in resRBData+vecRBData:
4059	exclList = ['X' for i in range(len(rbObj['Ids']))]
4060	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
4061	testRBObj = data.get('testRBObj',{})
4062	rbObj = testRBObj.get('rbObj',{})
4063	MCSA = data.get('MCSA',{})
4064	mcsaModels = MCSA.get('Models',[])
4065	if len(mcsaModels) > 1:
4066	XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA)
4067	mcsaXYZ = []
4068	mcsaTypes = []
4069	neqv = 0
4070	for xyz,atyp in zip(XYZs,Types):
4071	equiv = G2spc.GenAtom(xyz,SGData,All=True,Move=False)
4072	neqv = max(neqv,len(equiv))
4073	for item in equiv:
4074	mcsaXYZ.append(item[0])
4075	mcsaTypes.append(atyp)
4076	mcsaXYZ = np.array(mcsaXYZ)
4077	mcsaTypes = np.array(mcsaTypes)
4078	nuniq = mcsaXYZ.shape[0]/neqv
4079	mcsaXYZ = np.reshape(mcsaXYZ,(nuniq,neqv,3))
4080	mcsaTypes = np.reshape(mcsaTypes,(nuniq,neqv))
4081	cent = np.fix(np.sum(mcsaXYZ+2.,axis=0)/nuniq)-2
4082	cent[0] = [0,0,0] #make sure 1st one isn't moved
4083	mcsaXYZ = np.swapaxes(mcsaXYZ,0,1)-cent[:,np.newaxis,:]
4084	mcsaTypes = np.swapaxes(mcsaTypes,0,1)
4085	mcsaXYZ = np.reshape(mcsaXYZ,(nuniq*neqv,3))
4086	mcsaTypes = np.reshape(mcsaTypes,(nuniq*neqv))
4087	mcsaBonds = FindPeaksBonds(mcsaXYZ)
4088	drawAtoms = drawingData.get('Atoms',[])
4089	mapData = {}
4090	flipData = {}
4091	rhoXYZ = []
4092	showBonds = False
4093	if 'Map' in generalData:
4094	mapData = generalData['Map']
4095	showBonds = mapData.get('Show bonds',False)
4096	if 'Flip' in generalData:
4097	flipData = generalData['Flip']
4098	Wt = np.array([255,255,255])
4099	Rd = np.array([255,0,0])
4100	Gr = np.array([0,255,0])
4101	wxGreen = wx.Colour(0,255,0)
4102	Bl = np.array([0,0,255])
4103	Or = np.array([255,128,0])
4104	wxOrange = wx.Colour(255,128,0)
4105	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]])
4106	uEdges = np.array([
4107	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
4108	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
4109	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
4110	mD = 0.1
4111	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
4112	mapPeakVecs = np.inner(mV,Bmat)
4113
4114	backColor = np.array(list(drawingData['backColor'])+[0,])
4115	Bc = np.array(list(drawingData['backColor']))
4116	uColors = [Rd,Gr,Bl,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc]
4117	altDown = False
4118	shiftDown = False
4119	ctrlDown = False
4120	G2frame.tau = 0.
4121
4122	def OnKeyBox(event):
4123	mode = cb.GetValue()
4124	if mode in ['jpeg','bmp','tiff',]:
4125	try:
4126	import Image as Im
4127	except ImportError:
4128	try:
4129	from PIL import Image as Im
4130	except ImportError:
4131	print "PIL/pillow Image module not present. Cannot save images without this"
4132	raise Exception("PIL/pillow Image module not found")
4133	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
4134	size = Page.canvas.GetSize()
4135	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
4136	if mode in ['jpeg',]:
4137	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
4138	im = Im.new("RGBA", (size[0],size[1]))
4139	else:
4140	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
4141	im = Im.new("RGB", (size[0],size[1]))
4142	im.fromstring(Pix)
4143	im.save(Fname,mode)
4144	cb.SetValue(' save as/key:')
4145	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
4146	else:
4147	event.key = cb.GetValue()[0]
4148	cb.SetValue(' save as/key:')
4149	wx.CallAfter(OnKey,event)
4150	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
4151
4152	def OnKey(event): #on key UP!!
4153	try:
4154	keyCode = event.GetKeyCode()
4155	if keyCode > 255:
4156	keyCode = 0
4157	key = chr(keyCode)
4158	except AttributeError: #if from OnKeyBox above
4159	key = str(event.key).upper()
4160	indx = drawingData['selectedAtoms']
4161	cx,ct = drawingData['atomPtrs'][:2]
4162	if key in ['C']:
4163	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
4164	drawingData['viewDir'] = [0,0,1]
4165	drawingData['oldxy'] = []
4166	V0 = np.array([0,0,1])
4167	V = np.inner(Amat,V0)
4168	V /= np.sqrt(np.sum(V**2))
4169	A = np.arccos(np.sum(V*V0))
4170	Q = G2mth.AV2Q(A,[0,1,0])
4171	drawingData['Quaternion'] = Q
4172	SetViewPointText(drawingData['viewPoint'][0])
4173	SetViewDirText(drawingData['viewDir'])
4174	Q = drawingData['Quaternion']
4175	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4176	elif key in ['N']:
4177	drawAtoms = drawingData['Atoms']
4178	if not len(drawAtoms): #no atoms
4179	return
4180	pI = drawingData['viewPoint'][1]
4181	if not len(pI):
4182	pI = [0,0]
4183	if indx:
4184	pI[0] = indx[pI[1]]
4185	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4186	pI[1] += 1
4187	if pI[1] >= len(indx):
4188	pI[1] = 0
4189	else:
4190	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4191	pI[0] += 1
4192	if pI[0] >= len(drawAtoms):
4193	pI[0] = 0
4194	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
4195	SetViewPointText(drawingData['viewPoint'][0])
4196	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
4197
4198	elif key in ['P']:
4199	drawAtoms = drawingData['Atoms']
4200	if not len(drawAtoms): #no atoms
4201	return
4202	pI = drawingData['viewPoint'][1]
4203	if not len(pI):
4204	pI = [0,0]
4205	if indx:
4206	pI[0] = indx[pI[1]]
4207	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4208	pI[1] -= 1
4209	if pI[1] < 0:
4210	pI[1] = len(indx)-1
4211	else:
4212	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4213	pI[0] -= 1
4214	if pI[0] < 0:
4215	pI[0] = len(drawAtoms)-1
4216	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
4217	SetViewPointText(drawingData['viewPoint'][0])
4218	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
4219	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
4220	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
4221	SetMapRoll(dirDict[key])
4222	if 'rho' in generalData.get('4DmapData',{}):
4223	Set4DMapRoll(dirDict[key])
4224	SetPeakRoll(dirDict[key])
4225	SetMapPeaksText(mapPeaks)
4226	elif key in ['+','-','0'] and generalData['Type'] in ['modulated','magnetic']:
4227	if key == '0':
