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source: trunk/GSASIIplot.py @ 1779

Last change on this file since 1779 was 1779, checked in by vondreele, 8 years ago
Add FWHM to exported peak lists change default F2 refinement to False Add histogram name to axial dist plots from DData
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 223.2 KB

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1	# -- coding: utf-8 --
2	'''
3	GSASIIplot: plotting routines
4	===============================
5
6	'''
7	########### SVN repository information ###################
8	# $Date: 2015-04-06 20:45:25 +0000 (Mon, 06 Apr 2015) $
9	# $Author: vondreele $
10	# $Revision: 1779 $
11	# $URL: trunk/GSASIIplot.py $
12	# $Id: GSASIIplot.py 1779 2015-04-06 20:45:25Z 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: 1779 $")
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 GSASIIctrls as G2G
40	import pytexture as ptx
41	from OpenGL.GL import *
42	from OpenGL.GLU import *
43	from OpenGL.GLE import *
44	import gltext
45	from matplotlib.backends.backend_wx import _load_bitmap
46	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
47	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
48
49	# useful degree trig functions
50	sind = lambda x: math.sin(x*math.pi/180.)
51	cosd = lambda x: math.cos(x*math.pi/180.)
52	tand = lambda x: math.tan(x*math.pi/180.)
53	asind = lambda x: 180.*math.asin(x)/math.pi
54	acosd = lambda x: 180.*math.acos(x)/math.pi
55	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
56	atand = lambda x: 180.*math.atan(x)/math.pi
57	# numpy versions
58	npsind = lambda x: np.sin(x*np.pi/180.)
59	npcosd = lambda x: np.cos(x*np.pi/180.)
60	nptand = lambda x: np.tan(x*np.pi/180.)
61	npacosd = lambda x: 180.*np.arccos(x)/np.pi
62	npasind = lambda x: 180.*np.arcsin(x)/np.pi
63	npatand = lambda x: 180.*np.arctan(x)/np.pi
64	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
65	GkDelta = unichr(0x0394)
66
67	class G2PlotMpl(wx.Panel):
68	'needs a doc string'
69	def __init__(self,parent,id=-1,dpi=None,**kwargs):
70	wx.Panel.__init__(self,parent,id=id,**kwargs)
71	mpl.rcParams['legend.fontsize'] = 10
72	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6))
73	self.canvas = Canvas(self,-1,self.figure)
74	self.toolbar = GSASIItoolbar(self.canvas)
75
76	self.toolbar.Realize()
77
78	sizer=wx.BoxSizer(wx.VERTICAL)
79	sizer.Add(self.canvas,1,wx.EXPAND)
80	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
81	self.SetSizer(sizer)
82
83	class G2PlotOgl(wx.Panel):
84	'needs a doc string'
85	def __init__(self,parent,id=-1,dpi=None,**kwargs):
86	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
87	if 'win' in sys.platform: #Windows (& Mac) already double buffered
88	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
89	else: #fix from Jim Hester for X systems
90	attribs = (wx.glcanvas.WX_GL_DOUBLEBUFFER,)
91	self.canvas = wx.glcanvas.GLCanvas(self,-1,attribList=attribs,**kwargs)
92	# create GL context for wx > 2.8
93	i,j= wx.__version__.split('.')[0:2]
94	if int(i)+int(j)/10. > 2.8:
95	self.context = wx.glcanvas.GLContext(self.canvas)
96	self.canvas.SetCurrent(self.context)
97	else:
98	self.context = None
99	self.camera = {}
100	sizer=wx.BoxSizer(wx.VERTICAL)
101	sizer.Add(self.canvas,1,wx.EXPAND)
102	self.SetSizer(sizer)
103
104	class G2Plot3D(wx.Panel):
105	'needs a doc string'
106	def __init__(self,parent,id=-1,dpi=None,**kwargs):
107	wx.Panel.__init__(self,parent,id=id,**kwargs)
108	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
109	self.canvas = Canvas(self,-1,self.figure)
110	self.toolbar = GSASIItoolbar(self.canvas)
111
112	self.toolbar.Realize()
113
114	sizer=wx.BoxSizer(wx.VERTICAL)
115	sizer.Add(self.canvas,1,wx.EXPAND)
116	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
117	self.SetSizer(sizer)
118
119	class G2PlotNoteBook(wx.Panel):
120	'create a tabbed window for plotting'
121	def __init__(self,parent,id=-1):
122	wx.Panel.__init__(self,parent,id=id)
123	#so one can't delete a plot page!!
124	self.nb = wx.aui.AuiNotebook(self, \
125	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
126	sizer = wx.BoxSizer()
127	sizer.Add(self.nb,1,wx.EXPAND)
128	self.SetSizer(sizer)
129	self.status = parent.CreateStatusBar()
130	self.status.SetFieldsCount(2)
131	self.status.SetStatusWidths([150,-1])
132	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
133	self.nb.Bind(wx.EVT_KEY_UP,self.OnNotebookKey)
134
135	self.plotList = []
136
137	def OnNotebookKey(self,event):
138	'''Called when a keystroke event gets picked up by the notebook window
139	rather the child. This is not expected, but somehow it does sometimes
140	on the Mac and perhaps Linux.
141
142	Assume that the page associated with the currently displayed tab
143	has a child, .canvas; give that child the focus and pass it the event.
144	'''
145	try:
146	Page = self.nb.GetPage(self.nb.GetSelection())
147	except ValueError: # occurs with no plot tabs
148	return
149	try:
150	Page.canvas.SetFocus()
151	wx.PostEvent(Page.canvas,event)
152	except AttributeError:
153	pass
154
155	def addMpl(self,name=""):
156	'Add a tabbed page with a matplotlib plot'
157	page = G2PlotMpl(self.nb)
158	self.nb.AddPage(page,name)
159
160	self.plotList.append(name)
161
162	return page.figure
163
164	def add3D(self,name=""):
165	'Add a tabbed page with a 3D plot'
166	page = G2Plot3D(self.nb)
167	self.nb.AddPage(page,name)
168
169	self.plotList.append(name)
170
171	return page.figure
172
173	def addOgl(self,name=""):
174	'Add a tabbed page with an openGL plot'
175	page = G2PlotOgl(self.nb)
176	self.nb.AddPage(page,name)
177
178	self.plotList.append(name)
179
180	return page.figure
181
182	def Delete(self,name):
183	'delete a tabbed page'
184	try:
185	item = self.plotList.index(name)
186	del self.plotList[item]
187	self.nb.DeletePage(item)
188	except ValueError: #no plot of this name - do nothing
189	return
190
191	def clear(self):
192	'clear all pages from plot window'
193	while self.nb.GetPageCount():
194	self.nb.DeletePage(0)
195	self.plotList = []
196	self.status.DestroyChildren()
197
198	def Rename(self,oldName,newName):
199	'rename a tab'
200	try:
201	item = self.plotList.index(oldName)
202	self.plotList[item] = newName
203	self.nb.SetPageText(item,newName)
204	except ValueError: #no plot of this name - do nothing
205	return
206
207	def OnPageChanged(self,event):
208	'respond to someone pressing a tab on the plot window'
209	if self.plotList:
210	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
211	self.status.DestroyChildren() #get rid of special stuff on status bar
212
213	class GSASIItoolbar(Toolbar):
214	'Override the matplotlib toolbar so we can add more icons'
215	ON_MPL_HELP = wx.NewId()
216	ON_MPL_KEY = wx.NewId()
217	arrows = {}
218	for direc in ('left','right','up','down','Expand X',
219	'Shrink X','Expand Y','Shrink Y'):
220	arrows[direc] = wx.NewId()
221	def __init__(self,plotCanvas):
222	'''Adds additional icons to toolbar'''
223	Toolbar.__init__(self,plotCanvas)
224	self.plotCanvas = plotCanvas
225	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6 # remove one button, nos. start at 1!
226	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
227	self.parent = self.GetParent()
228	key = os.path.join(os.path.split(__file__)[0],'key.ico')
229	self.AddSimpleTool(self.ON_MPL_KEY,_load_bitmap(key),'Key press','Select key press')
230	wx.EVT_TOOL(self,self.ON_MPL_KEY,self.OnKey)
231	help = os.path.join(os.path.split(__file__)[0],'help.ico')
232	self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
233	wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
234	# add arrow keys to control zooming
235	for direc in ('left','right','up','down'):
236	wx.EVT_TOOL(self,self.arrows[direc],self.OnArrow)
237	icon = os.path.join(os.path.split(__file__)[0],direc[0]+'arrow.ico')
238	self.AddSimpleTool(self.arrows[direc],_load_bitmap(icon),
239	'Shift '+direc,'Shift plot '+direc)
240	for direc in ('Expand X','Shrink X','Expand Y','Shrink Y'):
241	fil = ''.join([i[0].lower() for i in direc.split()]+['arrow.ico'])
242	wx.EVT_TOOL(self,self.arrows[direc],self.OnArrow)
243	icon = os.path.join(os.path.split(__file__)[0],fil)
244	self.AddSimpleTool(self.arrows[direc],_load_bitmap(icon),
245	direc,'Zoom: '+direc)
246	def OnArrow(self,event):
247	'reposition limits to scan or zoom by button press'
248	ax = self.plotCanvas.figure.get_axes()[0]
249	xmin,xmax,ymin,ymax = ax.axis()
250	#print xmin,xmax,ymin,ymax
251	if event.Id == self.arrows['right']:
252	delta = (xmax-xmin)/10.
253	xmin -= delta
254	xmax -= delta
255	elif event.Id == self.arrows['left']:
256	delta = (xmax-xmin)/10.
257	xmin += delta
258	xmax += delta
259	elif event.Id == self.arrows['up']:
260	delta = (ymax-ymin)/10.
261	ymin -= delta
262	ymax -= delta
263	elif event.Id == self.arrows['down']:
264	delta = (ymax-ymin)/10.
265	ymin += delta
266	ymax += delta
267	elif event.Id == self.arrows['Expand X']:
268	delta = (xmax-xmin)/10.
269	xmin += delta
270	xmax -= delta
271	elif event.Id == self.arrows['Expand Y']:
272	delta = (ymax-ymin)/10.
273	ymin += delta
274	ymax -= delta
275	elif event.Id == self.arrows['Shrink X']:
276	delta = (xmax-xmin)/10.
277	xmin -= delta
278	xmax += delta
279	elif event.Id == self.arrows['Shrink Y']:
280	delta = (ymax-ymin)/10.
281	ymin -= delta
282	ymax += delta
283	else:
284	# should not happen!
285	GSASIIpath.IPyBreak()
286	self.parent.toolbar.push_current()
287	ax.axis((xmin,xmax,ymin,ymax))
288	#print xmin,xmax,ymin,ymax
289	self.plotCanvas.figure.canvas.draw()
290	self.parent.toolbar.draw()
291	# self.parent.toolbar.push_current()
292
293	def OnHelp(self,event):
294	'Respond to press of help button on plot toolbar'
295	Page = self.GetParent().GetParent()
296	pageNo = Page.GetSelection()
297	bookmark = Page.GetPageText(pageNo)
298	bookmark = bookmark.strip(')').replace('(','_')
299	G2G.ShowHelp(bookmark,self.TopLevelParent)
300	def OnKey(self,event):
301	'''Provide user with list of keystrokes defined for plot as well as an
302	alternate way to access the same functionality
303	'''
304	parent = self.GetParent()
305	if parent.Choice:
306	dlg = wx.SingleChoiceDialog(parent,'Select','Key press',list(parent.Choice))
307	if dlg.ShowModal() == wx.ID_OK:
308	sel = dlg.GetSelection()
309	event.key = parent.Choice[sel][0]
310	parent.keyPress(event)
311	dlg.Destroy()
312
313	################################################################################
314	##### PlotSngl
315	################################################################################
316
317	def PlotSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=''):
318	'''Structure factor plotting package - displays zone of reflections as rings proportional
319	to F, F**2, etc. as requested
320	'''
321	from matplotlib.patches import Circle,CirclePolygon
322	global HKL,HKLF
323
324	def OnSCKeyPress(event):
325	i = zones.index(Data['Zone'])
326	newPlot = False
327	pwdrChoice = {'f':'Fo','s':'Fosq','u':'Unit Fc'}
328	hklfChoice = {'1':'\|DFsq\|>sig','3':'\|DFsq\|>3sig','w':'\|DFsq\|/sig','f':'Fo','s':'Fosq','i':'Unit Fc'}
329	if event.key == 'h':
330	Data['Zone'] = '100'
331	newPlot = True
332	elif event.key == 'k':
333	Data['Zone'] = '010'
334	newPlot = True
335	elif event.key == 'l':
336	Data['Zone'] = '001'
337	newPlot = True
338	elif event.key == 'i':
339	Data['Scale'] *= 1.1
340	elif event.key == 'd':
341	Data['Scale'] /= 1.1
342	elif event.key in ['+','=']:
343	Data['Layer'] = min(Data['Layer']+1,HKLmax[i])
344	elif event.key == '-':
345	Data['Layer'] = max(Data['Layer']-1,HKLmin[i])
346	elif event.key == '0':
347	Data['Layer'] = 0
348	Data['Scale'] = 1.0
349	elif event.key in hklfChoice and 'HKLF' in Name:
350	Data['Type'] = hklfChoice[event.key]
351	newPlot = True
352	elif event.key in pwdrChoice and 'PWDR' in Name:
353	Data['Type'] = pwdrChoice[event.key]
354	newPlot = True
355	PlotSngl(G2frame,newPlot,Data,hklRef,Title)
356
357	def OnSCMotion(event):
358	xpos = event.xdata
359	if xpos:
360	xpos = round(xpos) #avoid out of frame mouse position
361	ypos = round(event.ydata)
362	zpos = Data['Layer']
363	if '100' in Data['Zone']:
364	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
365	elif '010' in Data['Zone']:
366	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
367	elif '001' in Data['Zone']:
368	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
369	Page.canvas.SetToolTipString(HKLtxt)
370	G2frame.G2plotNB.status.SetStatusText('HKL = '+HKLtxt,0)
371	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
372
373	def OnSCPress(event):
374	zpos = Data['Layer']
375	xpos = event.xdata
376	if xpos:
377	pos = int(round(event.xdata)),int(round(event.ydata))
378	if '100' in Data['Zone']:
379	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
380	hkl = np.array([zpos,pos[0],pos[1]])
381	elif '010' in Data['Zone']:
382	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
383	hkl = np.array([pos[0],zpos,pos[1]])
384	elif '001' in Data['Zone']:
385	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
386	hkl = np.array([pos[0],pos[1],zpos])
387	h,k,l = hkl
388	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
389	if len(hklf):
390	Fosq,sig,Fcsq = hklf[0]
391	HKLtxt = '( %.2f %.3f %.2f %.2f)'%(Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
392	G2frame.G2plotNB.status.SetStatusText('Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt,1)
393
394	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
395	if not Title:
396	Title = Name
397	try:
398	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
399	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
400	if not newPlot:
401	Plot = Page.figure.gca() #get previous powder plot & get limits
402	xylim = Plot.get_xlim(),Plot.get_ylim()
403	Page.figure.clf()
404	Plot = Page.figure.gca() #get a fresh plot after clf()
405	except ValueError:
406	Plot = G2frame.G2plotNB.addMpl('Structure Factors').gca()
407	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
408	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
409	Page.canvas.mpl_connect('button_press_event', OnSCPress)
410	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
411	Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
412	Page.keyPress = OnSCKeyPress
413	Page.Choice = (' key press','i: increase scale','d: decrease scale',
414	'h: select 100 zone','k: select 010 zone','l: select 001 zone',
415	'f: select Fo','s: select Fosq','u: select unit Fc',
416	'+: increase index','-: decrease index','0: zero layer',)
417	if 'HKLF' in Name:
418	Page.Choice += ('w: select \|DFsq\|/sig','1: select \|DFsq\|>sig','3: select \|DFsq\|>3sig',)
419	Page.SetFocus()
420
421	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
422	Plot.set_aspect(aspect='equal')
423
424	Type = Data['Type']
425	scale = Data['Scale']
426	HKLmax = Data['HKLmax']
427	HKLmin = Data['HKLmin']
428	FosqMax = Data['FoMax']
429	Super = Data['Super']
430	SuperVec = []
431	if Super:
432	SuperVec = np.array(Data['SuperVec'][0])
433	FoMax = math.sqrt(FosqMax)
434	xlabel = ['k, h=','h, k=','h, l=']
435	ylabel = ['l','l','k']
436	zones = ['100','010','001']
437	pzone = [[1,2],[0,2],[0,1]]
438	izone = zones.index(Data['Zone'])
439	Plot.set_title(Data['Type']+' for '+Title)
440	HKL = []
441	HKLF = []
442	time0 = time.time()
443	for refl in hklRef:
444	H = refl[:3]
445	if 'HKLF' in Name:
446	Fosq,sig,Fcsq = refl[5+Super:8+Super]
447	else:
448	Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super]
449	if Super:
450	HKL.append(H+SuperVec*refl[3])
451	else:
452	HKL.append(H)
453	HKLF.append([Fosq,sig,Fcsq])
454	if H[izone] == Data['Layer']:
455	A = 0
456	B = 0
457	if Type == 'Fosq':
458	A = scale*Fosq/FosqMax
459	B = scale*Fcsq/FosqMax
460	C = abs(A-B)
461	elif Type == 'Fo':
462	A = scale*math.sqrt(max(0,Fosq))/FoMax
463	B = scale*math.sqrt(max(0,Fcsq))/FoMax
464	C = abs(A-B)
465	elif Type == 'Unit Fc':
466	A = scale/2
467	B = scale/2
468	C = 0.0
469	if Fcsq and Fosq > 0:
470	A *= min(1.0,Fosq/Fcsq)
471	C = abs(A-B)
472	elif Type == '\|DFsq\|/sig':
473	if sig > 0.:
474	A = (Fosq-Fcsq)/(3*sig)
475	B = 0
476	elif Type == '\|DFsq\|>sig':
477	if sig > 0.:
478	A = (Fosq-Fcsq)/(3*sig)
479	if abs(A) < 1.0: A = 0
480	B = 0
481	elif Type == '\|DFsq\|>3sig':
482	if sig > 0.:
483	A = (Fosq-Fcsq)/(3*sig)
484	if abs(A) < 3.0: A = 0
485	B = 0
486	if Super:
487	h = H+SuperVec*refl[3]
488	else:
489	h = H
490	xy = (h[pzone[izone][0]],h[pzone[izone][1]])
491	if Type in ['\|DFsq\|/sig','\|DFsq\|>sig','\|DFsq\|>3sig']:
492	if A > 0.0:
493	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
494	else:
495	Plot.add_artist(Circle(xy,radius=-A,ec='r',fc='w'))
496	else:
497	if A > 0.0 and A > B:
498	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
499	if B:
500	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
501	if A < B:
502	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
503	radius = C
504	if radius > 0:
505	if A > B:
506	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
507	else:
508	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
509	# print 'plot time: %.3f'%(time.time()-time0)
510	HKL = np.array(HKL)
511	HKLF = np.array(HKLF)
512	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
513	Plot.set_ylabel(ylabel[izone],fontsize=12)
514	if not newPlot:
515	Page.toolbar.push_current()
516	Plot.set_xlim(xylim[0])
517	Plot.set_ylim(xylim[1])
518	# xylim = []
519	Page.toolbar.push_current()
520	Page.toolbar.draw()
521	else:
522	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
523	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
524	Page.canvas.draw()
525
526	################################################################################
527	##### Plot3DSngl
528	################################################################################
529
530	def Plot3DSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=False):
531	'''3D Structure factor plotting package - displays reflections as rings proportional
532	to F, F**2, etc. as requested as 3D array
533	'''
534
535	global ifBox
536	ifBox = False
537	def OnKeyBox(event):
538	mode = cb.GetValue()
539	if mode in ['jpeg','bmp','tiff',]:
540	try:
541	import Image as Im
542	except ImportError:
543	try:
544	from PIL import Image as Im
545	except ImportError:
546	print "PIL/pillow Image module not present. Cannot save images without this"
547	raise Exception("PIL/pillow Image module not found")
548	try:
549	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
550	except NameError: #for when generalData doesn't exist!