4228	G2frame.tau = 0.
4229	elif key =='+':
4230	G2frame.tau += 0.05
4231	elif key =='-':
4232	G2frame.tau -= 0.05
4233	G2frame.tau %= 1. #force 0-1 range
4234	Draw('key')
4235
4236	def GetTruePosition(xy,Add=False):
4237	View = glGetIntegerv(GL_VIEWPORT)
4238	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
4239	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
4240	Zmax = 1.
4241	if Add:
4242	Indx = GetSelectedAtoms()
4243	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
4244	for i,peak in enumerate(mapPeaks):
4245	x,y,z = peak[1:4]
4246	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
4247	XY = [int(X),int(View[3]-Y)]
4248	if np.allclose(xy,XY,atol=10) and Z < Zmax:
4249	Zmax = Z
4250	try:
4251	Indx.remove(i)
4252	ClearSelectedAtoms()
4253	for id in Indx:
4254	SetSelectedAtoms(id,Add)
4255	except:
4256	SetSelectedAtoms(i,Add)
4257	else:
4258	cx = drawingData['atomPtrs'][0]
4259	for i,atom in enumerate(drawAtoms):
4260	x,y,z = atom[cx:cx+3]
4261	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
4262	XY = [int(X),int(View[3]-Y)]
4263	if np.allclose(xy,XY,atol=10) and Z < Zmax:
4264	Zmax = Z
4265	try:
4266	Indx.remove(i)
4267	ClearSelectedAtoms()
4268	for id in Indx:
4269	SetSelectedAtoms(id,Add)
4270	except:
4271	SetSelectedAtoms(i,Add)
4272
4273	def OnMouseDown(event):
4274	xy = event.GetPosition()
4275	if event.ShiftDown():
4276	if event.LeftIsDown():
4277	GetTruePosition(xy)
4278	elif event.RightIsDown():
4279	GetTruePosition(xy,True)
4280	else:
4281	drawingData['oldxy'] = list(xy)
4282
4283	def OnMouseMove(event):
4284	if event.ShiftDown(): #don't want any inadvertant moves when picking
4285	return
4286	newxy = event.GetPosition()
4287
4288	if event.Dragging():
4289	if event.AltDown() and rbObj:
4290	if event.LeftIsDown():
4291	SetRBRotation(newxy)
4292	Q = rbObj['Orient'][0]
4293	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4294	elif event.RightIsDown():
4295	SetRBTranslation(newxy)
4296	Tx,Ty,Tz = rbObj['Orig'][0]
4297	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
4298	elif event.MiddleIsDown():
4299	SetRBRotationZ(newxy)
4300	Q = rbObj['Orient'][0]
4301	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4302	Draw('move')
4303	elif not event.ControlDown():
4304	if event.LeftIsDown():
4305	SetRotation(newxy)
4306	Q = drawingData['Quaternion']
4307	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4308	elif event.RightIsDown():
4309	SetTranslation(newxy)
4310	Tx,Ty,Tz = drawingData['viewPoint'][0]
4311	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
4312	elif event.MiddleIsDown():
4313	SetRotationZ(newxy)
4314	Q = drawingData['Quaternion']
4315	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4316	Draw('move')
4317
4318
4319	def OnMouseWheel(event):
4320	if event.ShiftDown():
4321	return
4322	drawingData['cameraPos'] += event.GetWheelRotation()/24.
4323	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
4324	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
4325	page = getSelection()
4326	if page:
4327	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
4328	G2frame.dataDisplay.cameraPosTxt.SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
4329	G2frame.dataDisplay.cameraSlider.SetValue(drawingData['cameraPos'])
4330	Draw('wheel')
4331
4332	def getSelection():
4333	try:
4334	return G2frame.dataDisplay.GetSelection()
4335	except AttributeError:
4336	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!',1)
4337	return 0
4338
4339	def SetViewPointText(VP):
4340	page = getSelection()
4341	if page:
4342	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
4343	G2frame.dataDisplay.viewPoint.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
4344
4345	def SetRBOrigText():
4346	page = getSelection()
4347	if page:
4348	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
4349	for i,sizer in enumerate(testRBObj['Sizers']['Xsizers']):
4350	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orig'][0][i]))
4351
4352	def SetRBOrienText():
4353	page = getSelection()
4354	if page:
4355	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
4356	for i,sizer in enumerate(testRBObj['Sizers']['Osizers']):
4357	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orient'][0][i]))
4358
4359	def SetViewDirText(VD):
4360	page = getSelection()
4361	if page:
4362	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
4363	G2frame.dataDisplay.viewDir.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
4364
4365	def SetMapPeaksText(mapPeaks):
4366	page = getSelection()
4367	if page:
4368	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
4369	G2frame.MapPeaksTable.SetData(mapPeaks)
4370	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
4371	names = [child.GetName() for child in panel]
4372	panel[names.index('grid window')].Refresh()
4373
4374	def ClearSelectedAtoms():
4375	page = getSelection()
4376	if page:
4377	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
4378	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
4379	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
4380	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
4381	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
4382	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
4383
4384
4385	def SetSelectedAtoms(ind,Add=False):
4386	page = getSelection()
4387	if page:
4388	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
4389	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
4390	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
4391	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
4392	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
4393	Id = drawAtoms[ind][-3]
4394	for i,atom in enumerate(atomData):
4395	if atom[-1] == Id:
4396	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
4397
4398	def GetSelectedAtoms():
4399	page = getSelection()
4400	Ind = []
4401	if page:
4402	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
4403	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
4404	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
4405	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
4406	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
4407	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
4408	return Ind
4409
4410	def SetBackground():
4411	R,G,B,A = Page.camera['backColor']
4412	glClearColor(R,G,B,A)
4413	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
4414
4415	def SetLights():
4416	glEnable(GL_DEPTH_TEST)
4417	glShadeModel(GL_SMOOTH)
4418	glEnable(GL_LIGHTING)
4419	glEnable(GL_LIGHT0)
4420	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
4421	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
4422	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
4423
4424	def GetRoll(newxy,rhoshape):
4425	Q = drawingData['Quaternion']
4426	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
4427	dxy = np.array(dxy*rhoshape)
4428	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
4429	return roll
4430
4431	def SetMapRoll(newxy):
4432	rho = mapData['rho']
4433	roll = GetRoll(newxy,rho.shape)
4434	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
4435	drawingData['oldxy'] = list(newxy)
4436
4437	def Set4DMapRoll(newxy):
4438	rho = generalData['4DmapData']['rho']
4439	roll = GetRoll(newxy,rho.shape[:3])
4440	generalData['4DmapData']['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
4441
4442	def SetPeakRoll(newxy):
4443	rho = mapData['rho']
4444	roll = GetRoll(newxy,rho.shape)
4445	steps = 1./np.array(rho.shape)
4446	dxy = roll*steps
4447	for peak in mapPeaks:
4448	peak[1:4] += dxy
4449	peak[1:4] %= 1.
4450	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
4451
4452	def SetTranslation(newxy):
4453	#first get translation vector in screen coords.
4454	oldxy = drawingData['oldxy']
4455	if not len(oldxy): oldxy = list(newxy)
4456	dxy = newxy-oldxy
4457	drawingData['oldxy'] = list(newxy)
4458	V = np.array([-dxy[0],dxy[1],0.])
4459	#then transform to rotated crystal coordinates & apply to view point
4460	Q = drawingData['Quaternion']
4461	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
4462	Tx,Ty,Tz = drawingData['viewPoint'][0]
4463	Tx += V[0]*0.01
4464	Ty += V[1]*0.01
4465	Tz += V[2]*0.01
4466	drawingData['viewPoint'][0] = Tx,Ty,Tz
4467	SetViewPointText([Tx,Ty,Tz])
4468
4469	def SetRBTranslation(newxy):
4470	#first get translation vector in screen coords.
4471	oldxy = drawingData['oldxy']
4472	if not len(oldxy): oldxy = list(newxy)
4473	dxy = newxy-oldxy
4474	drawingData['oldxy'] = list(newxy)
4475	V = np.array([-dxy[0],dxy[1],0.])
4476	#then transform to rotated crystal coordinates & apply to RB origin
4477	Q = drawingData['Quaternion']
4478	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
4479	Tx,Ty,Tz = rbObj['Orig'][0]
4480	Tx -= V[0]*0.01
4481	Ty -= V[1]*0.01
4482	Tz -= V[2]*0.01
4483	rbObj['Orig'][0] = Tx,Ty,Tz
4484	SetRBOrigText()
4485
4486	def SetRotation(newxy):
4487	'Perform a rotation in x-y space due to a left-mouse drag'
4488	#first get rotation vector in screen coords. & angle increment
4489	oldxy = drawingData['oldxy']
4490	if not len(oldxy): oldxy = list(newxy)
4491	dxy = newxy-oldxy
4492	drawingData['oldxy'] = list(newxy)
4493	V = np.array([dxy[1],dxy[0],0.])
4494	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
4495	if not A: return # nothing changed, nothing to do
4496	# next transform vector back to xtal coordinates via inverse quaternion
4497	# & make new quaternion
4498	Q = drawingData['Quaternion']
4499	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
4500	DQ = G2mth.AVdeg2Q(A,V)
4501	Q = G2mth.prodQQ(Q,DQ)
4502	drawingData['Quaternion'] = Q
4503	# finally get new view vector - last row of rotation matrix
4504	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
4505	VD /= np.sqrt(np.sum(VD**2))
4506	drawingData['viewDir'] = VD
4507	SetViewDirText(VD)
4508
4509	def SetRotationZ(newxy):
4510	#first get rotation vector (= view vector) in screen coords. & angle increment
4511	View = glGetIntegerv(GL_VIEWPORT)
4512	cent = [View[2]/2,View[3]/2]
4513	oldxy = drawingData['oldxy']
4514	if not len(oldxy): oldxy = list(newxy)
4515	dxy = newxy-oldxy
4516	drawingData['oldxy'] = list(newxy)
4517	V = drawingData['viewDir']
4518	A = [0,0]
4519	A[0] = dxy[1]*.25
4520	A[1] = dxy[0]*.25
4521	if newxy[0] > cent[0]:
4522	A[0] *= -1
4523	if newxy[1] < cent[1]:
4524	A[1] *= -1
4525	# next transform vector back to xtal coordinates & make new quaternion
4526	Q = drawingData['Quaternion']
4527	V = np.inner(Amat,V)
4528	Qx = G2mth.AVdeg2Q(A[0],V)
4529	Qy = G2mth.AVdeg2Q(A[1],V)
4530	Q = G2mth.prodQQ(Q,Qx)
4531	Q = G2mth.prodQQ(Q,Qy)
4532	drawingData['Quaternion'] = Q
4533
4534	def SetRBRotation(newxy):
4535	#first get rotation vector in screen coords. & angle increment
4536	oldxy = drawingData['oldxy']
4537	if not len(oldxy): oldxy = list(newxy)
4538	dxy = newxy-oldxy
4539	drawingData['oldxy'] = list(newxy)