551	Fname = os.path.join(Mydir,'unknown'+'.'+mode)
552	print Fname+' saved'
553	size = Page.canvas.GetSize()
554	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
555	if mode in ['jpeg',]:
556	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
557	im = Im.new("RGBA", (size[0],size[1]))
558	else:
559	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
560	im = Im.new("RGB", (size[0],size[1]))
561	im.fromstring(Pix)
562	im.save(Fname,mode)
563	cb.SetValue(' save as/key:')
564	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
565	else:
566	event.key = cb.GetValue()[0]
567	cb.SetValue(' save as/key:')
568	wx.CallAfter(OnKey,event)
569	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
570
571	def OnKey(event): #on key UP!!
572	global ifBox
573	Choice = {'F':'Fo','S':'Fosq','U':'Unit','D':'dFsq','W':'dFsq/sig'}
574	try:
575	keyCode = event.GetKeyCode()
576	if keyCode > 255:
577	keyCode = 0
578	key = chr(keyCode)
579	except AttributeError: #if from OnKeyBox above
580	key = str(event.key).upper()
581	if key in ['C']:
582	drawingData['viewPoint'][0] = drawingData['default']
583	drawingData['viewDir'] = [0,0,1]
584	drawingData['oldxy'] = []
585	V0 = np.array([0,0,1])
586	V = np.inner(Amat,V0)
587	V /= np.sqrt(np.sum(V**2))
588	A = np.arccos(np.sum(V*V0))
589	Q = G2mth.AV2Q(A,[0,1,0])
590	drawingData['Quaternion'] = Q
591	Q = drawingData['Quaternion']
592	elif key in 'B':
593	ifBox = not ifBox
594	elif key in ['+','=']:
595	Data['Scale'] *= 1.25
596	elif key == '-':
597	Data['Scale'] /= 1.25
598	elif key == '0':
599	drawingData['viewPoint'][0] = [0,0,0]
600	Data['Scale'] = 1.0
601	elif key == 'I':
602	Data['Iscale'] = not Data['Iscale']
603	elif key in Choice:
604	Data['Type'] = Choice[key]
605	Draw('key')
606
607	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
608	if Title: #NB: save image as e.g. jpeg will fail if False; MyDir is unknown
609	generalData = G2frame.GetPhaseData()[Title]['General']
610	cell = generalData['Cell'][1:7]
611	Mydir = generalData['Mydir']
612	else:
613	cell = [10,10,10,90,90,90]
614	Mydir = G2frame.dirname
615	drawingData = Data['Drawing']
616	Super = Data['Super']
617	SuperVec = []
618	if Super:
619	SuperVec = np.array(Data['SuperVec'][0])
620	defaultViewPt = copy.copy(drawingData['viewPoint'])
621	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
622	Gmat,gmat = G2lat.cell2Gmat(cell)
623	invcell = G2lat.Gmat2cell(Gmat)
624	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
625	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
626	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Bmat,[0,0,1]))
627	Wt = np.array([255,255,255])
628	Rd = np.array([255,0,0])
629	Gr = np.array([0,255,0])
630	wxGreen = wx.Colour(0,255,0)
631	Bl = np.array([0,0,255])
632	Or = np.array([255,128,0])
633	wxOrange = wx.Colour(255,128,0)
634	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]])
635	uEdges = np.array([
636	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
637	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
638	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
639	uColors = [Rd,Gr,Bl, Wt,Wt,Wt, Wt,Wt,Wt, Wt,Wt,Wt]
640	def FillHKLRC():
641	R = np.zeros(len(hklRef))
642	C = []
643	HKL = []
644	RC = []
645	for i,refl in enumerate(hklRef):
646	H = refl[:3]
647	if 'HKLF' in Name:
648	Fosq,sig,Fcsq = refl[5+Super:8+Super]
649	else:
650	Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super]
651	if Super:
652	HKL.append(H+SuperVec*refl[3])
653	else:
654	HKL.append(H)
655	if Data['Type'] == 'Unit':
656	R[i] = 0.1
657	C.append(Gr)
658	elif Data['Type'] == 'Fosq':
659	if Fosq > 0:
660	R[i] = Fosq
661	C.append(Gr)
662	else:
663	R[i] = -Fosq
664	C.append(Rd)
665	elif Data['Type'] == 'Fo':
666	if Fosq > 0:
667	R[i] = np.sqrt(Fosq)
668	C.append(Gr)
669	else:
670	R[i] = np.sqrt(-Fosq)
671	C.append(Rd)
672	elif Data['Type'] == 'dFsq/sig':
673	dFsig = (Fosq-Fcsq)/sig
674	if dFsig > 0:
675	R[i] = dFsig
676	C.append(Gr)
677	else:
678	R[i] = -dFsig
679	C.append(Rd)
680	elif Data['Type'] == 'dFsq':
681	dF = Fosq-Fcsq
682	if dF > 0:
683	R[i] = dF
684	C.append(Gr)
685	else:
686	R[i] = -dF
687	C.append(Rd)
688	R /= np.max(R)
689	R *= Data['Scale']
690	R = np.where(R<1.e-5,1.e-5,R)
691	if Data['Iscale']:
692	R = np.where(R<=1.,R,1.)
693	C = np.array(C)
694	C = (C.T*R).T
695	R = np.ones_like(R)*0.05
696	return HKL,zip(list(R),C)
697
698	def SetTranslation(newxy):
699	#first get translation vector in screen coords.
700	oldxy = drawingData['oldxy']
701	if not len(oldxy): oldxy = list(newxy)
702	dxy = newxy-oldxy
703	drawingData['oldxy'] = list(newxy)
704	V = np.array([-dxy[0],dxy[1],0.])
705	#then transform to rotated crystal coordinates & apply to view point
706	Q = drawingData['Quaternion']
707	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
708	Tx,Ty,Tz = drawingData['viewPoint'][0]
709	Tx += V[0]*0.1
710	Ty += V[1]*0.1
711	Tz += V[2]*0.1
712	drawingData['viewPoint'][0] = Tx,Ty,Tz
713
714	def SetRotation(newxy):
715	'Perform a rotation in x-y space due to a left-mouse drag'
716	#first get rotation vector in screen coords. & angle increment
717	oldxy = drawingData['oldxy']
718	if not len(oldxy): oldxy = list(newxy)
719	dxy = newxy-oldxy
720	drawingData['oldxy'] = list(newxy)
721	V = np.array([dxy[1],dxy[0],0.])
722	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
723	if not A: return # nothing changed, nothing to do
724	# next transform vector back to xtal coordinates via inverse quaternion
725	# & make new quaternion
726	Q = drawingData['Quaternion']
727	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
728	DQ = G2mth.AVdeg2Q(A,V)
729	Q = G2mth.prodQQ(Q,DQ)
730	drawingData['Quaternion'] = Q
731	# finally get new view vector - last row of rotation matrix
732	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
733	VD /= np.sqrt(np.sum(VD**2))
734	drawingData['viewDir'] = VD
735
736	def SetRotationZ(newxy):
737	#first get rotation vector (= view vector) in screen coords. & angle increment
738	View = glGetIntegerv(GL_VIEWPORT)
739	cent = [View[2]/2,View[3]/2]
740	oldxy = drawingData['oldxy']
741	if not len(oldxy): oldxy = list(newxy)
742	dxy = newxy-oldxy
743	drawingData['oldxy'] = list(newxy)
744	V = drawingData['viewDir']
745	A = [0,0]
746	A[0] = dxy[1]*.25
747	A[1] = dxy[0]*.25
748	if newxy[0] > cent[0]:
749	A[0] *= -1
750	if newxy[1] < cent[1]:
751	A[1] *= -1
752	# next transform vector back to xtal coordinates & make new quaternion
753	Q = drawingData['Quaternion']
754	V = np.inner(Amat,V)
755	Qx = G2mth.AVdeg2Q(A[0],V)
756	Qy = G2mth.AVdeg2Q(A[1],V)
757	Q = G2mth.prodQQ(Q,Qx)
758	Q = G2mth.prodQQ(Q,Qy)
759	drawingData['Quaternion'] = Q
760
761	def OnMouseDown(event):
762	xy = event.GetPosition()
763	drawingData['oldxy'] = list(xy)
764
765	def OnMouseMove(event):
766	if event.ShiftDown(): #don't want any inadvertant moves when picking
767	return
768	newxy = event.GetPosition()
769
770	if event.Dragging():
771	if event.LeftIsDown():
772	SetRotation(newxy)
773	Q = drawingData['Quaternion']
774	elif event.RightIsDown():
775	SetTranslation(newxy)
776	Tx,Ty,Tz = drawingData['viewPoint'][0]
777	elif event.MiddleIsDown():
778	SetRotationZ(newxy)
779	Q = drawingData['Quaternion']
780	Draw('move')
781
782	def OnMouseWheel(event):
783	if event.ShiftDown():
784	return
785	drawingData['cameraPos'] += event.GetWheelRotation()/120.
786	drawingData['cameraPos'] = max(0.1,min(20.00,drawingData['cameraPos']))
787	Draw('wheel')
788
789	def SetBackground():
790	R,G,B,A = Page.camera['backColor']
791	glClearColor(R,G,B,A)
792	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
793
794	def SetLights():
795	glEnable(GL_DEPTH_TEST)
796	glShadeModel(GL_SMOOTH)
797	glEnable(GL_LIGHTING)
798	glEnable(GL_LIGHT0)
799	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
800	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
801	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
802
803	def RenderBox(x,y,z):
804	xyz = np.array([x,y,z])
805	glEnable(GL_COLOR_MATERIAL)
806	glLineWidth(1)
807	glPushMatrix()
808	glTranslate(x,y,z)
809	glColor4ubv([0,0,0,0])
810	glBegin(GL_LINES)
811	for line,color in zip(uEdges,uColors):
812	glColor3ubv(color)
813	glVertex3fv(line[0])
814	glVertex3fv(line[1])
815	glEnd()
816	glPopMatrix()
817	glColor4ubv([0,0,0,0])
818	glDisable(GL_COLOR_MATERIAL)
819
820	def RenderUnitVectors(x,y,z):
821	xyz = np.array([x,y,z])
822	glEnable(GL_COLOR_MATERIAL)
823	glLineWidth(1)
824	glPushMatrix()
825	glTranslate(x,y,z)
826	glBegin(GL_LINES)
827	for line,color in zip(uEdges,uColors)[:3]:
828	glColor3ubv(color)
829	glVertex3fv(-line[1])
830	glVertex3fv(line[1])
831	glEnd()
832	glPopMatrix()
833	glColor4ubv([0,0,0,0])
834	glDisable(GL_COLOR_MATERIAL)
835
836	def RenderDots(XYZ,RC):
837	glEnable(GL_COLOR_MATERIAL)
838	XYZ = np.array(XYZ)
839	glPushMatrix()
840	for xyz,rc in zip(XYZ,RC):
841	x,y,z = xyz
842	r,c = rc
843	glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,c)
844	glPointSize(r*50)
845	glBegin(GL_POINTS)
846	glVertex3fv(xyz)
847	glEnd()
848	glPopMatrix()
849	glColor4ubv([0,0,0,0])
850	glDisable(GL_COLOR_MATERIAL)
851
852	def Draw(caller=''):
853	#useful debug?
854	# if caller:
855	# print caller
856	# end of useful debug
857	G2frame.G2plotNB.status.SetStatusText('Plot type = %s for %s'%(Data['Type'],Name),1)
858	VS = np.array(Page.canvas.GetSize())
859	aspect = float(VS[0])/float(VS[1])
860	cPos = drawingData['cameraPos']
861	Zclip = drawingData['Zclip']*cPos/20.
862	Q = drawingData['Quaternion']
863	Tx,Ty,Tz = drawingData['viewPoint'][0]
864	G,g = G2lat.cell2Gmat(cell)
865	GS = G
866	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
867	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
868	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
869
870	HKL,RC = FillHKLRC()
871
872	SetBackground()
873	glInitNames()
874	glPushName(0)
875
876	glMatrixMode(GL_PROJECTION)
877	glLoadIdentity()
878	glViewport(0,0,VS[0],VS[1])
879	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
880	gluLookAt(0,0,cPos,0,0,0,0,1,0)
881	SetLights()
882
883	glMatrixMode(GL_MODELVIEW)
884	glLoadIdentity()
885	matRot = G2mth.Q2Mat(Q)
886	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
887	glMultMatrixf(matRot.T)
888	glMultMatrixf(B4mat.T)
889	glTranslate(-Tx,-Ty,-Tz)
890	x,y,z = drawingData['viewPoint'][0]
891	if ifBox:
892	RenderBox(x,y,z)
893	else:
894	RenderUnitVectors(x,y,z)
895	RenderUnitVectors(0,0,0)
896	RenderDots(HKL,RC)
897	time0 = time.time()
898	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
899	Page.canvas.SwapBuffers()
900
901	# PlotStructure execution starts here (N.B. initialization above)
902	try:
903	plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors')
904	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
905	except ValueError:
906	Plot = G2frame.G2plotNB.addOgl('3D Structure Factors')
907	plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors')
908	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
909	Page.views = False
910	view = False
911	altDown = False
912	Font = Page.GetFont()
913	Page.SetFocus()
914	Page.Choice = None
915	choice = [' save as/key:','jpeg','tiff','bmp','c: recenter to default','b: toggle box ','+: increase scale',
916	'-: decrease scale','f: Fobs','s: Fobs**2','u: unit','d: Fo-Fc','w: DF/sig','i: toggle intensity scaling']
917	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
918	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
919	cb.SetValue(' save as/key:')
920	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
921	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
922	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
923	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
924	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
925	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
926	# Page.canvas.Bind(wx.EVT_SIZE, OnSize)
927	Page.camera['position'] = drawingData['cameraPos']
928	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
929	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
930	Page.controls = Data
931	try:
932	Page.canvas.SetCurrent()
933	except:
934	pass
935	Draw('main')
936	# if firstCall: Draw('main') # draw twice the first time that graphics are displayed
937
938
939	################################################################################
940	##### PlotPatterns
941	################################################################################
942
943	def PlotPatterns(G2frame,newPlot=False,plotType='PWDR'):
944	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
945	2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I
946	plotting available.
947	'''
948	global HKL
949	global exclLines
950	global DifLine
951	global Ymax
952	plottype = plotType
953	#patch
954	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
955	if 'Offset' not in data[0] and plotType in ['PWDR','SASD']: #plot offset data
956	data[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,
957	'refDelt':0.01,})
958	G2frame.PatternTree.SetItemPyData(G2frame.PickId,data)
959	#end patch
960	def OnPlotKeyPress(event):
961	try: #one way to check if key stroke will work on plot
962	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
963	except TypeError:
964	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1)
965	return
966	newPlot = False
967	if event.key == 'w':
968	G2frame.Weight = not G2frame.Weight
969	if not G2frame.Weight and 'PWDR' in plottype:
970	G2frame.SinglePlot = True
971	newPlot = True
972	elif event.key == 'e' and 'SASD' in plottype:
973	G2frame.ErrorBars = not G2frame.ErrorBars
974	elif event.key == 'b':
975	G2frame.SubBack = not G2frame.SubBack
976	if not G2frame.SubBack:
977	G2frame.SinglePlot = True
978	elif event.key == 'n':
979	if G2frame.Contour:
980	pass
981	else:
982	G2frame.logPlot = not G2frame.logPlot
983	if not G2frame.logPlot:
984	Pattern[0]['Offset'][0] = 0
985	newPlot = True
986	elif event.key == 's' and 'PWDR' in plottype:
987	if G2frame.Contour:
988	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
989	choice.sort()
990	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
991	if dlg.ShowModal() == wx.ID_OK:
992	sel = dlg.GetSelection()
993	G2frame.ContourColor = choice[sel]
994	else:
995	G2frame.ContourColor = 'Paired'
996	dlg.Destroy()
997	elif G2frame.SinglePlot:
998	G2frame.plotStyle['sqrtPlot'] = not G2frame.plotStyle['sqrtPlot']
999	if G2frame.plotStyle['sqrtPlot']:
1000	Pattern[0]['delOffset'] = .002
1001	Pattern[0]['refOffset'] = -1.0
1002	Pattern[0]['refDelt'] = .001
1003	else:
1004	Pattern[0]['delOffset'] = .02
1005	Pattern[0]['refOffset'] = -1.0
1006	Pattern[0]['refDelt'] = .01
1007	newPlot = True
1008	elif event.key == 'u' and (G2frame.Contour or not G2frame.SinglePlot):
1009	if G2frame.Contour:
1010	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1011	elif Pattern[0]['Offset'][0] < 100.:
1012	Pattern[0]['Offset'][0] += 1.
1013	elif event.key == 'd' and (G2frame.Contour or not G2frame.SinglePlot):
1014	if G2frame.Contour:
1015	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1016	elif Pattern[0]['Offset'][0] > 0.:
1017	Pattern[0]['Offset'][0] -= 1.
1018	elif event.key == 'l' and not G2frame.SinglePlot:
1019	Pattern[0]['Offset'][1] -= 1.
1020	elif event.key == 'r' and not G2frame.SinglePlot:
1021	Pattern[0]['Offset'][1] += 1.
1022	elif event.key == 'o' and not G2frame.SinglePlot:
1023	G2frame.Cmax = 1.0
1024	Pattern[0]['Offset'] = [0,0]
1025	elif event.key == 'c' and 'PWDR' in plottype:
1026	newPlot = True
1027	if not G2frame.Contour:
1028	G2frame.SinglePlot = False
1029	Pattern[0]['Offset'] = [0.,0.]
1030	else:
1031	G2frame.SinglePlot = True
1032	G2frame.Contour = not G2frame.Contour
1033	elif event.key == 'q':
1034	if 'PWDR' in plottype:
1035	newPlot = True
1036	G2frame.plotStyle['qPlot'] = not G2frame.plotStyle['qPlot']
1037	G2frame.plotStyle['dPlot'] = False
1038	elif 'SASD' in plottype:
1039	newPlot = True
1040	G2frame.plotStyle['sqPlot'] = not G2frame.plotStyle['sqPlot']
1041	elif event.key == 't' and 'PWDR' in plottype:
1042	G2frame.plotStyle['dPlot'] = not G2frame.plotStyle['dPlot']
1043	G2frame.plotStyle['qPlot'] = False
1044	newPlot = True
1045	elif event.key == 'm':
1046	G2frame.plotStyle['sqrtPlot'] = False
1047	G2frame.SinglePlot = not G2frame.SinglePlot
1048	newPlot = True
1049	elif event.key in ['+','=']:
1050	if G2frame.PickId:
1051	G2frame.PickId = False
1052	elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot
1053	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1054	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1055	'mitchell','sinc','lanczos']
1056	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1057	if dlg.ShowModal() == wx.ID_OK:
1058	sel = dlg.GetSelection()
1059	G2frame.Interpolate = choice[sel]
1060	else:
1061	G2frame.Interpolate = 'nearest'
1062	dlg.Destroy()
1063	else:
1064	# print 'no binding for key',event.key
1065	#GSASIIpath.IPyBreak()
1066	return
1067	wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype)
1068
1069	def OnMotion(event):
1070	xpos = event.xdata
1071	if xpos: #avoid out of frame mouse position
1072	ypos = event.ydata
1073	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1074	try:
1075	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
1076	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
1077	q = xpos
1078	dsp = 2.*np.pi/q
1079	try:
1080	xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos)
1081	except ValueError: #avoid bad value in asin beyond upper limit
1082	pass
1083	elif 'SASD' in plottype:
1084	q = xpos
1085	dsp = 2.*np.pi/q
1086	elif G2frame.plotStyle['dPlot']:
1087	dsp = xpos
1088	q = 2.*np.pi/dsp
1089	xpos = G2lat.Dsp2pos(Parms,xpos)
1090	elif G2frame.Contour and 'T' in Parms['Type'][0]:
1091	xpos = X[xpos]
1092	dsp = G2lat.Pos2dsp(Parms,xpos)
1093	q = 2.*np.pi/dsp
1094	else:
1095	dsp = G2lat.Pos2dsp(Parms,xpos)
1096	q = 2.*np.pi/dsp
1097	if G2frame.Contour: #PWDR only
1098	if 'C' in Parms['Type'][0]:
1099	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
1100	else:
1101	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
1102	else:
1103	if 'C' in Parms['Type'][0]:
1104	if 'PWDR' in plottype:
1105	if G2frame.plotStyle['sqrtPlot']:
1106	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
1107	else:
1108	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
1109	elif 'SASD' in plottype:
1110	G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1)
1111	else:
1112	if G2frame.plotStyle['sqrtPlot']:
1113	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
1114	else:
1115	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
1116	if G2frame.itemPicked:
1117	Page.canvas.SetToolTipString('%9.5f'%(xpos))
1118	if G2frame.PickId:
1119	found = []
1120	pickIdText = G2frame.PatternTree.GetItemText(G2frame.PickId)
1121	if pickIdText in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
1122	'PWDR' in pickIdText:
1123	indx = -1
1124	if pickIdText in ['Index Peak List','Unit Cells List',]:
1125	indx = -2
1126	if len(HKL):
1127	view = Page.toolbar._views.forward()[0][:2]
1128	wid = view[1]-view[0]
1129	found = HKL[np.where(np.fabs(HKL.T[indx]-xpos) < 0.002*wid)]
1130	if len(found):
1131	if len(found[0]) > 6: #SS reflections
1132	h,k,l,m = found[0][:4]
1133	Page.canvas.SetToolTipString('%d,%d,%d,%d'%(int(h),int(k),int(l),int(m)))
1134	else:
1135	h,k,l = found[0][:3]
1136	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
1137	else:
1138	Page.canvas.SetToolTipString('')
1139
1140	except TypeError:
1141	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1)
1142
1143	def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots
1144	olderr = np.seterr(invalid='ignore')
1145
1146	def OnPick(event):
1147	if G2frame.itemPicked is not None: return
1148	PatternId = G2frame.PatternId
1149	try:
1150	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
1151	except TypeError:
1152	return
1153	PickId = G2frame.PickId
1154	pick = event.artist
1155	mouse = event.mouseevent
1156	xpos = pick.get_xdata()
1157	ypos = pick.get_ydata()
1158	ind = event.ind
1159	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
1160	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
1161	if ind.all() != [0] and ObsLine[0].get_label() in str(pick): #picked a data point
1162	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
1163	if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta
1164	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
1165	elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta
1166	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
1167	XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
1168	data['peaks'].append(XY)
1169	data['sigDict'] = {} #now invalid
1170	G2pdG.UpdatePeakGrid(G2frame,data)
1171	PlotPatterns(G2frame,plotType=plottype)
1172	else: #picked a peak list line
1173	G2frame.itemPicked = pick
1174	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
1175	if ind.all() != [0]: #picked a data point
1176	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1177	data = G2frame.PatternTree.GetItemPyData(LimitId)
1178	if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta
1179	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
1180	elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta
1181	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
1182	if G2frame.ifGetExclude:
1183	excl = [0,0]
1184	excl[0] = max(data[1][0],min(xy[0],data[1][1]))
1185	excl[1] = excl[0]+0.1
1186	data.append(excl)
1187	G2frame.ifGetExclude = False
1188	else:
1189	if mouse.button==1:
1190	data[1][0] = min(xy[0],data[1][1])
1191	if mouse.button==3:
1192	data[1][1] = max(xy[0],data[1][0])
1193	G2frame.PatternTree.SetItemPyData(LimitId,data)
1194	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
1195	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
1196	else: #picked a limit line
1197	G2frame.itemPicked = pick
1198	elif G2frame.PatternTree.GetItemText(PickId) == 'Models':
1199	if ind.all() != [0]: #picked a data point
1200	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
1201	data = G2frame.PatternTree.GetItemPyData(LimitId)
1202	if mouse.button==1:
1203	data[1][0] = min(xy[0],data[1][1])
1204	if mouse.button==3:
1205	data[1][1] = max(xy[0],data[1][0])
1206	G2frame.PatternTree.SetItemPyData(LimitId,data)
1207	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
1208	else: #picked a limit line
1209	G2frame.itemPicked = pick
1210	elif G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
1211	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1212	G2frame.itemPicked = pick
1213	pick = str(pick)
1214
1215	def OnRelease(event):
1216	if G2frame.itemPicked is None: return
1217	PickId = G2frame.PickId
1218	if str(DifLine[0]) == str(G2frame.itemPicked):
1219	data = G2frame.PatternTree.GetItemPyData(PickId)
1220	ypos = event.ydata
1221	data[0]['delOffset'] = -ypos/Ymax
1222	G2frame.itemPicked = None
1223	G2frame.PatternTree.SetItemPyData(PickId,data)
1224	PlotPatterns(G2frame,plotType=plottype)
1225	return
1226	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
1227	xpos = event.xdata
1228	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
1229	lines = []
1230	for line in G2frame.Lines:
1231	lines.append(line.get_xdata()[0])
1232	try:
1233	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
1234	except ValueError:
1235	lineNo = -1
1236	if lineNo in [0,1] or lineNo in exclLines:
1237	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
1238	limits = G2frame.PatternTree.GetItemPyData(LimitId)
1239	id = lineNo/2+1
1240	id2 = lineNo%2
1241	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
1242	limits[id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
1243	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype:
1244	limits[id][id2] = G2lat.Dsp2pos(Parms,xpos)
1245	else:
1246	limits[id][id2] = xpos
1247	if id > 1 and limits[id][0] > limits[id][1]:
1248	limits[id].reverse()
1249	limits[1][0] = min(max(limits[0][0],limits[1][0]),limits[1][1])
1250	limits[1][1] = max(min(limits[0][1],limits[1][1]),limits[1][0])
1251	G2frame.PatternTree.SetItemPyData(LimitId,limits)
1252	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
1253	G2pdG.UpdateLimitsGrid(G2frame,limits,plottype)
1254	elif lineNo > 1:
1255	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
1256	peaks = G2frame.PatternTree.GetItemPyData(PeakId)
1257	if event.button == 3:
1258	del peaks['peaks'][lineNo-2]
1259	else:
1260	if G2frame.plotStyle['qPlot']:
1261	peaks['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
1262	elif G2frame.plotStyle['dPlot']:
1263	peaks['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,xpos)
1264	else:
1265	peaks['peaks'][lineNo-2][0] = xpos
1266	peaks['sigDict'] = {} #no longer valid
1267	G2frame.PatternTree.SetItemPyData(PeakId,peaks)
1268	G2pdG.UpdatePeakGrid(G2frame,peaks)
1269	elif G2frame.PatternTree.GetItemText(PickId) in ['Models',] and xpos:
1270	lines = []
1271	for line in G2frame.Lines:
1272	lines.append(line.get_xdata()[0])
1273	try:
1274	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
1275	except ValueError:
1276	lineNo = -1
1277	if lineNo in [0,1]:
1278	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
1279	data = G2frame.PatternTree.GetItemPyData(LimitId)
1280	data[1][lineNo] = xpos
1281	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
1282	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
1283	G2frame.PatternTree.SetItemPyData(LimitId,data)
1284	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
1285	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
1286	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1287	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
1288	if 'line' not in pick: #avoid data points, etc.
1289	data = G2frame.PatternTree.GetItemPyData(PickId)
1290	num = Phases.keys().index(pick)
1291	if num:
1292	data[0]['refDelt'] = -(event.ydata-Pattern[0]['refOffset'])/(num*Ymax)
1293	else: #1st row of refl ticks
1294	data[0]['refOffset'] = event.ydata
1295	G2frame.PatternTree.SetItemPyData(PickId,data)
1296	PlotPatterns(G2frame,plotType=plottype)
1297	G2frame.itemPicked = None
1298
1299	try:
1300	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
1301	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1302	if not newPlot:
1303	Plot = Page.figure.gca() #get previous powder plot & get limits
1304	xylim = Plot.get_xlim(),Plot.get_ylim()
1305	Page.figure.clf()
1306	Plot = Page.figure.gca() #get a fresh plot after clf()
1307	except ValueError:
1308	if plottype == 'SASD':
1309	G2frame.logPlot = True
1310	G2frame.ErrorBars = True
1311	newPlot = True
1312	G2frame.Cmax = 1.0
1313	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
1314	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
1315	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1316	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1317	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1318	Page.canvas.mpl_connect('pick_event', OnPick)
1319	Page.canvas.mpl_connect('button_release_event', OnRelease)
1320	Page.canvas.mpl_connect('button_press_event',OnPress)
1321	if plottype == 'PWDR': # avoids a very nasty clash with KILL_FOCUS in SASD TextCtrl?