4540	V = np.array([dxy[1],dxy[0],0.])
4541	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
4542	# next transform vector back to xtal coordinates via inverse quaternion
4543	# & make new quaternion
4544	Q = rbObj['Orient'][0] #rotate RB to Cart
4545	QC = drawingData['Quaternion'] #rotate Cart to drawing
4546	V = G2mth.prodQVQ(G2mth.invQ(QC),V)
4547	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
4548	DQ = G2mth.AVdeg2Q(A,V)
4549	Q = G2mth.prodQQ(Q,DQ)
4550	rbObj['Orient'][0] = Q
4551	SetRBOrienText()
4552
4553	def SetRBRotationZ(newxy):
4554	#first get rotation vector (= view vector) in screen coords. & angle increment
4555	View = glGetIntegerv(GL_VIEWPORT)
4556	cent = [View[2]/2,View[3]/2]
4557	oldxy = drawingData['oldxy']
4558	if not len(oldxy): oldxy = list(newxy)
4559	dxy = newxy-oldxy
4560	drawingData['oldxy'] = list(newxy)
4561	V = drawingData['viewDir']
4562	A = [0,0]
4563	A[0] = dxy[1]*.25
4564	A[1] = dxy[0]*.25
4565	if newxy[0] < cent[0]:
4566	A[0] *= -1
4567	if newxy[1] > cent[1]:
4568	A[1] *= -1
4569	# next transform vector back to RB coordinates & make new quaternion
4570	Q = rbObj['Orient'][0] #rotate RB to cart
4571	V = np.inner(Amat,V)
4572	V = -G2mth.prodQVQ(G2mth.invQ(Q),V)
4573	Qx = G2mth.AVdeg2Q(A[0],V)
4574	Qy = G2mth.AVdeg2Q(A[1],V)
4575	Q = G2mth.prodQQ(Q,Qx)
4576	Q = G2mth.prodQQ(Q,Qy)
4577	rbObj['Orient'][0] = Q
4578	SetRBOrienText()
4579
4580	def RenderBox():
4581	glEnable(GL_COLOR_MATERIAL)
4582	glLineWidth(2)
4583	glEnable(GL_BLEND)
4584	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
4585	glEnable(GL_LINE_SMOOTH)
4586	glBegin(GL_LINES)
4587	for line,color in zip(uEdges,uColors):
4588	glColor3ubv(color)
4589	glVertex3fv(line[0])
4590	glVertex3fv(line[1])
4591	glEnd()
4592	glColor4ubv([0,0,0,0])
4593	glDisable(GL_LINE_SMOOTH)
4594	glDisable(GL_BLEND)
4595	glDisable(GL_COLOR_MATERIAL)
4596
4597	def RenderUnitVectors(x,y,z):
4598	xyz = np.array([x,y,z])
4599	glEnable(GL_COLOR_MATERIAL)
4600	glLineWidth(1)
4601	glPushMatrix()
4602	glTranslate(x,y,z)
4603	glScalef(1/cell[0],1/cell[1],1/cell[2])
4604	glBegin(GL_LINES)
4605	for line,color in zip(uEdges,uColors)[:3]:
4606	glColor3ubv(color)
4607	glVertex3fv(-line[1]/2.)
4608	glVertex3fv(line[1]/2.)
4609	glEnd()
4610	glPopMatrix()
4611	glColor4ubv([0,0,0,0])
4612	glDisable(GL_COLOR_MATERIAL)
4613
4614	def RenderSphere(x,y,z,radius,color):
4615	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4616	glPushMatrix()
4617	glTranslate(x,y,z)
4618	glMultMatrixf(B4mat.T)
4619	q = gluNewQuadric()
4620	gluSphere(q,radius,20,10)
4621	glPopMatrix()
4622
4623	def RenderDots(XYZ,RC):
4624	glEnable(GL_COLOR_MATERIAL)
4625	XYZ = np.array(XYZ)
4626	glPushMatrix()
4627	for xyz,rc in zip(XYZ,RC):
4628	x,y,z = xyz
4629	r,c = rc
4630	glColor3ubv(c)
4631	glPointSize(r*50)
4632	glBegin(GL_POINTS)
4633	glVertex3fv(xyz)
4634	glEnd()
4635	glPopMatrix()
4636	glColor4ubv([0,0,0,0])
4637	glDisable(GL_COLOR_MATERIAL)
4638
4639	def RenderSmallSphere(x,y,z,radius,color):
4640	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4641	glPushMatrix()
4642	glTranslate(x,y,z)
4643	glMultMatrixf(B4mat.T)
4644	q = gluNewQuadric()
4645	gluSphere(q,radius,4,2)
4646	glPopMatrix()
4647
4648	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
4649	s1,s2,s3 = E
4650	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4651	glPushMatrix()
4652	glTranslate(x,y,z)
4653	glMultMatrixf(B4mat.T)
4654	glMultMatrixf(R4.T)
4655	glEnable(GL_NORMALIZE)
4656	glScale(s1,s2,s3)
4657	q = gluNewQuadric()
4658	gluSphere(q,ellipseProb,20,10)
4659	glDisable(GL_NORMALIZE)
4660	glPopMatrix()
4661
4662	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
4663	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4664	glPushMatrix()
4665	glTranslate(x,y,z)
4666	glMultMatrixf(B4mat.T)
4667	for bond in Bonds:
4668	glPushMatrix()
4669	Dx = np.inner(Amat,bond)
4670	Z = np.sqrt(np.sum(Dx**2))
4671	if Z:
4672	azm = atan2d(-Dx[1],-Dx[0])
4673	phi = acosd(Dx[2]/Z)
4674	glRotate(-azm,0,0,1)
4675	glRotate(phi,1,0,0)
4676	q = gluNewQuadric()
4677	gluCylinder(q,radius,radius,Z,slice,2)
4678	glPopMatrix()
4679	glPopMatrix()
4680
4681	def RenderLines(x,y,z,Bonds,color):
4682	glShadeModel(GL_FLAT)
4683	xyz = np.array([x,y,z])
4684	glEnable(GL_COLOR_MATERIAL)
4685	glLineWidth(1)
4686	glColor3fv(color)
4687	glPushMatrix()
4688	glBegin(GL_LINES)
4689	for bond in Bonds:
4690	glVertex3fv(xyz)
4691	glVertex3fv(xyz+bond)
4692	glEnd()
4693	glColor4ubv([0,0,0,0])
4694	glPopMatrix()
4695	glDisable(GL_COLOR_MATERIAL)
4696	glShadeModel(GL_SMOOTH)
4697
4698	def RenderPolyhedra(x,y,z,Faces,color):
4699	glShadeModel(GL_FLAT)
4700	glPushMatrix()
4701	glTranslate(x,y,z)
4702	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
4703	glShadeModel(GL_SMOOTH)
4704	glMultMatrixf(B4mat.T)
4705	for face,norm in Faces:
4706	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