1322	Page.SetFocus()
1323	G2frame.G2plotNB.status.DestroyChildren()
1324	if G2frame.Contour:
1325	Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
1326	'i: interpolation method','s: color scheme','c: contour off')
1327	else:
1328	if G2frame.logPlot:
1329	if 'PWDR' in plottype:
1330	if G2frame.SinglePlot:
1331	Page.Choice = (' key press','n: log(I) off',
1332	'c: contour on','q: toggle q plot','t: toggle d-spacing plot',
1333	'm: toggle multidata plot','w: toggle divide by sig','+: no selection')
1334	else:
1335	Page.Choice = (' key press','n: log(I) off',
1336	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
1337	'c: contour on','q: toggle q plot','t: toggle d-spacing plot',
1338	'm: toggle multidata plot','w: toggle divide by sig','+: no selection')
1339	elif 'SASD' in plottype:
1340	if G2frame.SinglePlot:
1341	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
1342	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1343	else:
1344	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
1345	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
1346	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1347	else:
1348	if 'PWDR' in plottype:
1349	if G2frame.SinglePlot:
1350	Page.Choice = (' key press',
1351	'b: toggle subtract background','n: log(I) on','s: toggle sqrt plot','c: contour on',
1352	'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot',
1353	'w: toggle divide by sig','+: no selection')
1354	else:
1355	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down',
1356	'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on',
1357	'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot',
1358	'w: toggle divide by sig','+: no selection')
1359	elif 'SASD' in plottype:
1360	if G2frame.SinglePlot:
1361	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
1362	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1363	else:
1364	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
1365	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
1366	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
1367
1368	Page.keyPress = OnPlotKeyPress
1369	PickId = G2frame.PickId
1370	PatternId = G2frame.PatternId
1371	colors=['b','g','r','c','m','k']
1372	Lines = []
1373	exclLines = []
1374	if G2frame.SinglePlot and PatternId:
1375	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1376	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1377	PlotList = [Pattern,]
1378	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
1379	G2frame.PatternId, 'Instrument Parameters'))
1380	Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
1381	ParmList = [Parms,]
1382	SampleList = [Sample,]
1383	Title = Pattern[-1]
1384	else:
1385	Title = os.path.split(G2frame.GSASprojectfile)[1]
1386	PlotList = []
1387	ParmList = []
1388	SampleList = []
1389	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1390	while item:
1391	if plottype in G2frame.PatternTree.GetItemText(item):
1392	Pattern = G2frame.PatternTree.GetItemPyData(item)
1393	if len(Pattern) < 3: # put name on end if needed
1394	Pattern.append(G2frame.PatternTree.GetItemText(item))
1395	if 'Offset' not in Pattern[0]: #plot offset data
1396	Pattern[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,})
1397	PlotList.append(Pattern)
1398	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
1399	item,'Instrument Parameters'))[0])
1400	SampleList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
1401	item, 'Sample Parameters')))
1402	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1403	lenX = 0
1404	if PickId:
1405	if G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists']:
1406	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1407	HKL = []
1408	if Phases:
1409	try:
1410	for peak in Phases[G2frame.RefList]['RefList']:
1411	if len(peak) > 15:
1412	HKL.append(peak[:7]) #SS reflection list - need peak[:7]
1413	else:
1414	HKL.append(peak[:6])
1415	except TypeError: #old style patch
1416	for peak in Phases[G2frame.RefList]:
1417	HKL.append(peak[:6])
1418	HKL = np.array(HKL)
1419	else:
1420	HKL = np.array(G2frame.HKL)
1421	Ymax = None
1422	for Pattern in PlotList:
1423	xye = Pattern[1]
1424	if xye[1] is None: continue
1425	if Ymax is None: Ymax = max(xye[1])
1426	Ymax = max(Ymax,max(xye[1]))
1427	if Ymax is None: return # nothing to plot
1428	offsetX = Pattern[0]['Offset'][1]
1429	offsetY = Pattern[0]['Offset'][0]
1430	if G2frame.logPlot:
1431	Title = 'log('+Title+')'
1432	Plot.set_title(Title)
1433	if G2frame.plotStyle['qPlot'] or 'SASD' in plottype and not G2frame.Contour:
1434	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=16)
1435	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype and not G2frame.Contour:
1436	Plot.set_xlabel(r'$d, \AA$',fontsize=16)
1437	else:
1438	if 'C' in ParmList[0]['Type'][0]:
1439	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=16)
1440	else:
1441	if G2frame.Contour:
1442	Plot.set_xlabel(r'Channel no.',fontsize=16)
1443	else:
1444	Plot.set_xlabel(r'$TOF, \mathsf{\mu}$s',fontsize=16)
1445	if G2frame.Weight:
1446	if 'PWDR' in plottype:
1447	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=16)
1448	elif 'SASD' in plottype:
1449	Plot.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16)
1450	else:
1451	if 'C' in ParmList[0]['Type'][0]:
1452	if 'PWDR' in plottype:
1453	if G2frame.plotStyle['sqrtPlot']:
1454	Plot.set_ylabel(r'$\sqrt{Intensity}$',fontsize=16)
1455	else:
1456	Plot.set_ylabel(r'$Intensity$',fontsize=16)
1457	elif 'SASD' in plottype:
1458	if G2frame.sqPlot:
1459	Plot.set_ylabel(r'$S(Q)=I*Q^{4}$',fontsize=16)
1460	else:
1461	Plot.set_ylabel(r'$Intensity, cm^{-1}$',fontsize=16)
1462	else:
1463	if G2frame.plotStyle['sqrtPlot']:
1464	Plot.set_ylabel(r'$\sqrt{Normalized\ intensity}$',fontsize=16)
1465	else:
1466	Plot.set_ylabel(r'$Normalized\ intensity$',fontsize=16)
1467	if G2frame.Contour:
1468	ContourZ = []
1469	ContourY = []
1470	Nseq = 0
1471	for N,Pattern in enumerate(PlotList):
1472	Parms = ParmList[N]
1473	Sample = SampleList[N]
1474	if 'C' in Parms['Type'][0]:
1475	wave = G2mth.getWave(Parms)
1476	else:
1477	difC = Parms['difC'][1]
1478	ifpicked = False
1479	LimitId = 0
1480	if Pattern[1] is None: continue # skip over uncomputed simulations
1481	xye = ma.array(ma.getdata(Pattern[1]))
1482	Zero = Parms.get('Zero',[0.,0.])[1]
1483	if PickId:
1484	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1485	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId,'Limits')
1486	limits = G2frame.PatternTree.GetItemPyData(LimitId)
1487	excls = limits[2:]
1488	for excl in excls:
1489	xye[0] = ma.masked_inside(xye[0],excl[0],excl[1])
1490	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
1491	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
1492	X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye[0])
1493	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype:
1494	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
1495	X = G2lat.Pos2dsp(Parms,xye[0])
1496	else:
1497	X = xye[0]
1498	if not lenX:
1499	lenX = len(X)
1500	if 'PWDR' in plottype:
1501	if G2frame.plotStyle['sqrtPlot']:
1502	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
1503	Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1]))
1504	np.seterr(invalid=olderr['invalid'])
1505	else:
1506	Y = xye[1]+offsetYNYmax/100.0
1507	elif 'SASD' in plottype:
1508	B = xye[5]
1509	if G2frame.sqPlot:
1510	Y = xye[1]Sample['Scale'][0](1.05)*(offsetYN)X*4
1511	else:
1512	Y = xye[1]Sample['Scale'][0](1.05)*(offsetYN)
1513	if LimitId and ifpicked:
1514	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
1515	lims = limits[1]
1516	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
1517	lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims)
1518	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype:
1519	lims = G2lat.Pos2dsp(Parms,lims)
1520	Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.))
1521	Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.))
1522	for i,item in enumerate(limits[2:]):
1523	Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))
1524	Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.))
1525	exclLines += [2i+2,2i+3]
1526	if G2frame.Contour:
1527	if lenX == len(X):
1528	ContourY.append(N)
1529	ContourZ.append(Y)
1530	if 'C' in ParmList[0]['Type'][0]:
1531	ContourX = X
1532	else: #'T'OF
1533	ContourX = range(lenX)
1534	Nseq += 1
1535	Plot.set_ylabel('Data sequence',fontsize=12)
1536	else:
1537	if 'SASD' in plottype and G2frame.logPlot:
1538	X = (1.01)(offsetXN)
1539	else:
1540	X += offsetX.005N
1541	Xum = ma.getdata(X)
1542	DifLine = ['']
1543	if ifpicked:
1544	if G2frame.plotStyle['sqrtPlot']:
1545	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
1546	Z = np.where(xye[3]>=0.,np.sqrt(xye[3]),-np.sqrt(-xye[3]))
1547	np.seterr(invalid=olderr['invalid'])
1548	else:
1549	Z = xye[3]+offsetYNYmax/100.0
1550	if 'PWDR' in plottype:
1551	if G2frame.plotStyle['sqrtPlot']:
1552	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
1553	W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4]))
1554	np.seterr(invalid=olderr['invalid'])
1555	D = np.where(xye[5],(Y-Z),0.)-Ymax*Pattern[0]['delOffset']
1556	else:
1557	W = xye[4]+offsetYNYmax/100.0
1558	D = xye[5]-Ymax*Pattern[0]['delOffset'] #powder background
1559	elif 'SASD' in plottype:
1560	if G2frame.sqPlot:
1561	W = xye[4]X*4
1562	Z = xye[3]X*4
1563	B = BX*4
1564	else:
1565	W = xye[4]
1566	if G2frame.SubBack:
1567	YB = Y-B
1568	ZB = Z
1569	else:
1570	YB = Y
1571	ZB = Z+B
1572	Plot.set_yscale("log",nonposy='mask')
1573	if np.any(W>0.):
1574	Plot.set_ylim(bottom=np.min(np.trim_zeros(W))/2.,top=np.max(Y)*2.)
1575	else:
1576	Plot.set_ylim(bottom=np.min(np.trim_zeros(YB))/2.,top=np.max(Y)*2.)
1577	if G2frame.logPlot:
1578	if 'PWDR' in plottype:
1579	Plot.set_yscale("log",nonposy='mask')
1580	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1581	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
1582	Plot.plot(X,W,colors[(N+2)%6],picker=False) #background
1583	elif 'SASD' in plottype:
1584	Plot.set_xscale("log",nonposx='mask')
1585	Ibeg = np.searchsorted(X,limits[1][0])
1586	Ifin = np.searchsorted(X,limits[1][1])
1587	if G2frame.Weight:
1588	Plot.set_yscale("linear")
1589	DS = (YB-ZB)*np.sqrt(xye[2])
1590	Plot.plot(X[Ibeg:Ifin],DS[Ibeg:Ifin],colors[(N+3)%6],picker=False)
1591	Plot.axhline(0.,color=wx.BLACK)
1592	Plot.set_ylim(bottom=np.min(DS[Ibeg:Ifin])1.2,top=np.max(DS[Ibeg:Ifin])1.2)
1593	else:
1594	Plot.set_yscale("log",nonposy='mask')
1595	if G2frame.ErrorBars:
1596	if G2frame.sqPlot:
1597	Plot.errorbar(X,YB,yerr=X*4Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
1598	ecolor=colors[N%6],picker=3.,clip_on=False)
1599	else:
1600	Plot.errorbar(X,YB,yerr=Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
1601	ecolor=colors[N%6],picker=3.,clip_on=False)
1602	else:
1603	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1604	Plot.plot(X,W,colors[(N+2)%6],picker=False) #const. background
1605	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1606	elif G2frame.Weight and 'PWDR' in plottype:
1607	DY = xye[1]*np.sqrt(xye[2])
1608	Ymax = max(DY)
1609	DZ = xye[3]*np.sqrt(xye[2])
1610	DS = xye[5]np.sqrt(xye[2])-YmaxPattern[0]['delOffset']
1611	ObsLine = Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False) #Io/sig(Io)
1612	Plot.plot(X,DZ,colors[(N+1)%6],picker=False) #Ic/sig(Io)
1613	DifLine = Plot.plot(X,DS,colors[(N+3)%6],picker=1.) #(Io-Ic)/sig(Io)
1614	Plot.axhline(0.,color=wx.BLACK)
1615	else:
1616	if G2frame.SubBack:
1617	if 'PWDR' in plottype:
1618	Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=False,clip_on=False) #Io-Ib
1619	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False) #Ic-Ib
1620	else:
1621	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1622	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1623	else:
1624	if 'PWDR' in plottype:
1625	ObsLine = Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False) #Io
1626	Plot.plot(X,Z,colors[(N+1)%6],picker=False) #Ic
1627	else:
1628	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
1629	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
1630	if 'PWDR' in plottype:
1631	Plot.plot(X,W,colors[(N+2)%6],picker=False) #Ib
1632	DifLine = Plot.plot(X,D,colors[(N+3)%6],picker=1.) #Io-Ic
1633	Plot.axhline(0.,color=wx.BLACK)
1634	Page.canvas.SetToolTipString('')
1635	if PickId:
1636	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
1637	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
1638	Page.canvas.SetToolTipString(tip)
1639	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
1640	for item in data['peaks']:
1641	if G2frame.plotStyle['qPlot']:
1642	Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
1643	elif G2frame.plotStyle['dPlot']:
1644	Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
1645	else:
1646	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
1647	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
1648	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
1649	Page.canvas.SetToolTipString(tip)
1650	data = G2frame.LimitsTable.GetData()
1651
1652	else: #not picked
1653	if G2frame.logPlot:
1654	if 'PWDR' in plottype:
1655	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1656	elif 'SASD' in plottype:
1657	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
1658	else:
1659	if 'PWDR' in plottype:
1660	Plot.plot(X,Y,colors[N%6],picker=False)
1661	elif 'SASD' in plottype:
1662	Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask')
1663	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1664
1665	if G2frame.logPlot and 'PWDR' in plottype:
1666	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
1667	if PickId and not G2frame.Contour:
1668	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
1669	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
1670	peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))
1671	if not len(peaks): return # are there any peaks?
1672	for peak in peaks[0]:
1673	if peak[2]:
1674	if G2frame.plotStyle['qPlot']:
1675	Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b')
1676	if G2frame.plotStyle['dPlot']:
1677	Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b')
1678	else:
1679	Plot.axvline(peak[0],color='b')
1680	for hkl in G2frame.HKL:
1681	clr = 'r'
1682	if len(hkl) > 6 and hkl[3]:
1683	clr = 'g'
1684	if G2frame.plotStyle['qPlot']:
1685	Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5))
1686	if G2frame.plotStyle['dPlot']:
1687	Plot.axvline(G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5))
1688	else:
1689	Plot.axvline(hkl[-2],color=clr,dashes=(5,5))
1690	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
1691	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
1692	refColors=['b','r','c','g','m','k']
1693	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
1694	for pId,phase in enumerate(Phases):
1695	try: #patch for old style reflection lists
1696	peaks = Phases[phase]['RefList']
1697	except TypeError:
1698	peaks = Phases[phase]
1699	if not len(peaks):
1700	continue
1701	if Phases[phase].get('Super',False):
1702	peak = np.array([[peak[5],peak[6]] for peak in peaks])
1703	else:
1704	peak = np.array([[peak[4],peak[5]] for peak in peaks])
1705	pos = Pattern[0]['refOffset']-pIdYmaxPattern[0]['refDelt']*np.ones_like(peak)
1706	if G2frame.plotStyle['qPlot']:
1707	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1708	elif G2frame.plotStyle['dPlot']:
1709	Plot.plot(peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1710	else:
1711	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
1712	if len(Phases):
1713	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
1714	if handles:
1715	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
1716
1717	if G2frame.Contour:
1718	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1719	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1720	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1721	Page.figure.colorbar(Img)
1722	else:
1723	G2frame.Lines = Lines
1724	if not newPlot:
1725	Page.toolbar.push_current()
1726	Plot.set_xlim(xylim[0])
1727	Plot.set_ylim(xylim[1])
1728	# xylim = []
1729	Page.toolbar.push_current()
1730	Page.toolbar.draw()
1731	else:
1732	Page.canvas.draw()
1733	olderr = np.seterr(invalid='ignore') #ugh - this removes a matplotlib error for mouse clicks in log plots
1734	# and sqrt(-ve) in np.where usage
1735	# G2frame.Pwdr = True
1736
1737	################################################################################
1738	##### PlotDeltSig
1739	################################################################################
1740
1741	def PlotDeltSig(G2frame,kind):
1742	'needs a doc string'
1743	try:
1744	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1745	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1746	Page.figure.clf()
1747	Plot = Page.figure.gca() #get a fresh plot after clf()
1748	except ValueError:
1749	newPlot = True
1750	G2frame.Cmax = 1.0
1751	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
1752	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
1753	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1754	Page.Choice = None
1755	PatternId = G2frame.PatternId
1756	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
1757	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
1758	wtFactor = Pattern[0]['wtFactor']
1759	if kind == 'PWDR':
1760	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
1761	xye = np.array(Pattern[1])
1762	xmin = np.searchsorted(xye[0],limits[0])
1763	xmax = np.searchsorted(xye[0],limits[1])
1764	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
1765	elif kind == 'HKLF':
1766	refl = Pattern[1]
1767	DS = []
1768	for ref in refl:
1769	if ref[6] > 0.:
1770	DS.append((ref[5]-ref[7])/ref[6])
1771	Page.SetFocus()
1772	G2frame.G2plotNB.status.DestroyChildren()
1773	DS.sort()
1774	EDS = np.zeros_like(DS)
1775	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
1776	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
1777	T = np.sqrt(np.log(1.0/DX**2))
1778	top = 2.515517+0.802853T+0.010328T**2
1779	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
1780	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
1781	low1 = np.searchsorted(EDS,-1.)
1782	hi1 = np.searchsorted(EDS,1.)