4707	glFrontFace(GL_CW)
4708	glNormal3fv(norm)
4709	glBegin(GL_TRIANGLES)
4710	for vert in face:
4711	glVertex3fv(vert)
4712	glEnd()
4713	glPopMatrix()
4714	glShadeModel(GL_SMOOTH)
4715
4716	def RenderMapPeak(x,y,z,color,den):
4717	glShadeModel(GL_FLAT)
4718	xyz = np.array([x,y,z])
4719	glEnable(GL_COLOR_MATERIAL)
4720	glLineWidth(3)
4721	glColor3fv(color*den/255)
4722	glPushMatrix()
4723	glBegin(GL_LINES)
4724	for vec in mapPeakVecs:
4725	glVertex3fv(vec[0]+xyz)
4726	glVertex3fv(vec[1]+xyz)
4727	glEnd()
4728	glColor4ubv([0,0,0,0])
4729	glPopMatrix()
4730	glDisable(GL_COLOR_MATERIAL)
4731	glShadeModel(GL_SMOOTH)
4732
4733	def RenderBackbone(Backbone,BackboneColor,radius):
4734	glPushMatrix()
4735	glMultMatrixf(B4mat.T)
4736	glEnable(GL_COLOR_MATERIAL)
4737	glShadeModel(GL_SMOOTH)
4738	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
4739	glePolyCylinder(Backbone,BackboneColor,radius)
4740	glPopMatrix()
4741	glDisable(GL_COLOR_MATERIAL)
4742
4743	def RenderLabel(x,y,z,label,r,color,matRot):
4744	'''
4745	color wx.Colour object
4746	'''
4747	glPushMatrix()
4748	glTranslate(x,y,z)
4749	glMultMatrixf(B4mat.T)
4750	glDisable(GL_LIGHTING)
4751	glRasterPos3f(0,0,0)
4752	glMultMatrixf(matRot)
4753	glRotate(180,1,0,0) #fix to flip about x-axis
4754	text = gltext.Text(text=label,font=Font,foreground=color)
4755	text.draw_text(scale=0.025)
4756	glEnable(GL_LIGHTING)
4757	glPopMatrix()
4758
4759	def RenderMap(rho,rhoXYZ,indx,Rok):
4760	glShadeModel(GL_FLAT)
4761	cLevel = drawingData['contourLevel']
4762	XYZ = []
4763	RC = []
4764	for i,xyz in enumerate(rhoXYZ):
4765	if not Rok[i]:
4766	x,y,z = xyz
4767	I,J,K = indx[i]
4768	alpha = 1.0
4769	if cLevel < 1.:
4770	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
4771	if rho[I,J,K] < 0.:
4772	XYZ.append(xyz)
4773	RC.append([0.1*alpha,Rd])
4774	else:
4775	XYZ.append(xyz)
4776	RC.append([0.1*alpha,Gr])
4777	RenderDots(XYZ,RC)
4778	glShadeModel(GL_SMOOTH)
4779
4780	def Draw(caller=''):
4781	#useful debug?
4782	# if caller:
4783	# print caller
4784	# end of useful debug
4785	mapData = generalData['Map']
4786	pageName = ''
4787	page = getSelection()
4788	if page:
4789	pageName = G2frame.dataDisplay.GetPageText(page)
4790	rhoXYZ = []
4791	if len(mapData['rho']):
4792	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
4793	contLevel = drawingData['contourLevel']*mapData['rhoMax']
4794	if 'delt-F' in mapData['MapType'] or 'N' in mapData['Type']:
4795	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
4796	else:
4797	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
4798	steps = 1./np.array(rho.shape)
4799	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
4800	Vsteps = -np.array(VP/steps,dtype='i')
4801	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
4802	indx = np.array(ma.nonzero(rho)).T
4803	rhoXYZ = indx*steps+VP-incre
4804	Nc = len(rhoXYZ)
4805	rcube = 2000.Vol/(ForthirdPINc)
4806	rmax = math.exp(math.log(rcube)/3.)**2
4807	radius = min(drawingData['mapSize']**2,rmax)
4808	view = np.array(drawingData['viewPoint'][0])
4809	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
4810	Ind = GetSelectedAtoms()
4811	VS = np.array(Page.canvas.GetSize())
4812	aspect = float(VS[0])/float(VS[1])
4813	cPos = drawingData['cameraPos']
4814	Zclip = drawingData['Zclip']*cPos/200.
4815	Q = drawingData['Quaternion']
4816	Tx,Ty,Tz = drawingData['viewPoint'][0]
4817	cx,ct,cs,ci = drawingData['atomPtrs']
4818	bondR = drawingData['bondRadius']
4819	G,g = G2lat.cell2Gmat(cell)
4820	GS = G
4821	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
4822	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
4823	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
4824	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
4825
4826	SetBackground()
4827	glInitNames()
4828	glPushName(0)
4829
4830	glMatrixMode(GL_PROJECTION)
4831	glLoadIdentity()
4832	glViewport(0,0,VS[0],VS[1])
4833	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
4834	gluLookAt(0,0,cPos,0,0,0,0,1,0)
4835	SetLights()
4836
4837	glMatrixMode(GL_MODELVIEW)
4838	glLoadIdentity()
4839	matRot = G2mth.Q2Mat(Q)
4840	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4841	glMultMatrixf(matRot.T)
4842	glMultMatrixf(A4mat.T)
4843	glTranslate(-Tx,-Ty,-Tz)
4844	if drawingData['unitCellBox']:
4845	RenderBox()
4846	if drawingData['showABC']:
4847	x,y,z = drawingData['viewPoint'][0]
4848	RenderUnitVectors(x,y,z)
4849	Backbones = {}
4850	BackboneColor = []
4851	time0 = time.time()
4852	# glEnable(GL_BLEND)
4853	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
4854	for iat,atom in enumerate(drawingData['Atoms']):
4855	x,y,z = atom[cx:cx+3]
4856	Bonds = atom[-2]
4857	Faces = atom[-1]
4858	try:
4859	atNum = generalData['AtomTypes'].index(atom[ct])
4860	except ValueError:
4861	atNum = -1
4862	CL = atom[cs+2]
4863	atColor = np.array(CL)/255.