1783	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
1784	frac = 100.*(hi1-low1)/len(DS)
1785	G2frame.G2plotNB.status.SetStatusText( \
1786	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
1787	Plot.set_title('Normal probability for '+Pattern[-1])
1788	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
1789	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
1790	Plot.plot(EDS,DS,'r+',label='result')
1791	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
1792	Plot.legend(loc='upper left')
1793	np.seterr(invalid='warn')
1794	Page.canvas.draw()
1795
1796	################################################################################
1797	##### PlotISFG
1798	################################################################################
1799
1800	def PlotISFG(G2frame,newPlot=False,type=''):
1801	''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
1802	or multiple plots with waterfall and contour plots as options
1803	'''
1804	if not type:
1805	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
1806	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
1807	return
1808	superMinusOne = unichr(0xaf)+unichr(0xb9)
1809
1810	def OnPlotKeyPress(event):
1811	newPlot = False
1812	if event.key == 'u':
1813	if G2frame.Contour:
1814	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
1815	elif Pattern[0]['Offset'][0] < 100.:
1816	Pattern[0]['Offset'][0] += 1.
1817	elif event.key == 'd':
1818	if G2frame.Contour:
1819	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
1820	elif Pattern[0]['Offset'][0] > 0.:
1821	Pattern[0]['Offset'][0] -= 1.
1822	elif event.key == 'l':
1823	Pattern[0]['Offset'][1] -= 1.
1824	elif event.key == 'r':
1825	Pattern[0]['Offset'][1] += 1.
1826	elif event.key == 'o':
1827	Pattern[0]['Offset'] = [0,0]
1828	elif event.key == 'c':
1829	newPlot = True
1830	G2frame.Contour = not G2frame.Contour
1831	if not G2frame.Contour:
1832	G2frame.SinglePlot = False
1833	Pattern[0]['Offset'] = [0.,0.]
1834	elif event.key == 's':
1835	if G2frame.Contour:
1836	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
1837	choice.sort()
1838	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
1839	if dlg.ShowModal() == wx.ID_OK:
1840	sel = dlg.GetSelection()
1841	G2frame.ContourColor = choice[sel]
1842	else:
1843	G2frame.ContourColor = 'Paired'
1844	dlg.Destroy()
1845	else:
1846	G2frame.SinglePlot = not G2frame.SinglePlot
1847	elif event.key == 'i': #for smoothing contour plot
1848	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
1849	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
1850	'mitchell','sinc','lanczos']
1851	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
1852	if dlg.ShowModal() == wx.ID_OK:
1853	sel = dlg.GetSelection()
1854	G2frame.Interpolate = choice[sel]
1855	else:
1856	G2frame.Interpolate = 'nearest'
1857	dlg.Destroy()
1858	elif event.key == 't' and not G2frame.Contour:
1859	G2frame.Legend = not G2frame.Legend
1860	PlotISFG(G2frame,newPlot=newPlot,type=type)
1861
1862	def OnKeyBox(event):
1863	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
1864	event.key = cb.GetValue()[0]
1865	cb.SetValue(' key press')
1866	wx.CallAfter(OnPlotKeyPress,event)
1867	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
1868
1869	def OnMotion(event):
1870	xpos = event.xdata
1871	if xpos: #avoid out of frame mouse position
1872	ypos = event.ydata
1873	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1874	try:
1875	if G2frame.Contour:
1876	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
1877	else:
1878	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
1879	except TypeError:
1880	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
1881
1882	xylim = []
1883	try:
1884	plotNum = G2frame.G2plotNB.plotList.index(type)
1885	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1886	if not newPlot:
1887	Plot = Page.figure.gca() #get previous plot & get limits
1888	xylim = Plot.get_xlim(),Plot.get_ylim()
1889	Page.figure.clf()
1890	Plot = Page.figure.gca()
1891	except ValueError:
1892	newPlot = True
1893	G2frame.Cmax = 1.0
1894	Plot = G2frame.G2plotNB.addMpl(type).gca()
1895	plotNum = G2frame.G2plotNB.plotList.index(type)
1896	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
1897	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
1898	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1899
1900	Page.SetFocus()
1901	G2frame.G2plotNB.status.DestroyChildren()
1902	if G2frame.Contour:
1903	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
1904	'i: interpolation method','s: color scheme','c: contour off')
1905	else:
1906	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
1907	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
1908	Page.keyPress = OnPlotKeyPress
1909	PatternId = G2frame.PatternId
1910	PickId = G2frame.PickId
1911	Plot.set_title(type)
1912	if type == 'G(R)':
1913	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
1914	else:
1915	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
1916	Plot.set_ylabel(r''+type,fontsize=14)
1917	colors=['b','g','r','c','m','k']
1918	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
1919	Pattern = []
1920	if G2frame.SinglePlot:
1921	name = G2frame.PatternTree.GetItemText(PatternId)
1922	name = type+name[4:]
1923	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
1924	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1925	if Pattern:
1926	Pattern.append(name)
1927	PlotList = [Pattern,]
1928	else:
1929	PlotList = []
1930	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1931	while item:
1932	if 'PDF' in G2frame.PatternTree.GetItemText(item):
1933	name = type+G2frame.PatternTree.GetItemText(item)[4:]
1934	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
1935	Pattern = G2frame.PatternTree.GetItemPyData(Id)
1936	if Pattern:
1937	Pattern.append(name)
1938	PlotList.append(Pattern)
1939	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1940	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
1941	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
1942	Xb = [0.,10.]
1943	Yb = [0.,-40.np.pinumbDen]
1944	Ymax = 1.0
1945	lenX = 0
1946	for Pattern in PlotList:
1947	try:
1948	xye = Pattern[1]
1949	except IndexError:
1950	return
1951	Ymax = max(Ymax,max(xye[1]))
1952	offset = Pattern[0]['Offset'][0]*Ymax/100.0
1953	if G2frame.Contour:
1954	ContourZ = []
1955	ContourY = []
1956	Nseq = 0
1957	for N,Pattern in enumerate(PlotList):
1958	xye = Pattern[1]
1959	if PickId:
1960	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
1961	X = xye[0]
1962	if not lenX:
1963	lenX = len(X)
1964	Y = xye[1]+offset*N
1965	if G2frame.Contour:
1966	if lenX == len(X):
1967	ContourY.append(N)
1968	ContourZ.append(Y)
1969	ContourX = X
1970	Nseq += 1
1971	Plot.set_ylabel('Data sequence',fontsize=12)
1972	else:
1973	X = xye[0]+Pattern[0]['Offset'][1].005N
1974	if ifpicked:
1975	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
1976	Page.canvas.SetToolTipString('')
1977	else:
1978	if G2frame.Legend:
1979	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
1980	else:
1981	Plot.plot(X,Y,colors[N%6],picker=False)
1982	if type == 'G(R)':
1983	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
1984	elif type == 'F(Q)':
1985	Plot.axhline(0.,color=wx.BLACK)
1986	elif type == 'S(Q)':
1987	Plot.axhline(1.,color=wx.BLACK)
1988	if G2frame.Contour:
1989	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
1990	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
1991	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
1992	Page.figure.colorbar(Img)
1993	elif G2frame.Legend:
1994	Plot.legend(loc='best')
1995	if not newPlot:
1996	Page.toolbar.push_current()
1997	Plot.set_xlim(xylim[0])
1998	Plot.set_ylim(xylim[1])
1999	xylim = []
2000	Page.toolbar.push_current()
2001	Page.toolbar.draw()
2002	else:
2003	Page.canvas.draw()
2004
2005	################################################################################
2006	##### PlotCalib
2007	################################################################################
2008
2009	def PlotCalib(G2frame,Inst,XY,Sigs,newPlot=False):
2010	'''plot of CW or TOF peak calibration
2011	'''
2012	def OnMotion(event):
2013	xpos = event.xdata
2014	if xpos: #avoid out of frame mouse position
2015	ypos = event.ydata
2016	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2017	try:
2018	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3g'%(xpos,Title,ypos),1)
2019	except TypeError:
2020	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
2021	found = []
2022	wid = 1
2023	view = Page.toolbar._views.forward()
2024	if view:
2025	view = view[0][:2]
2026	wid = view[1]-view[0]
2027	found = XY[np.where(np.fabs(XY.T[0]-xpos) < 0.005*wid)]
2028	if len(found):
2029	pos = found[0][1]
2030	if 'C' in Inst['Type'][0]:
2031	Page.canvas.SetToolTipString('position=%.4f'%(pos))
2032	else:
2033	Page.canvas.SetToolTipString('position=%.2f'%(pos))
2034	else:
2035	Page.canvas.SetToolTipString('')
2036
2037	Title = 'Position calibration'
2038	try:
2039	plotNum = G2frame.G2plotNB.plotList.index(Title)
2040	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2041	if not newPlot:
2042	Plot = Page.figure.gca()
2043	xylim = Plot.get_xlim(),Plot.get_ylim()
2044	Page.figure.clf()
2045	Plot = Page.figure.gca()
2046	except ValueError:
2047	newPlot = True
2048	Plot = G2frame.G2plotNB.addMpl(Title).gca()
2049	plotNum = G2frame.G2plotNB.plotList.index(Title)
2050	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2051	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2052
2053	Page.Choice = None
2054	Page.SetFocus()
2055	G2frame.G2plotNB.status.DestroyChildren()
2056	Plot.set_title(Title)
2057	Plot.set_xlabel(r'd-spacing',fontsize=14)
2058	if 'C' in Inst['Type'][0]:
2059	Plot.set_ylabel(r'$\mathsf{\Delta(2\theta)}$',fontsize=14)
2060	else:
2061	Plot.set_ylabel(r'$\mathsf{\Delta}T/T$',fontsize=14)
2062	for ixy,xyw in enumerate(XY):
2063	if len(xyw) > 2:
2064	X,Y,W = xyw
2065	else:
2066	X,Y = xyw
2067	W = 0.
2068	Yc = G2lat.Dsp2pos(Inst,X)
2069	if 'C' in Inst['Type'][0]:
2070	Y = Y-Yc
2071	E = Sigs[ixy]
2072	bin = W/2.
2073	else:
2074	Y = (Y-Yc)/Yc
2075	E = Sigs[ixy]/Yc
2076	bin = W/(2.*Yc)
2077	if E:
2078	Plot.errorbar(X,Y,ecolor='k',yerr=E)
2079	if ixy:
2080	Plot.plot(X,Y,'kx',picker=3)
2081	else:
2082	Plot.plot(X,Y,'kx',label='peak')
2083	if W:
2084	if ixy:
2085	Plot.plot(X,bin,'b+')
2086	else:
2087	Plot.plot(X,bin,'b+',label='bin width')
2088	Plot.plot(X,-bin,'b+')
2089	Plot.axhline(0.,color='r',linestyle='--')
2090	Plot.legend(loc='best')
2091	if not newPlot:
2092	Page.toolbar.push_current()
2093	Plot.set_xlim(xylim[0])
2094	Plot.set_ylim(xylim[1])
2095	# xylim = []
2096	Page.toolbar.push_current()
2097	Page.toolbar.draw()
2098	else:
2099	Page.canvas.draw()
2100
2101	################################################################################
2102	##### PlotXY
2103	################################################################################
2104
2105	def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,Title=''):
2106	'''simple plot of xy data, used for diagnostic purposes
2107	'''
2108	def OnMotion(event):
2109	xpos = event.xdata
2110	if xpos: #avoid out of frame mouse position
2111	ypos = event.ydata
2112	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2113	try:
2114	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,Title,ypos),1)
2115	except TypeError:
2116	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
2117
2118	try:
2119	plotNum = G2frame.G2plotNB.plotList.index(Title)
2120	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2121	if not newPlot:
2122	Plot = Page.figure.gca()
2123	xylim = Plot.get_xlim(),Plot.get_ylim()
2124	Page.figure.clf()
2125	Plot = Page.figure.gca()
2126	except ValueError:
2127	newPlot = True
2128	Plot = G2frame.G2plotNB.addMpl(Title).gca()
2129	plotNum = G2frame.G2plotNB.plotList.index(Title)
2130	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2131	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2132
2133	Page.Choice = None
2134	Page.SetFocus()
2135	G2frame.G2plotNB.status.DestroyChildren()
2136	Plot.set_title(Title)
2137	if labelX:
2138	Plot.set_xlabel(r''+labelX,fontsize=14)
2139	else:
2140	Plot.set_xlabel(r'X',fontsize=14)
2141	if labelY:
2142	Plot.set_ylabel(r''+labelY,fontsize=14)
2143	else:
2144	Plot.set_ylabel(r'Y',fontsize=14)
2145	colors=['b','g','r','c','m','k']
2146	for ixy,xy in enumerate(XY):
2147	X,Y = xy
2148	Plot.plot(X,Y,colors[ixy%6]+'+',picker=False)
2149	if len(XY2):
2150	for ixy,xy in enumerate(XY2):
2151	X,Y = xy
2152	Plot.plot(X,Y,colors[ixy%6],picker=False)
2153	if not newPlot:
2154	Page.toolbar.push_current()
2155	Plot.set_xlim(xylim[0])
2156	Plot.set_ylim(xylim[1])
2157	xylim = []
2158	Page.toolbar.push_current()
2159	Page.toolbar.draw()
2160	else:
2161	Page.canvas.draw()
2162
2163	################################################################################
2164	##### PlotStrain
2165	################################################################################
2166
2167	def PlotStrain(G2frame,data,newPlot=False):
2168	'''plot of strain data, used for diagnostic purposes
2169	'''
2170	def OnMotion(event):
2171	xpos = event.xdata
2172	if xpos: #avoid out of frame mouse position
2173	ypos = event.ydata
2174	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2175	try:
2176	G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1)
2177	except TypeError:
2178	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
2179
2180	try:
2181	plotNum = G2frame.G2plotNB.plotList.index('Strain')
2182	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2183	if not newPlot:
2184	Plot = Page.figure.gca()
2185	xylim = Plot.get_xlim(),Plot.get_ylim()
2186	Page.figure.clf()
2187	Plot = Page.figure.gca()
2188	except ValueError:
2189	newPlot = True
2190	Plot = G2frame.G2plotNB.addMpl('Strain').gca()
2191	plotNum = G2frame.G2plotNB.plotList.index('Strain')
2192	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2193	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2194
2195	Page.Choice = None
2196	Page.SetFocus()
2197	G2frame.G2plotNB.status.DestroyChildren()
2198	Plot.set_title('Strain')
2199	Plot.set_ylabel(r'd-spacing',fontsize=14)
2200	Plot.set_xlabel(r'Azimuth',fontsize=14)
2201	colors=['b','g','r','c','m','k']
2202	for N,item in enumerate(data['d-zero']):
2203	Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y
2204	Plot.plot(X,Y,colors[N%6]+'+',picker=False)
2205	Y,X = np.array(item['ImtaCalc'])
2206	Plot.plot(X,Y,colors[N%6],picker=False)
2207	if not newPlot:
2208	Page.toolbar.push_current()
2209	Plot.set_xlim(xylim[0])
2210	Plot.set_ylim(xylim[1])
2211	xylim = []
2212	Page.toolbar.push_current()
2213	Page.toolbar.draw()
2214	else:
2215	Page.canvas.draw()
2216
2217	################################################################################
2218	##### PlotSASDSizeDist
2219	################################################################################
2220
2221	def PlotSASDSizeDist(G2frame):
2222
2223	def OnPageChanged(event):
2224	PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
2225	if 'Powder' in PlotText:
2226	PlotPatterns(G2frame,plotType='SASD',newPlot=True)
2227	elif 'Size' in PlotText:
2228	PlotSASDSizeDist(G2frame)
2229
2230	def OnMotion(event):
2231	xpos = event.xdata
2232	if xpos: #avoid out of frame mouse position
2233	ypos = event.ydata
2234	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2235	try:
2236	G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1)
2237	except TypeError:
2238	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
2239
2240	try:
2241	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
2242	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2243	Page.figure.clf()
2244	Plot = Page.figure.gca() #get a fresh plot after clf()
2245	except ValueError:
2246	newPlot = True
2247	Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca()
2248	G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged)
2249	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
2250	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2251	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2252	Page.Choice = None
2253	Page.SetFocus()
2254	PatternId = G2frame.PatternId
2255	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models'))
2256	Bins,Dbins,BinMag = data['Size']['Distribution']
2257	Plot.set_title('Size Distribution')
2258	Plot.set_xlabel(r'$D, \AA$',fontsize=14)
2259	Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
2260	if data['Size']['logBins']:
2261	Plot.set_xscale("log",nonposy='mask')
2262	Plot.set_xlim([np.min(2.Bins)/2.,np.max(2.Bins)*2.])
2263	Plot.bar(2.Bins-Dbins,BinMag,2.Dbins,facecolor='white') #plot diameters
2264	if 'Size Calc' in data:
2265	Rbins,Dist = data['Size Calc']
2266	for i in range(len(Rbins)):
2267	if len(Rbins[i]):
2268	Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters
2269	Page.canvas.draw()
2270
2271	################################################################################
2272	##### PlotPowderLines
2273	################################################################################
2274
2275	def PlotPowderLines(G2frame):
2276	''' plotting of powder lines (i.e. no powder pattern) as sticks
2277	'''
2278	global HKL
2279
2280	def OnMotion(event):
2281	xpos = event.xdata
2282	if xpos: #avoid out of frame mouse position
2283	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2284	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
2285	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
2286	found = []
2287	if len(HKL):
2288	view = Page.toolbar._views.forward()[0][:2]
2289	wid = view[1]-view[0]
2290	found = HKL[np.where(np.fabs(HKL.T[-1]-xpos) < 0.002*wid)]
2291	if len(found):
2292	h,k,l = found[0][:3]
2293	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
2294	else:
2295	Page.canvas.SetToolTipString('')
2296
2297	try:
2298	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
2299	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2300	Page.figure.clf()
2301	Plot = Page.figure.gca()
2302	except ValueError:
2303	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
2304	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
2305	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2306	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2307
2308	Page.Choice = None
2309	Page.SetFocus()
2310	Plot.set_title('Powder Pattern Lines')
2311	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
2312	PickId = G2frame.PickId
2313	PatternId = G2frame.PatternId
2314	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))[0]
2315	for peak in peaks:
2316	Plot.axvline(peak[0],color='b')
2317	HKL = np.array(G2frame.HKL)
2318	for hkl in G2frame.HKL:
2319	Plot.axvline(hkl[-1],color='r',dashes=(5,5))
2320	xmin = peaks[0][0]
2321	xmax = peaks[-1][0]
2322	delt = xmax-xmin
2323	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
2324	Plot.set_xlim(xlim)
2325	Page.canvas.draw()
2326	Page.toolbar.push_current()
2327
2328	################################################################################
2329	##### PlotPeakWidths
2330	################################################################################
2331
2332	def PlotPeakWidths(G2frame):
2333	''' Plotting of instrument broadening terms as function of 2-theta
2334	Seen when "Instrument Parameters" chosen from powder pattern data tree
2335	'''
2336	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
2337	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
2338	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.)