4864	if drawingData['showRigidBodies'] and atom[ci] in rbAtmDict:
4865	bndColor = Or
4866	else:
4867	bndColor = atColor
4868	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
4869	atColor = np.array(Gr)/255.
4870	# color += [.25,]
4871	radius = 0.5
4872	if atom[cs] != '':
4873	try:
4874	glLoadName(atom[-3])
4875	except: #problem with old files - missing code
4876	pass
4877	if 'balls' in atom[cs]:
4878	vdwScale = drawingData['vdwScale']
4879	ballScale = drawingData['ballScale']
4880	if atNum < 0:
4881	radius = 0.2
4882	elif 'H' == atom[ct]:
4883	if drawingData['showHydrogen']:
4884	if 'vdW' in atom[cs] and atNum >= 0:
4885	radius = vdwScale*generalData['vdWRadii'][atNum]
4886	else:
4887	radius = ballScale*drawingData['sizeH']
4888	else:
4889	radius = 0.0
4890	else:
4891	if 'vdW' in atom[cs]:
4892	radius = vdwScale*generalData['vdWRadii'][atNum]
4893	else:
4894	radius = ballScale*generalData['BondRadii'][atNum]
4895	RenderSphere(x,y,z,radius,atColor)
4896	if 'sticks' in atom[cs]:
4897	RenderBonds(x,y,z,Bonds,bondR,bndColor)
4898	elif 'ellipsoids' in atom[cs]:
4899	RenderBonds(x,y,z,Bonds,bondR,bndColor)
4900	if atom[cs+3] == 'A':
4901	Uij = atom[cs+5:cs+11]
4902	U = np.multiply(G2spc.Uij2U(Uij),GS)
4903	U = np.inner(Amat,np.inner(U,Amat).T)
4904	E,R = nl.eigh(U)
4905	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4906	E = np.sqrt(E)
4907	if atom[ct] == 'H' and not drawingData['showHydrogen']:
4908	pass
4909	else:
4910	RenderEllipsoid(x,y,z,ellipseProb,E,R4,atColor)
4911	else:
4912	if atom[ct] == 'H' and not drawingData['showHydrogen']:
4913	pass
4914	else:
4915	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
4916	RenderSphere(x,y,z,radius,atColor)
4917	elif 'lines' in atom[cs]:
4918	radius = 0.1
4919	RenderLines(x,y,z,Bonds,bndColor)
4920	# RenderBonds(x,y,z,Bonds,0.05,color,6)
4921	elif atom[cs] == 'sticks':
4922	radius = 0.1
4923	RenderBonds(x,y,z,Bonds,bondR,bndColor)
4924	elif atom[cs] == 'polyhedra':
4925	RenderPolyhedra(x,y,z,Faces,atColor)
4926	elif atom[cs] == 'backbone':
4927	if atom[ct-1].split()[0] in ['C','N']:
4928	if atom[2] not in Backbones:
4929	Backbones[atom[2]] = []
4930	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
4931	BackboneColor.append(list(atColor))
4932
4933	if atom[cs+1] == 'type':
4934	RenderLabel(x,y,z,' '+atom[ct],radius,wxGreen,matRot)
4935	elif atom[cs+1] == 'name':
4936	RenderLabel(x,y,z,' '+atom[ct-1],radius,wxGreen,matRot)
4937	elif atom[cs+1] == 'number':
4938	RenderLabel(x,y,z,' '+str(iat),radius,wxGreen,matRot)
4939	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
4940	RenderLabel(x,y,z,' '+atom[ct-4],radius,wxGreen,matRot)
4941	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
4942	RenderLabel(x,y,z,' '+atom[ct-3],radius,wxGreen,matRot)
4943	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
4944	RenderLabel(x,y,z,' '+atom[ct-2],radius,wxGreen,matRot)
4945	# glDisable(GL_BLEND)
4946	if len(rhoXYZ):
4947	RenderMap(rho,rhoXYZ,indx,Rok)
4948	if len(mapPeaks):
4949	XYZ = mapPeaks.T[1:4].T
4950	mapBonds = FindPeaksBonds(XYZ)
4951	for ind,[mag,x,y,z,d] in enumerate(mapPeaks):
4952	if ind in Ind and pageName == 'Map peaks':
4953	RenderMapPeak(x,y,z,Gr,1.0)
4954	else:
4955	if mag > 0.:
4956	RenderMapPeak(x,y,z,Wt,mag/peakMax)
4957	else:
4958	RenderMapPeak(x,y,z,Rd,-mag/peakMax)
4959	if showBonds:
4960	RenderLines(x,y,z,mapBonds[ind],Wt)
4961	if len(testRBObj) and pageName == 'RB Models':
4962	XYZ = G2mth.UpdateRBXYZ(Bmat,testRBObj['rbObj'],testRBObj['rbData'],testRBObj['rbType'])[0]
4963	rbBonds = FindPeaksBonds(XYZ)
4964	for ind,[x,y,z] in enumerate(XYZ):
4965	aType = testRBObj['rbAtTypes'][ind]
4966	name = ' '+aType+str(ind)
4967	color = np.array(testRBObj['AtInfo'][aType][1])
4968	RenderSphere(x,y,z,0.2,color/255.)
4969	RenderBonds(x,y,z,rbBonds[ind],0.03,Gr)
4970	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4971	if len(mcsaModels) > 1 and pageName == 'MC/SA': #skip the default MD entry
4972	for ind,[x,y,z] in enumerate(mcsaXYZ):
4973	aType = mcsaTypes[ind]
4974	name = ' '+aType+str(ind)
4975	color = np.array(MCSA['AtInfo'][aType][1])