2339	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
2340	PatternId = G2frame.PatternId
2341	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
2342	if limitID:
2343	limits = G2frame.PatternTree.GetItemPyData(limitID)[:2]
2344	else:
2345	return
2346	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
2347	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
2348	if 'C' in Parms['Type'][0]:
2349	lam = G2mth.getWave(Parms)
2350	else:
2351	difC = Parms['difC'][0]
2352	try: # PATCH: deal with older peak lists, before changed to dict to implement TOF
2353	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))['peaks']
2354	except TypeError:
2355	print "Your peak list needs reformatting...",
2356	item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
2357	G2frame.PatternTree.SelectItem(item)
2358	item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters')
2359	G2frame.PatternTree.SelectItem(item)
2360	print "done"
2361	return
2362	try:
2363	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
2364	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2365	Page.figure.clf()
2366	Plot = Page.figure.gca()
2367	except ValueError:
2368	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
2369	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
2370	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2371	Page.Choice = None
2372	Page.SetFocus()
2373
2374	Page.canvas.SetToolTipString('')
2375	colors=['b','g','r','c','m','k']
2376	X = []
2377	Y = []
2378	Z = []
2379	W = []
2380	if 'C' in Parms['Type'][0]:
2381	Plot.set_title('Instrument and sample peak widths')
2382	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
2383	Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14)
2384	try:
2385	Xmin,Xmax = limits[1]
2386	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
2387	Q = 4.np.pinpsind(X/2.)/lam
2388	Z = np.ones_like(X)
2389	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
2390	s = 1.17741np.sqrt(data[4])np.pi/18000.
2391	g = data[6]*np.pi/18000.
2392	G = G2pwd.getgamFW(g,s)
2393	Y = s/nptand(X/2.)
2394	Z = g/nptand(X/2.)
2395	W = G/nptand(X/2.)
2396	Plot.plot(Q,Y,color='r',label='Gaussian')
2397	Plot.plot(Q,Z,color='g',label='Lorentzian')
2398	Plot.plot(Q,W,color='b',label='G+L')
2399
2400	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
2401	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
2402	gf = fit[6]*np.pi/18000.
2403	Gf = G2pwd.getgamFW(gf,sf)
2404	Yf = sf/nptand(X/2.)
2405	Zf = gf/nptand(X/2.)
2406	Wf = Gf/nptand(X/2.)
2407	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
2408	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
2409	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
2410
2411	X = []
2412	Y = []
2413	Z = []
2414	W = []
2415	V = []
2416	for peak in peaks:
2417	X.append(4.0math.pisind(peak[0]/2.0)/lam)
2418	try:
2419	s = 1.17741math.sqrt(peak[4])math.pi/18000.
2420	except ValueError:
2421	s = 0.01
2422	g = peak[6]*math.pi/18000.
2423	G = G2pwd.getgamFW(g,s)
2424	Y.append(s/tand(peak[0]/2.))
2425	Z.append(g/tand(peak[0]/2.))
2426	W.append(G/tand(peak[0]/2.))
2427	if len(peaks):
2428	Plot.plot(X,Y,'+',color='r',label='G peak')
2429	Plot.plot(X,Z,'+',color='g',label='L peak')
2430	Plot.plot(X,W,'+',color='b',label='G+L peak')
2431	Plot.legend(loc='best')
2432	Page.canvas.draw()
2433	except ValueError:
2434	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
2435	'%.3f'%(2*theta)
2436	G2frame.G2plotNB.Delete('Peak Widths')
2437	else: #'T'OF
2438	Plot.set_title('Instrument and sample peak coefficients')
2439	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
2440	Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14)
2441	Xmin,Xmax = limits[1]
2442	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
2443	Z = np.ones_like(T)
2444	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
2445	ds = T/difC
2446	Q = 2.*np.pi/ds
2447	A = data[4]
2448	B = data[6]
2449	S = 1.17741*np.sqrt(data[8])/T
2450	G = data[10]/T
2451	Plot.plot(Q,A,color='r',label='Alpha')
2452	Plot.plot(Q,B,color='g',label='Beta')
2453	Plot.plot(Q,S,color='b',label='Gaussian')
2454	Plot.plot(Q,G,color='m',label='Lorentzian')
2455
2456	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
2457	ds = T/difC
2458	Q = 2.*np.pi/ds
2459	Af = fit[4]
2460	Bf = fit[6]
2461	Sf = 1.17741*np.sqrt(fit[8])/T
2462	Gf = fit[10]/T
2463	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
2464	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
2465	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
2466	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
2467
2468	T = []
2469	A = []
2470	B = []
2471	S = []
2472	G = []
2473	W = []
2474	Q = []
2475	V = []
2476	for peak in peaks:
2477	T.append(peak[0])
2478	A.append(peak[4])
2479	B.append(peak[6])
2480	Q.append(2.np.pidifC/peak[0])
2481	S.append(1.17741*np.sqrt(peak[8])/peak[0])
2482	G.append(peak[10]/peak[0])
2483
2484
2485	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
2486	Plot.plot(Q,B,'+',color='g',label='Beta peak')
2487	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
2488	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
2489	Plot.legend(loc='best')
2490	Page.canvas.draw()
2491
2492
2493	################################################################################
2494	##### PlotSizeStrainPO
2495	################################################################################
2496
2497	def PlotSizeStrainPO(G2frame,data,hist='',Start=False):
2498	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
2499	'''
2500
2501	PatternId = G2frame.PatternId
2502	generalData = data['General']
2503	SGData = generalData['SGData']
2504	SGLaue = SGData['SGLaue']
2505	if Start: #initialize the spherical harmonics qlmn arrays
2506	ptx.pyqlmninit()
2507	Start = False
2508	# MuStrKeys = G2spc.MustrainNames(SGData)
2509	cell = generalData['Cell'][1:]
2510	A,B = G2lat.cell2AB(cell[:6])
2511	Vol = cell[6]
2512	useList = data['Histograms']
2513	phase = generalData['Name']
2514	plotType = generalData['Data plot type']
2515	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
2516	for ptype in plotDict:
2517	G2frame.G2plotNB.Delete(ptype)
2518	if plotType in ['None']:
2519	return
2520	if hist == '':
2521	hist = useList.keys()[0]
2522	numPlots = len(useList)
2523
2524	if plotType in ['Mustrain','Size']:
2525	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
2526	else:
2527	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
2528	plotNum = G2frame.G2plotNB.plotList.index(plotType)
2529	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2530	Page.Choice = None
2531	Page.SetFocus()
2532	G2frame.G2plotNB.status.SetStatusText('',1)
2533	if not Page.IsShown():
2534	Page.Show()
2535
2536	PHI = np.linspace(0.,360.,30,True)
2537	PSI = np.linspace(0.,180.,30,True)
2538	X = np.outer(npsind(PHI),npsind(PSI))
2539	Y = np.outer(npcosd(PHI),npsind(PSI))
2540	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
2541	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
2542	coeff = useList[hist][plotDict[plotType]]
2543	except KeyError:
2544	return
2545	if plotType in ['Mustrain','Size']:
2546	if coeff[0] == 'isotropic':
2547	X *= coeff[1][0]
2548	Y *= coeff[1][0]
2549	Z *= coeff[1][0]
2550	elif coeff[0] == 'uniaxial':
2551
2552	def uniaxCalc(xyz,iso,aniso,axes):
2553	Z = np.array(axes)
2554	cp = abs(np.dot(xyz,Z))
2555	sp = np.sqrt(1.-cp**2)
2556	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
2557	return R*xyz
2558
2559	iso,aniso = coeff[1][:2]
2560	axes = np.inner(A,np.array(coeff[3]))
2561	axes /= nl.norm(axes)
2562	Shkl = np.array(coeff[1])
2563	XYZ = np.dstack((X,Y,Z))
2564	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
2565	X,Y,Z = np.dsplit(XYZ,3)
2566	X = X[:,:,0]
2567	Y = Y[:,:,0]
2568	Z = Z[:,:,0]
2569
2570	elif coeff[0] == 'ellipsoidal':
2571
2572	def ellipseCalc(xyz,E,R):
2573	XYZ = xyz*E.T
2574	return np.inner(XYZ.T,R)
2575
2576	S6 = coeff[4]
2577	Sij = G2lat.U6toUij(S6)
2578	E,R = nl.eigh(Sij)
2579	XYZ = np.dstack((X,Y,Z))
2580	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
2581	X,Y,Z = np.dsplit(XYZ,3)
2582	X = X[:,:,0]
2583	Y = Y[:,:,0]
2584	Z = Z[:,:,0]
2585
2586	elif coeff[0] == 'generalized':
2587
2588	def genMustrain(xyz,SGData,A,Shkl):
2589	uvw = np.inner(A.T,xyz)
2590	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
2591	Sum = np.sum(np.multiply(Shkl,Strm))
2592	Sum = np.where(Sum > 0.01,Sum,0.01)
2593	Sum = np.sqrt(Sum)
2594	return Sum*xyz
2595
2596	Shkl = np.array(coeff[4])
2597	if np.any(Shkl):
2598	XYZ = np.dstack((X,Y,Z))
2599	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
2600	X,Y,Z = np.dsplit(XYZ,3)
2601	X = X[:,:,0]
2602	Y = Y[:,:,0]
2603	Z = Z[:,:,0]
2604
2605	if np.any(X) and np.any(Y) and np.any(Z):
2606	errFlags = np.seterr(all='ignore')
2607	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
2608	np.seterr(all='ignore')
2609	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
2610	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
2611	Plot.set_xlim3d(XYZlim)
2612	Plot.set_ylim3d(XYZlim)
2613	Plot.set_zlim3d(XYZlim)
2614	Plot.set_aspect('equal')
2615	if plotType == 'Size':
2616	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
2617	Plot.set_xlabel(r'X, $\mu$m')
2618	Plot.set_ylabel(r'Y, $\mu$m')
2619	Plot.set_zlabel(r'Z, $\mu$m')
2620	else:
2621	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
2622	Plot.set_xlabel(r'X, $\mu$strain')
2623	Plot.set_ylabel(r'Y, $\mu$strain')
2624	Plot.set_zlabel(r'Z, $\mu$strain')
2625	else:
2626	h,k,l = generalData['POhkl']
2627	if coeff[0] == 'MD':
2628	print 'March-Dollase preferred orientation plot'
2629
2630	else:
2631	PH = np.array(generalData['POhkl'])
2632	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
2633	SHCoef = {}
2634	for item in coeff[5]:
2635	L,N = eval(item.strip('C'))
2636	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
2637	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
2638	X = np.linspace(0,90.0,26)
2639	Y = G2lat.polfcal(ODFln,'0',X,0.0)
2640	Plot.plot(X,Y,color='k',label=str(PH))
2641	Plot.legend(loc='best')
2642	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase+'\n'+hist)
2643	Plot.set_xlabel(r'$\psi$',fontsize=16)
2644	Plot.set_ylabel('MRD',fontsize=14)
2645	Page.canvas.draw()
2646
2647	################################################################################
2648	##### PlotTexture
2649	################################################################################
2650
2651	def PlotTexture(G2frame,data,Start=False):
2652	'''Pole figure, inverse pole figure, 3D pole distribution and 3D inverse pole distribution
2653	plotting.
2654	dict generalData contains all phase info needed which is in data
2655	'''
2656
2657	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
2658	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
2659	PatternId = G2frame.PatternId
2660	generalData = data['General']
2661	SGData = generalData['SGData']
2662	textureData = generalData['SH Texture']
2663	G2frame.G2plotNB.Delete('Texture')
2664	if not textureData['Order']:
2665	return #no plot!!
2666	SHData = generalData['SH Texture']
2667	SHCoef = SHData['SH Coeff'][1]
2668	cell = generalData['Cell'][1:7]
2669	Amat,Bmat = G2lat.cell2AB(cell)
2670	sq2 = 1.0/math.sqrt(2.0)
2671
2672	def rp2xyz(r,p):
2673	z = npcosd(r)
2674	xy = np.sqrt(1.-z**2)
2675	return xynpsind(p),xynpcosd(p),z
2676
2677	def OnMotion(event):
2678	SHData = data['General']['SH Texture']
2679	if event.xdata and event.ydata: #avoid out of frame errors
2680	xpos = event.xdata
2681	ypos = event.ydata
2682	if 'Inverse' in SHData['PlotType']:
2683	r = xpos2+ypos2
2684	if r <= 1.0:
2685	if 'equal' in G2frame.Projection:
2686	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
2687	else:
2688	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
2689	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
2690	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
2691	y,x,z = list(xyz/np.max(np.abs(xyz)))
2692
2693	G2frame.G2plotNB.status.SetFields(['',
2694	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
2695
2696	elif 'Axial' in SHData['PlotType']:
2697	pass
2698
2699	else: #ordinary pole figure
2700	z = xpos2+ypos2
2701	if z <= 1.0:
2702	z = np.sqrt(z)
2703	if 'equal' in G2frame.Projection:
2704	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
2705	else:
2706	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
2707	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
2708	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
2709
2710	try:
2711	plotNum = G2frame.G2plotNB.plotList.index('Texture')
2712	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2713	Page.figure.clf()
2714	Plot = Page.figure.gca()
2715	if not Page.IsShown():
2716	Page.Show()
2717	except ValueError:
2718	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
2719	plotNum = G2frame.G2plotNB.plotList.index('Texture')
2720	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2721	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2722
2723	Page.Choice = None
2724	Page.SetFocus()
2725	G2frame.G2plotNB.status.SetFields(['',''])
2726	PH = np.array(SHData['PFhkl'])
2727	phi,beta = G2lat.CrsAng(PH,cell,SGData)
2728	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
2729	PX = np.array(SHData['PFxyz'])
2730	gam = atan2d(PX[0],PX[1])
2731	xy = math.sqrt(PX[0]2+PX[1]2)
2732	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
2733	psi = asind(xy/xyz)
2734	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
2735	if 'Axial' in SHData['PlotType']:
2736	X = np.linspace(0,90.0,26)
2737	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
2738	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
2739	Plot.legend(loc='best')
2740	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
2741	Plot.set_xlabel(r'$\psi$',fontsize=16)
2742	Plot.set_ylabel('MRD',fontsize=14)
2743
2744	else:
2745	npts = 201
2746	if 'Inverse' in SHData['PlotType']:
2747	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2748	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2749	if 'equal' in G2frame.Projection:
2750	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2751	else:
2752	R = np.where(R <= 1.,2.*npatand(R),0.0)
2753	Z = np.zeros_like(R)
2754	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
2755	Z = np.reshape(Z,(npts,npts))
2756	CS = Plot.contour(Y,X,Z,aspect='equal')
2757	Plot.clabel(CS,fontsize=9,inline=1)
2758	try:
2759	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2760	except ValueError:
2761	pass
2762	Page.figure.colorbar(Img)
2763	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
2764	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2765
2766	else:
2767	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
2768	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
2769	if 'equal' in G2frame.Projection:
2770	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
2771	else:
2772	R = np.where(R <= 1.,2.*npatand(R),0.0)
2773	Z = np.zeros_like(R)
2774	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
2775	Z = np.reshape(Z,(npts,npts))
2776	try:
2777	CS = Plot.contour(Y,X,Z,aspect='equal')
2778	Plot.clabel(CS,fontsize=9,inline=1)
2779	except ValueError:
2780	pass
2781	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
2782	Page.figure.colorbar(Img)
2783	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
2784	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
2785	Page.canvas.draw()
2786
2787	################################################################################
2788	##### Plot Modulation
2789	################################################################################
2790
2791	def ModulationPlot(G2frame,data,atom,ax,off=0):
2792	global Off,Atom,Ax
2793	Off = off
2794	Atom = atom
2795	Ax = ax
2796	def OnMotion(event):
2797	xpos = event.xdata
2798	if xpos: #avoid out of frame mouse position
2799	ypos = event.ydata
2800	Page.canvas.SetCursor(wx.CROSS_CURSOR)
2801	try:
2802	G2frame.G2plotNB.status.SetStatusText('t =%9.3f %s =%9.3f'%(xpos,GkDelta+Ax,ypos),1)
2803	except TypeError:
2804	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
2805
2806	def OnPlotKeyPress(event):
2807	global Off,Atom,Ax
2808	newPlot = False
2809	if event.key == '0':
2810	Off = 0
2811	elif event.key in ['+','=']:
2812	Off += 1
2813	elif event.key == '-':
2814	Off -= 1
2815	elif event.key in ['l','r',] and mapData['Flip']:
2816	roll = 1
2817	if event.key == 'l':
2818	roll = -1
2819	rho = Map['rho']
2820	Map['rho'] = np.roll(rho,roll,axis=3)
2821	wx.CallAfter(ModulationPlot,G2frame,data,Atom,Ax,Off)
2822
2823	try:
2824	plotNum = G2frame.G2plotNB.plotList.index('Modulation')
2825	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2826	Page.figure.clf()
2827	Plot = Page.figure.gca()
2828	if not Page.IsShown():
2829	Page.Show()
2830	except ValueError:
2831	Plot = G2frame.G2plotNB.addMpl('Modulation').gca()
2832	plotNum = G2frame.G2plotNB.plotList.index('Modulation')
2833	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2834	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2835	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2836
2837	Page.SetFocus()
2838	General = data['General']
2839	cx,ct,cs,cia = General['AtomPtrs']
2840	mapData = General['Map']
2841	if mapData['Flip']:
2842	Page.Choice = ['+: shift up','-: shift down','0: reset shift','l: move left','r: move right']
2843	else:
2844	Page.Choice = ['+: shift up','-: shift down','0: reset shift']
2845	Page.keyPress = OnPlotKeyPress
2846	Map = General['4DmapData']
2847	MapType = Map['MapType']
2848	rhoSize = np.array(Map['rho'].shape)
2849	atxyz = np.array(atom[cx:cx+3])
2850	waveType = atom[-1]['SS1']['waveType']
2851	Spos = atom[-1]['SS1']['Spos']
2852	tau = np.linspace(0.,2.,101)
2853	wave = np.zeros((3,101))
2854	if len(Spos):
2855	scof = []
2856	ccof = []
2857	for i,spos in enumerate(Spos):
2858	if waveType in ['Sawtooth','ZigZag'] and not i:
2859	Toff = spos[0][0]
2860	slopes = np.array(spos[0][1:])
2861	if waveType == 'Sawtooth':
2862	wave = G2mth.posSawtooth(tau,Toff,slopes)
2863	elif waveType == 'ZigZag':
2864	wave = G2mth.posZigZag(tau,Toff,slopes)
2865	else:
2866	scof.append(spos[0][:3])
2867	ccof.append(spos[0][3:])
2868	wave += G2mth.posFourier(tau,np.array(scof),np.array(ccof))
2869	if mapData['Flip']:
2870	Title = 'Charge flip'
2871	else:
2872	Title = MapType
2873	Title += ' map for atom '+atom[0]+ \
2874	' at %.4f %.4f %.4f'%(atxyz[0],atxyz[1],atxyz[2])
2875	ix = -np.array(np.rint(rhoSize[:3]*atxyz),dtype='i')
2876	ix += (rhoSize[:3]/2)
2877	ix = ix%rhoSize[:3]
2878	rho = np.roll(np.roll(np.roll(Map['rho'],ix[0],axis=0),ix[1],axis=1),ix[2],axis=2)
2879	ix = rhoSize[:3]/2
2880	ib = 4
2881	if Ax == 'x':
2882	slab = np.sum(np.sum(rho[:,ix[1]-ib:ix[1]+ib,ix[2]-ib:ix[2]+ib,:],axis=2),axis=1)
2883	Plot.plot(tau,wave[0])
2884	elif Ax == 'y':
2885	slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,:,ix[2]-ib:ix[2]+ib,:],axis=2),axis=0)
2886	Plot.plot(tau,wave[1])
2887	elif Ax == 'z':
2888	slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,ix[1]-ib:ix[1]+ib,:,:],axis=1),axis=0)
2889	Plot.plot(tau,wave[2])
2890	Plot.set_title(Title)
2891	Plot.set_xlabel('t')
2892	Plot.set_ylabel(r'$\mathsf{\Delta}$%s'%(Ax))
2893	Slab = np.hstack((slab,slab,slab))
2894	Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Off.005,.5+Off.005))
2895	Page.canvas.draw()
2896
2897	################################################################################
2898	##### PlotCovariance
2899	################################################################################
2900
2901	def PlotCovariance(G2frame,Data):
2902	'needs a doc string'
2903	if not Data:
2904	print 'No covariance matrix available'
2905	return
2906	varyList = Data['varyList']
2907	values = Data['variables']
2908	Xmax = len(varyList)
2909	covMatrix = Data['covMatrix']
2910	sig = np.sqrt(np.diag(covMatrix))
2911	xvar = np.outer(sig,np.ones_like(sig))
2912	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
2913	title = ' for\n'+Data['title']
2914	newAtomDict = Data.get('newAtomDict',{})
2915	G2frame.G2plotNB.Delete('Covariance')
2916
2917
2918	def OnPlotKeyPress(event):
2919	newPlot = False
2920	if event.key == 's':
2921	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
2922	choice.sort()
2923	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
2924	if dlg.ShowModal() == wx.ID_OK:
2925	sel = dlg.GetSelection()
2926	G2frame.VcovColor = choice[sel]
2927	else:
2928	G2frame.VcovColor = 'RdYlGn'
2929	dlg.Destroy()
2930	PlotCovariance(G2frame,Data)
2931
2932	def OnMotion(event):
2933	if event.button:
2934	ytics = imgAx.get_yticks()
2935	ytics = np.where(ytics<len(varyList),ytics,-1)
2936	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
2937	imgAx.set_yticklabels(ylabs)
2938	if event.xdata and event.ydata: #avoid out of frame errors
2939	xpos = int(event.xdata+.5)
2940	ypos = int(event.ydata+.5)
2941	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
2942	if xpos == ypos:
2943	value = values[xpos]
2944	name = varyList[xpos]
2945	if varyList[xpos] in newAtomDict:
2946	name,value = newAtomDict[name]
2947	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
2948	else:
2949	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
2950	Page.canvas.SetToolTipString(msg)
2951	G2frame.G2plotNB.status.SetFields(['',msg])
2952
2953	try:
2954	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2955	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2956	Page.figure.clf()
2957	Plot = Page.figure.gca()
2958	if not Page.IsShown():
2959	Page.Show()
2960	except ValueError:
2961	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
2962	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
2963	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
2964	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
2965	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
2966	Page.Choice = ['s: to change colors']
2967	Page.keyPress = OnPlotKeyPress
2968	Page.SetFocus()
2969	G2frame.G2plotNB.status.SetFields(['',''])
2970	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
2971	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower',
2972	vmin=-1.,vmax=1.)
2973	imgAx = Img.get_axes()
2974	ytics = imgAx.get_yticks()
2975	ylabs = [varyList[int(i)] for i in ytics[:-1]]
2976	imgAx.set_yticklabels(ylabs)
2977	colorBar = Page.figure.colorbar(Img)
2978	Plot.set_title('V-Cov matrix'+title)
2979	Plot.set_xlabel('Variable number')
2980	Plot.set_ylabel('Variable name')
2981	Page.canvas.draw()
2982
2983	################################################################################
2984	##### PlotTorsion
2985	################################################################################
2986
2987	def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]):
2988	'needs a doc string'
2989
2990	global names
2991	names = Names
2992	sum = np.sum(Torsion)
2993	torsion = np.log(2*Torsion+1.)/sum
2994	tMin = np.min(torsion)
2995	tMax = np.max(torsion)
2996	torsion = 3.*(torsion-tMin)/(tMax-tMin)
2997	X = np.linspace(0.,360.,num=45)
2998
2999	def OnPick(event):
3000	ind = event.ind[0]
3001	msg = 'atoms:'+names[ind]
3002	Page.canvas.SetToolTipString(msg)
3003	try:
3004	page = G2frame.dataDisplay.GetSelection()
3005	except:
3006	return
3007	if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints':
3008	torGrid = G2frame.dataDisplay.GetPage(page).Torsions
3009	torGrid.ClearSelection()
3010	for row in range(torGrid.GetNumberRows()):
3011	if names[ind] in torGrid.GetCellValue(row,0):
3012	torGrid.SelectRow(row)
3013	torGrid.ForceRefresh()
3014
3015	def OnMotion(event):
3016	if event.xdata and event.ydata: #avoid out of frame errors
3017	xpos = event.xdata
3018	ypos = event.ydata
3019	msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos)
3020	Page.canvas.SetToolTipString(msg)
3021
3022	try:
3023	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
3024	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3025	Page.figure.clf()
3026	Plot = Page.figure.gca()
3027	if not Page.IsShown():
3028	Page.Show()
3029	except ValueError:
3030	Plot = G2frame.G2plotNB.addMpl('Torsion').gca()
3031	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
3032	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3033	Page.canvas.mpl_connect('pick_event', OnPick)
3034	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3035
3036	Page.SetFocus()
3037	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms'])
3038	Plot.plot(X,torsion,'b+')
3039	if len(Coeff):
3040	X2 = np.linspace(0.,360.,45)
3041	Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2])
3042	Plot.plot(X2,Y2,'r')
3043	if len(Angles):
3044	Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles])
3045	Plot.plot(Angles,Eval,'ro',picker=5)
3046	Plot.set_xlim((0.,360.))
3047	Plot.set_title('Torsion angles for '+TorName+' in '+phaseName)
3048	Plot.set_xlabel('angle',fontsize=16)
3049	Plot.set_ylabel('Energy',fontsize=16)
3050	Page.canvas.draw()
3051
3052	################################################################################
3053	##### PlotRama
3054	################################################################################
3055
3056	def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]):
3057	'needs a doc string'
3058
3059	global names
3060	names = Names
3061	rama = np.log(2*Rama+1.)
3062	ramaMax = np.max(rama)
3063	rama = np.reshape(rama,(45,45))
3064	global Phi,Psi
3065	Phi = []
3066	Psi = []
3067
3068	def OnPlotKeyPress(event):
3069	newPlot = False
3070	if event.key == 's':
3071	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3072	choice.sort()
3073	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
3074	if dlg.ShowModal() == wx.ID_OK:
3075	sel = dlg.GetSelection()
3076	G2frame.RamaColor = choice[sel]
3077	else:
3078	G2frame.RamaColor = 'RdYlGn'
3079	dlg.Destroy()
3080	PlotRama(G2frame,phaseName,Rama)
3081
3082	def OnPick(event):
3083	ind = event.ind[0]
3084	msg = 'atoms:'+names[ind]
3085	Page.canvas.SetToolTipString(msg)
3086	try:
3087	page = G2frame.dataDisplay.GetSelection()
3088	except:
3089	return
3090	if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints':
3091	ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas
3092	ramaGrid.ClearSelection()
3093	for row in range(ramaGrid.GetNumberRows()):
3094	if names[ind] in ramaGrid.GetCellValue(row,0):
3095	ramaGrid.SelectRow(row)
3096	ramaGrid.ForceRefresh()
3097
3098	def OnMotion(event):
3099	if event.xdata and event.ydata: #avoid out of frame errors
3100	xpos = event.xdata
3101	ypos = event.ydata
3102	msg = 'phi/psi: %5.3f %5.3f'%(xpos,ypos)
3103	Page.canvas.SetToolTipString(msg)
3104
3105	try:
3106	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
3107	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3108	Page.figure.clf()
3109	Plot = Page.figure.gca()
3110	if not Page.IsShown():
3111	Page.Show()
3112	except ValueError:
3113	Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca()
3114	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
3115	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3116	Page.canvas.mpl_connect('pick_event', OnPick)
3117	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3118	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
3119
3120	Page.Choice = ['s: to change colors']
3121	Page.keyPress = OnPlotKeyPress
3122	Page.SetFocus()
3123	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms'])
3124	acolor = mpl.cm.get_cmap(G2frame.RamaColor)
3125	if RamaName == 'All' or '-1' in RamaName:
3126	if len(Coeff):
3127	X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45))
3128	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
3129	Plot.contour(X,Y,np.reshape(Z,(45,45)))
3130	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
3131	extent=[-180,180,-180,180],origin='lower')
3132	if len(PhiPsi):
3133	Phi,Psi = PhiPsi.T
3134	Phi = np.where(Phi>180.,Phi-360.,Phi)
3135	Psi = np.where(Psi>180.,Psi-360.,Psi)
3136	Plot.plot(Phi,Psi,'ro',picker=5)
3137	Plot.set_xlim((-180.,180.))
3138	Plot.set_ylim((-180.,180.))
3139	else:
3140	if len(Coeff):
3141	X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45))
3142	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
3143	Plot.contour(X,Y,np.reshape(Z,(45,45)))
3144	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
3145	extent=[0,360,0,360],origin='lower')
3146	if len(PhiPsi):
3147	Phi,Psi = PhiPsi.T
3148	Plot.plot(Phi,Psi,'ro',picker=5)
3149	Plot.set_xlim((0.,360.))
3150	Plot.set_ylim((0.,360.))
3151	Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName)
3152	Plot.set_xlabel(r'$\phi$',fontsize=16)
3153	Plot.set_ylabel(r'$\psi$',fontsize=16)
3154	colorBar = Page.figure.colorbar(Img)
3155	Page.canvas.draw()
3156
3157
3158	################################################################################
3159	##### PlotSeq
3160	################################################################################
3161	def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX,fitnum=None,fitvals=None):
3162	'''Plot a result from a sequential refinement
3163
3164	:param wx.Frame G2frame: The main GSAS-II tree "window"
3165	:param list ColumnList: list of int values corresponding to columns
3166	selected as y values
3167	:param function TableGet: a function that takes a column number
3168	as argument and returns the column label, the values and there ESDs (or None)
3169	:param function SelectX: a function that returns a selected column
3170	number (or None) as the X-axis selection
3171	'''
3172	global Title,xLabel,yLabel
3173	xLabel = yLabel = Title = ''
3174	def OnMotion(event):
3175	if event.xdata and event.ydata: #avoid out of frame errors
3176	xpos = event.xdata
3177	ypos = event.ydata
3178	msg = '%5.3f %.6g'%(xpos,ypos)
3179	Page.canvas.SetToolTipString(msg)
3180
3181	def OnKeyPress(event):
3182	global Title,xLabel,yLabel
3183	if event.key == 's':
3184	G2frame.seqXaxis = G2frame.seqXselect()
3185	Draw()
3186	elif event.key == 't':
3187	dlg = G2gd.MultiStringDialog(G2frame,'Set titles & labels',[' Title ',' x-Label ',' y-Label '],
3188	[Title,xLabel,yLabel])
3189	if dlg.Show():
3190	Title,xLabel,yLabel = dlg.GetValues()
3191	dlg.Destroy()
3192	Draw()
3193
3194	def Draw():
3195	global Title,xLabel,yLabel
3196	Page.SetFocus()
3197	G2frame.G2plotNB.status.SetStatusText('press s to select X axis, t to change titles',1)
3198	Plot.clear()
3199	if G2frame.seqXaxis is not None:
3200	xName,X,Xsig = Page.seqTableGet(G2frame.seqXaxis)
3201	else:
3202	X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1)
3203	xName = 'Data sequence number'
3204	for col in Page.seqYaxisList:
3205	name,Y,sig = Page.seqTableGet(col)
3206	# deal with missing (None) values
3207	Xnew = []
3208	Ynew = []
3209	Ysnew = []
3210	for i in range(len(X)):
3211	if X[i] is None or Y[i] is None: continue
3212	Xnew.append(X[i])
3213	Ynew.append(Y[i])
3214	if sig: Ysnew.append(sig[i])
3215	if Ysnew:
3216	if G2frame.seqReverse and not G2frame.seqXaxis:
3217	Ynew = Ynew[::-1]
3218	Ysnew = Ysnew[::-1]
3219	Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name)
3220	else:
3221	if G2frame.seqReverse and not G2frame.seqXaxis:
3222	Ynew = Ynew[::-1]
3223	Plot.plot(Xnew,Ynew)
3224	Plot.plot(Xnew,Ynew,'o',label=name)
3225	if Page.fitvals: # TODO: deal with fitting of None values
3226	if G2frame.seqReverse and not G2frame.seqXaxis:
3227	Page.fitvals = Page.fitvals[::-1]
3228	Plot.plot(X,Page.fitvals,label='Fit')
3229
3230	Plot.legend(loc='best')
3231	print Title,xLabel,yLabel
3232	if Title:
3233	Plot.set_title(Title)
3234	else:
3235	Plot.set_title('')
3236	if xLabel:
3237	Plot.set_xlabel(xLabel)
3238	else:
3239	Plot.set_xlabel(xName)
3240	if yLabel:
3241	Plot.set_ylabel(yLabel)
3242	else:
3243	Plot.set_ylabel('Parameter values')
3244	Page.canvas.draw()
3245
3246	G2frame.seqXselect = SelectX
3247	try:
3248	G2frame.seqXaxis
3249	except:
3250	G2frame.seqXaxis = None
3251
3252	if fitnum is None:
3253	label = 'Sequential refinement'
3254	else:
3255	label = 'Parametric fit #'+str(fitnum+1)
3256	try:
3257	plotNum = G2frame.G2plotNB.plotList.index(label)
3258	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3259	Page.figure.clf()
3260	Plot = Page.figure.gca()
3261	if not Page.IsShown():
3262	Page.Show()
3263	except ValueError:
3264	Plot = G2frame.G2plotNB.addMpl(label).gca()
3265	plotNum = G2frame.G2plotNB.plotList.index(label)
3266	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3267	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
3268	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3269	Page.Choice = ['s - select x-axis','t - change titles',]
3270	Page.keyPress = OnKeyPress
3271	Page.seqYaxisList = ColumnList
3272	Page.seqTableGet = TableGet
3273	Page.fitvals = fitvals
3274
3275	Draw()
3276	G2frame.G2plotNB.nb.SetSelection(plotNum) # raises plot tab
3277
3278	################################################################################
3279	##### PlotExposedImage & PlotImage
3280	################################################################################
3281
3282	def PlotExposedImage(G2frame,newPlot=False,event=None):
3283	'''General access module for 2D image plotting
3284	'''
3285	plotNo = G2frame.G2plotNB.nb.GetSelection()
3286	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
3287	PlotImage(G2frame,newPlot,event,newImage=True)
3288	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
3289	PlotIntegration(G2frame,newPlot,event)
3290
3291	def OnStartMask(G2frame):
3292	'''Initiate the start of a Frame or Polygon map
3293
3294	:param wx.Frame G2frame: The main GSAS-II tree "window"
3295	:param str eventkey: a single letter ('f' or 'p') that
3296	determines what type of mask is created.