4976	RenderSphere(x,y,z,0.2,color/255.)
4977	RenderBonds(x,y,z,mcsaBonds[ind],0.03,Gr)
4978	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
4979	if Backbones:
4980	for chain in Backbones:
4981	Backbone = Backbones[chain]
4982	RenderBackbone(Backbone,BackboneColor,bondR)
4983	# print time.time()-time0
4984	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
4985	Page.canvas.SwapBuffers()
4986
4987	def OnSize(event):
4988	Draw('size')
4989
4990	def OnFocus(event): #not needed?? Bind commented out below
4991	Draw('focus')
4992
4993	# PlotStructure execution starts here (N.B. initialization above)
4994	try:
4995	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
4996	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
4997	except ValueError:
4998	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
4999	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
5000	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
5001	Page.views = False
5002	view = False
5003	altDown = False
5004	G2frame.G2plotNB.nb.SetSelection(plotNum) # make sure plot tab is raised for wx >2.8
5005	Font = Page.GetFont()
5006	Page.SetFocus()
5007	Page.Choice = None
5008	if mapData.get('Flip',False):
5009	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2',
5010	'u: roll up','d: roll down','l: roll left','r: roll right']
5011	else:
5012	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
5013	if generalData['Type'] in ['modulated','magnetic',] and len(drawAtoms):
5014	choice += ['+: increase tau','-: decrease tau','0: set tau = 0']
5015
5016	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
5017	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
5018	cb.SetValue(' save as/key:')
5019	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
5020	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
5021	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
5022	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
5023	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
5024	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
5025	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
5026	# Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
5027	Page.camera['position'] = drawingData['cameraPos']
5028	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
5029	Page.camera['backColor'] = backColor/255.
5030	try:
5031	Page.canvas.SetCurrent()
5032	except:
5033	pass
5034	Draw('main')
5035	if firstCall: Draw('main') # draw twice the first time that graphics are displayed
5036
5037	################################################################################
5038	#### Plot Rigid Body
5039	################################################################################
5040
5041	def PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults):
5042	'''RB plotting package. Can show rigid body structures as balls & sticks
5043	'''
5044
5045	def FindBonds(XYZ):
5046	rbTypes = rbData['rbTypes']
5047	Radii = []
5048	for Atype in rbTypes:
5049	Radii.append(AtInfo[Atype][0])
5050	if Atype == 'H':
5051	Radii[-1] = 0.5
5052	Radii = np.array(Radii)
5053	Bonds = [[] for i in range(len(Radii))]
5054	for i,xyz in enumerate(XYZ):
5055	Dx = XYZ-xyz
5056	dist = np.sqrt(np.sum(Dx**2,axis=1))
5057	sumR = Radii[i]+Radii
5058	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
5059	for j in IndB[0]:
5060	Bonds[i].append(Dx[j]*Radii[i]/sumR[j])
5061	Bonds[j].append(-Dx[j]*Radii[j]/sumR[j])
5062	return Bonds
5063
5064	Wt = np.array([255,255,255])
5065	Rd = np.array([255,0,0])
5066	Gr = np.array([0,255,0])
5067	Bl = np.array([0,0,255])
5068	uBox = np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1]])
5069	uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]])
5070	uColors = [Rd,Gr,Bl]
5071	if rbType == 'Vector':
5072	atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['rbTypes'])]
5073	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
5074	for imag,mag in enumerate(rbData['VectMag']):
5075	XYZ += mag*rbData['rbVect'][imag]
5076	Bonds = FindBonds(XYZ)
5077	elif rbType == 'Residue':
5078	# atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['atNames'])]
5079	atNames = rbData['atNames']
5080	XYZ = np.copy(rbData['rbXYZ']) #don't mess with original!
5081	Seq = rbData['rbSeq']
5082	for ia,ib,ang,mv in Seq:
5083	va = XYZ[ia]-XYZ[ib]
5084	Q = G2mth.AVdeg2Q(ang,va)
5085	for im in mv:
5086	vb = XYZ[im]-XYZ[ib]
5087	vb = G2mth.prodQVQ(Q,vb)
5088	XYZ[im] = XYZ[ib]+vb
5089	Bonds = FindBonds(XYZ)
5090	elif rbType == 'Z-matrix':
5091	pass
5092
5093	# def SetRBOrigin():
5094	# page = getSelection()
5095	# if page:
5096	# if G2frame.dataDisplay.GetPageText(page) == 'Rigid bodies':
5097	# G2frame.MapPeaksTable.SetData(mapPeaks)
5098	# panel = G2frame.dataDisplay.GetPage(page).GetChildren()
5099	# names = [child.GetName() for child in panel]
5100	# panel[names.index('grid window')].Refresh()
5101
5102	def OnMouseDown(event):
5103	xy = event.GetPosition()
5104	defaults['oldxy'] = list(xy)
5105
5106	def OnMouseMove(event):
5107	newxy = event.GetPosition()
5108
5109	if event.Dragging():
5110	if event.LeftIsDown():
5111	SetRotation(newxy)
5112	Q = defaults['Quaternion']
5113	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
5114	# elif event.RightIsDown():
5115	# SetRBOrigin(newxy)
5116	elif event.MiddleIsDown():
5117	SetRotationZ(newxy)
5118	Q = defaults['Quaternion']
5119	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
5120	Draw('move')
5121
5122	def OnMouseWheel(event):
5123	defaults['cameraPos'] += event.GetWheelRotation()/24
5124	defaults['cameraPos'] = max(10,min(500,defaults['cameraPos']))
5125	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1)
5126	Draw('wheel')
5127
5128	def SetBackground():
5129	R,G,B,A = Page.camera['backColor']
5130	glClearColor(R,G,B,A)
5131	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
5132
5133	def SetLights():
5134	glEnable(GL_DEPTH_TEST)
5135	glShadeModel(GL_FLAT)
5136	glEnable(GL_LIGHTING)
5137	glEnable(GL_LIGHT0)
5138	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
5139	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
5140	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
5141
5142	# def SetRBOrigin(newxy):
5143	##first get translation vector in screen coords.
5144	# oldxy = defaults['oldxy']
5145	# if not len(oldxy): oldxy = list(newxy)
5146	# dxy = newxy-oldxy
5147	# defaults['oldxy'] = list(newxy)
5148	# V = np.array([dxy[0],-dxy[1],0.])/100.
5149	# Q = defaults['Quaternion']
5150	# V = G2mth.prodQVQ(G2mth.invQ(Q),V)
5151	# rbData['rbXYZ'] += V
5152	# PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults)
5153	#
5154	def SetRotation(newxy):
5155	#first get rotation vector in screen coords. & angle increment
5156	oldxy = defaults['oldxy']
5157	if not len(oldxy): oldxy = list(newxy)
5158	dxy = newxy-oldxy
5159	defaults['oldxy'] = list(newxy)
5160	V = np.array([dxy[1],dxy[0],0.])
5161	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
5162	# next transform vector back to xtal coordinates via inverse quaternion
5163	# & make new quaternion
5164	Q = defaults['Quaternion']
5165	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
5166	DQ = G2mth.AVdeg2Q(A,V)
5167	Q = G2mth.prodQQ(Q,DQ)
5168	defaults['Quaternion'] = Q
5169	# finally get new view vector - last row of rotation matrix
5170	VD = G2mth.Q2Mat(Q)[2]
5171	VD /= np.sqrt(np.sum(VD**2))
5172	defaults['viewDir'] = VD
5173
5174	def SetRotationZ(newxy):
5175	#first get rotation vector (= view vector) in screen coords. & angle increment
5176	View = glGetIntegerv(GL_VIEWPORT)
5177	cent = [View[2]/2,View[3]/2]
5178	oldxy = defaults['oldxy']
5179	if not len(oldxy): oldxy = list(newxy)
5180	dxy = newxy-oldxy
5181	defaults['oldxy'] = list(newxy)
5182	V = defaults['viewDir']
5183	A = [0,0]
5184	A[0] = dxy[1]*.25
5185	A[1] = dxy[0]*.25
5186	if newxy[0] > cent[0]:
5187	A[0] *= -1
5188	if newxy[1] < cent[1]:
5189	A[1] *= -1
5190	# next transform vector back to xtal coordinates & make new quaternion
5191	Q = defaults['Quaternion']
5192	Qx = G2mth.AVdeg2Q(A[0],V)
5193	Qy = G2mth.AVdeg2Q(A[1],V)
5194	Q = G2mth.prodQQ(Q,Qx)
5195	Q = G2mth.prodQQ(Q,Qy)
5196	defaults['Quaternion'] = Q
5197
5198	def RenderUnitVectors(x,y,z):
5199	xyz = np.array([x,y,z])
5200	glEnable(GL_COLOR_MATERIAL)
5201	glLineWidth(1)
5202	glPushMatrix()
5203	glTranslate(x,y,z)
5204	glBegin(GL_LINES)
5205	for line,color in zip(uEdges,uColors):
5206	glColor3ubv(color)
5207	glVertex3fv(-line[1])
5208	glVertex3fv(line[1])
5209	glEnd()
5210	glPopMatrix()
5211	glColor4ubv([0,0,0,0])
5212	glDisable(GL_COLOR_MATERIAL)
5213
5214	def RenderSphere(x,y,z,radius,color):
5215	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
5216	glPushMatrix()
5217	glTranslate(x,y,z)
5218	q = gluNewQuadric()
5219	gluSphere(q,radius,20,10)
5220	glPopMatrix()
5221
5222	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
5223	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
5224	glPushMatrix()
5225	glTranslate(x,y,z)
5226	for Dx in Bonds:
5227	glPushMatrix()
5228	Z = np.sqrt(np.sum(Dx**2))
5229	if Z:
5230	azm = atan2d(-Dx[1],-Dx[0])
5231	phi = acosd(Dx[2]/Z)
5232	glRotate(-azm,0,0,1)
5233	glRotate(phi,1,0,0)
5234	q = gluNewQuadric()
5235	gluCylinder(q,radius,radius,Z,slice,2)
5236	glPopMatrix()
5237	glPopMatrix()
5238
5239	def RenderLabel(x,y,z,label,matRot):
5240	glPushMatrix()
5241	glTranslate(x,y,z)
5242	glDisable(GL_LIGHTING)
5243	glRasterPos3f(0,0,0)
5244	glMultMatrixf(matRot)
5245	glRotate(180,1,0,0) #fix to flip about x-axis
5246	text = gltext.TextElement(text=label,font=Font,foreground=wx.WHITE)
5247	text.draw_text(scale=0.025)
5248	glEnable(GL_LIGHTING)
5249	glPopMatrix()
5250
5251	def Draw(caller=''):
5252	#useful debug?
5253	# if caller:
5254	# print caller
5255	# end of useful debug
5256	cPos = defaults['cameraPos']
5257	VS = np.array(Page.canvas.GetSize())
5258	aspect = float(VS[0])/float(VS[1])
5259	Zclip = 500.0
5260	Q = defaults['Quaternion']
5261	SetBackground()
5262	glInitNames()
5263	glPushName(0)
5264
5265	glMatrixMode(GL_PROJECTION)
5266	glLoadIdentity()
5267	glViewport(0,0,VS[0],VS[1])
5268	gluPerspective(20.,aspect,1.,500.)
5269	gluLookAt(0,0,cPos,0,0,0,0,1,0)
5270	SetLights()
5271
5272	glMatrixMode(GL_MODELVIEW)
5273	glLoadIdentity()
5274	matRot = G2mth.Q2Mat(Q)
5275	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
5276	glMultMatrixf(matRot.T)
5277	RenderUnitVectors(0.,0.,0.)
5278	radius = 0.2
5279	for iat,atom in enumerate(XYZ):
5280	x,y,z = atom
5281	CL = AtInfo[rbData['rbTypes'][iat]][1]
5282	color = np.array(CL)/255.
5283	RenderSphere(x,y,z,radius,color)
5284	RenderBonds(x,y,z,Bonds[iat],0.05,color)
5285	RenderLabel(x,y,z,' '+atNames[iat],matRot)
5286	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
5287	Page.canvas.SwapBuffers()
5288
5289	def OnSize(event):
5290	Draw('size')
5291
5292	try:
5293	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
5294	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
5295	except ValueError:
5296	Plot = G2frame.G2plotNB.addOgl('Rigid body')
5297	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
5298	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
5299	Page.views = False
5300	view = False
5301	altDown = False
5302	Page.SetFocus()
5303	Font = Page.GetFont()
5304	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
5305	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
5306	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
5307	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
5308	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
5309	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
5310	Page.camera['position'] = defaults['cameraPos']
5311	Page.camera['backColor'] = np.array([0,0,0,0])
5312	Page.canvas.SetCurrent()
5313	Draw('main')

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