3297	'''
3298	Masks = G2frame.PatternTree.GetItemPyData(
3299	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3300	if G2frame.MaskKey == 'f':
3301	Masks['Frames'] = []
3302	elif G2frame.MaskKey == 'p':
3303	Masks['Polygons'].append([])
3304	elif G2frame.MaskKey == 's':
3305	Masks['Points'].append([])
3306	elif G2frame.MaskKey == 'a':
3307	Masks['Arcs'].append([])
3308	elif G2frame.MaskKey == 'r':
3309	Masks['Rings'].append([])
3310	G2imG.UpdateMasks(G2frame,Masks)
3311	PlotImage(G2frame,newImage=True)
3312
3313	def OnStartNewDzero(G2frame):
3314	'''Initiate the start of adding a new d-zero to a strain data set
3315
3316	:param wx.Frame G2frame: The main GSAS-II tree "window"
3317	:param str eventkey: a single letter ('a') that
3318	triggers the addition of a d-zero.
3319	'''
3320	G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',0)
3321	G2frame.PickId = G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain')
3322	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
3323	return data
3324
3325	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
3326	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
3327	masks, etc.
3328	'''
3329	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
3330	import numpy.ma as ma
3331	Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.))
3332	global Data,Masks,StrSta
3333	colors=['b','g','r','c','m','k']
3334	Data = G2frame.PatternTree.GetItemPyData(
3335	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3336	# patch
3337	if 'invert_x' not in Data:
3338	Data['invert_x'] = False
3339	Data['invert_y'] = True
3340	# end patch
3341	Masks = G2frame.PatternTree.GetItemPyData(
3342	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
3343	try: #may be absent
3344	StrSta = G2frame.PatternTree.GetItemPyData(
3345	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
3346	except TypeError: #is missing
3347	StrSta = {}
3348
3349	def OnImMotion(event):
3350	Page.canvas.SetToolTipString('')
3351	sizexy = Data['size']
3352	FlatBkg = Data.get('Flat Bkg',0.)
3353	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
3354	Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata))
3355	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3356	item = G2frame.itemPicked
3357	pixelSize = Data['pixelSize']
3358	scalex = 1000./pixelSize[0]
3359	scaley = 1000./pixelSize[1]
3360	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
3361	if 'Text' in str(item):
3362	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
3363	else:
3364	xcent,ycent = Data['center']
3365	xpos = event.xdata-xcent
3366	ypos = event.ydata-ycent
3367	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
3368	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
3369	Page.canvas.SetToolTipString('%6d deg'%(azm))
3370	elif 'line1' in str(item) or 'line2' in str(item):
3371	Page.canvas.SetToolTipString('%8.3f deg'%(tth))
3372	else:
3373	xpos = event.xdata
3374	ypos = event.ydata
3375	xpix = xpos*scalex
3376	ypix = ypos*scaley
3377	Int = 0
3378	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
3379	Int = G2frame.ImageZ[ypix][xpix]-int(FlatBkg)
3380	tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
3381	Q = 2.*math.pi/dsp
3382	fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)]
3383	if G2frame.MaskKey in ['p','f']:
3384	fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon'
3385	elif G2frame.StrainKey:
3386	fields[0] = 'd-zero pick active'
3387	G2frame.G2plotNB.status.SetFields(fields)
3388
3389	def OnImPlotKeyPress(event):
3390	try:
3391	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
3392	except TypeError:
3393	return
3394	if PickName == 'Masks':
3395	if event.key in ['l','p','f','s','a','r']:
3396	G2frame.MaskKey = event.key
3397	OnStartMask(G2frame)
3398	PlotImage(G2frame,newPlot=False)
3399
3400	elif PickName == 'Stress/Strain':
3401	if event.key in ['a',]:
3402	G2frame.StrainKey = event.key
3403	StrSta = OnStartNewDzero(G2frame)
3404	PlotImage(G2frame,newPlot=False)
3405
3406	elif PickName == 'Image Controls':
3407	if event.key in ['c',]:
3408	Xpos = event.xdata
3409	if not Xpos: #got point out of frame
3410	return
3411	Ypos = event.ydata
3412	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
3413	'Center change',style=wx.OK\|wx.CANCEL)
3414	try:
3415	if dlg.ShowModal() == wx.ID_OK:
3416	print 'move center to: ',Xpos,Ypos
3417	Data['center'] = [Xpos,Ypos]
3418	G2imG.UpdateImageControls(G2frame,Data,Masks)
3419	PlotImage(G2frame,newPlot=False)
3420	finally:
3421	dlg.Destroy()
3422	return
3423	elif event.key == 'l':
3424	G2frame.logPlot = not G2frame.logPlot
3425	elif event.key in ['x',]:
3426	Data['invert_x'] = not Data['invert_x']
3427	elif event.key in ['y',]:
3428	Data['invert_y'] = not Data['invert_y']
3429	PlotImage(G2frame,newPlot=True)
3430
3431	def OnKeyBox(event):
3432	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
3433	event.key = cb.GetValue()[0]
3434	cb.SetValue(' key press')
3435	if event.key in ['l','s','a','r','p','x','y']:
3436	wx.CallAfter(OnImPlotKeyPress,event)
3437	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
3438
3439	def OnImPick(event):
3440	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
3441	return
3442	if G2frame.itemPicked is not None: return
3443	G2frame.itemPicked = event.artist
3444	G2frame.mousePicked = event.mouseevent
3445
3446	def OnImRelease(event):
3447	try:
3448	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
3449	except TypeError:
3450	return
3451	if PickName not in ['Image Controls','Masks','Stress/Strain']:
3452	return
3453	pixelSize = Data['pixelSize']
3454	FlatBkg = Data.get('Flat Bkg',0.)
3455	scalex = 1000./pixelSize[0]
3456	scaley = 1000./pixelSize[1]
3457	# pixLimit = Data['pixLimit'] #can be too tight
3458	pixLimit = 20 #this makes the search box 40x40 pixels
3459	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
3460	Xpos = event.xdata
3461	if not (Xpos and G2frame.ifGetRing): #got point out of frame
3462	return
3463	Ypos = event.ydata
3464	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
3465	if event.button == 1:
3466	Xpix = Xpos*scalex
3467	Ypix = Ypos*scaley
3468	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ-FlatBkg,pixLimit,Xpix,Ypix)
3469	if I and J:
3470	xpos += .5 #shift to pixel center
3471	ypos += .5
3472	xpos /= scalex #convert to mm
3473	ypos /= scaley
3474	Data['ring'].append([xpos,ypos])
3475	elif event.button == 3:
3476	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...',0)
3477	if G2img.ImageCalibrate(G2frame,Data):
3478	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check',0)
3479	print 'Calibration successful'
3480	else:
3481	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose',0)
3482	print 'Calibration failed'
3483	G2frame.ifGetRing = False
3484	G2imG.UpdateImageControls(G2frame,Data,Masks)
3485	return
3486	PlotImage(G2frame,newImage=False)
3487	return
3488	elif G2frame.MaskKey and PickName == 'Masks':
3489	Xpos,Ypos = [event.xdata,event.ydata]
3490	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
3491	return
3492	if G2frame.MaskKey == 's' and event.button == 1:
3493	Masks['Points'][-1] = [Xpos,Ypos,1.]
3494	G2frame.MaskKey = ''
3495	elif G2frame.MaskKey == 'r' and event.button == 1:
3496	tth = G2img.GetTth(Xpos,Ypos,Data)
3497	Masks['Rings'][-1] = [tth,0.1]
3498	G2frame.MaskKey = ''
3499	elif G2frame.MaskKey == 'a' and event.button == 1:
3500	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
3501	azm = int(azm)
3502	Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1]
3503	G2frame.MaskKey = ''
3504	elif G2frame.MaskKey =='p':
3505	polygon = Masks['Polygons'][-1]
3506	if len(polygon) > 2 and event.button == 3:
3507	x0,y0 = polygon[0]
3508	polygon.append([x0,y0])
3509	G2frame.MaskKey = ''
3510	G2frame.G2plotNB.status.SetFields(['','Polygon closed'])
3511	else:
3512	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)])
3513	polygon.append([Xpos,Ypos])
3514	elif G2frame.MaskKey =='f':
3515	frame = Masks['Frames']
3516	if len(frame) > 2 and event.button == 3:
3517	x0,y0 = frame[0]
3518	frame.append([x0,y0])
3519	G2frame.MaskKey = ''
3520	G2frame.G2plotNB.status.SetFields(['','Frame closed'])
3521	else:
3522	G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)])
3523	frame.append([Xpos,Ypos])
3524	G2imG.UpdateMasks(G2frame,Masks)
3525	PlotImage(G2frame,newImage=False)
3526	elif PickName == 'Stress/Strain' and G2frame.StrainKey:
3527	Xpos,Ypos = [event.xdata,event.ydata]
3528	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
3529	return
3530	dsp = G2img.GetDsp(Xpos,Ypos,Data)
3531	StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':0.5,
3532	'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]})
3533	R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ-FlatBkg,Data)
3534	if not len(R):
3535	del StrSta['d-zero'][-1]
3536	G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection')
3537	StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True)
3538	G2frame.StrainKey = ''
3539	G2imG.UpdateStressStrain(G2frame,StrSta)
3540	PlotStrain(G2frame,StrSta)
3541	PlotImage(G2frame,newPlot=False)
3542	else:
3543	Xpos,Ypos = [event.xdata,event.ydata]
3544	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
3545	return
3546	if G2frame.ifGetRing: #delete a calibration ring pick
3547	xypos = [Xpos,Ypos]
3548	rings = Data['ring']
3549	for ring in rings:
3550	if np.allclose(ring,xypos,.01,0):
3551	rings.remove(ring)
3552	else:
3553	tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3]
3554	itemPicked = str(G2frame.itemPicked)
3555	if 'Line2D' in itemPicked and PickName == 'Image Controls':
3556	if 'line1' in itemPicked:
3557	Data['IOtth'][0] = max(tth,0.001)
3558	elif 'line2' in itemPicked:
3559	Data['IOtth'][1] = tth
3560	elif 'line3' in itemPicked:
3561	Data['LRazimuth'][0] = int(azm)
3562	elif 'line4' in itemPicked and not Data['fullIntegrate']:
3563	Data['LRazimuth'][1] = int(azm)
3564
3565	Data['LRazimuth'][0] %= 360
3566	Data['LRazimuth'][1] %= 360
3567	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
3568	Data['LRazimuth'][1] += 360
3569	if Data['fullIntegrate']:
3570	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
3571
3572	if Data['IOtth'][0] > Data['IOtth'][1]:
3573	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
3574
3575	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
3576	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
3577	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
3578	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
3579	elif 'Circle' in itemPicked and PickName == 'Masks':
3580	spots = Masks['Points']
3581	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
3582	newPos = np.array([float(newPos[0]),float(newPos[1])])
3583	for spot in spots:
3584	if spot and np.allclose(np.array([spot[:2]]),newPos):
3585	spot[:2] = Xpos,Ypos
3586	G2imG.UpdateMasks(G2frame,Masks)
3587	elif 'Line2D' in itemPicked and PickName == 'Masks':
3588	Obj = G2frame.itemPicked.findobj()
3589	rings = Masks['Rings']
3590	arcs = Masks['Arcs']
3591	polygons = Masks['Polygons']
3592	frame = Masks['Frames']
3593	for ring in G2frame.ringList:
3594	if Obj == ring[0]:
3595	rN = ring[1]
3596	if ring[2] == 'o':
3597	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2.
3598	else:
3599	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2.
3600	for arc in G2frame.arcList:
3601	if Obj == arc[0]:
3602	aN = arc[1]
3603	if arc[2] == 'o':
3604	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2
3605	elif arc[2] == 'i':
3606	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2
3607	elif arc[2] == 'l':
3608	arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data))
3609	else:
3610	arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data))
3611	for poly in G2frame.polyList: #merging points problem here?
3612	if Obj == poly[0]:
3613	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
3614	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
3615	pN = poly[1]
3616	for i,xy in enumerate(polygons[pN]):
3617	if np.allclose(np.array([xy]),oldPos,atol=1.0):
3618	if event.button == 1:
3619	polygons[pN][i] = Xpos,Ypos
3620	elif event.button == 3:
3621	polygons[pN].insert(i,[Xpos,Ypos])
3622	break
3623	if frame:
3624	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
3625	for i,xy in enumerate(frame):
3626	if np.allclose(np.array([xy]),oldPos,atol=1.0):
3627	if event.button == 1:
3628	frame[i] = Xpos,Ypos
3629	elif event.button == 3:
3630	frame.insert(i,[Xpos,Ypos])
3631	break
3632	G2imG.UpdateMasks(G2frame,Masks)
3633	# else: #keep for future debugging
3634	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
3635	PlotImage(G2frame,newImage=True)
3636	G2frame.itemPicked = None
3637
3638	try:
3639	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
3640	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3641	if not newPlot:
3642	Plot = Page.figure.gca() #get previous powder plot & get limits
3643	xylim = Plot.get_xlim(),Plot.get_ylim()
3644	if newImage:
3645	Page.figure.clf()
3646	Plot = Page.figure.gca() #get a fresh plot after clf()
3647	except ValueError:
3648	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
3649	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
3650	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3651	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
3652	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
3653	Page.canvas.mpl_connect('pick_event', OnImPick)
3654	Page.canvas.mpl_connect('button_release_event', OnImRelease)
3655	xylim = []
3656	Page.Choice = None
3657	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
3658	Page.SetFocus()
3659	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
3660	G2frame.G2plotNB.status.DestroyChildren()
3661	if G2frame.logPlot:
3662	Title = 'log('+Title+')'
3663	Plot.set_title(Title)
3664	try:
3665	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
3666	Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',)
3667	if G2frame.logPlot:
3668	Page.Choice[1] = 'l: log(I) off'
3669	Page.keyPress = OnImPlotKeyPress
3670	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]:
3671	Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask',
3672	'p: polygon mask','f: frame mask',)
3673	if G2frame.logPlot:
3674	Page.Choice[1] = 'l: log(I) off'
3675	Page.keyPress = OnImPlotKeyPress
3676	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]:
3677	Page.Choice = (' key press','a: add new ring',)
3678	Page.keyPress = OnImPlotKeyPress
3679	except TypeError:
3680	pass
3681	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
3682	dark = Data.get('dark image',[0,''])
3683	if dark[0]:
3684	darkfile = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
3685	G2frame.root,dark[0]))[1]
3686	if imagefile != G2frame.oldImagefile:
3687	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
3688	if not imagefile:
3689	G2frame.G2plotNB.Delete('2D Powder Image')
3690	return
3691	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
3692	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
3693	if dark[0]:
3694	darkImg = G2IO.GetImageData(G2frame,darkfile,imageOnly=True)
3695	G2frame.ImageZ += dark[1]*darkImg
3696	G2frame.oldImagefile = imagefile
3697
3698	imScale = 1
3699	if len(G2frame.ImageZ) > 1024:
3700	imScale = len(G2frame.ImageZ)/1024
3701	sizexy = Data['size']
3702	pixelSize = Data['pixelSize']
3703	scalex = 1000./pixelSize[0]
3704	scaley = 1000./pixelSize[1]
3705	Xmax = sizexy[0]*pixelSize[0]/1000.
3706	Ymax = sizexy[1]*pixelSize[1]/1000.
3707	xlim = (0,Xmax)
3708	ylim = (Ymax,0)
3709	Imin,Imax = Data['range'][1]
3710	acolor = mpl.cm.get_cmap(Data['color'])
3711	xcent,ycent = Data['center']
3712	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
3713	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
3714	#do threshold mask - "real" mask - others are just bondaries
3715	Zlim = Masks['Thresholds'][1]
3716	FlatBkg = Data.get('Flat Bkg',0.0)
3717	wx.BeginBusyCursor()
3718	try:
3719
3720	if newImage:
3721	Imin,Imax = Data['range'][1]
3722	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]+FlatBkg),Zlim[1]+FlatBkg)
3723	MaskA = ma.getmaskarray(MA)
3724	A = G2img.ImageCompress(MA,imScale)-FlatBkg
3725	AM = G2img.ImageCompress(MaskA,imScale)
3726	if G2frame.logPlot:
3727	A = np.where(A>Imin,np.where(A<Imax,A,0),0)
3728	A = np.where(A>0,np.log(A),0)
3729	AM = np.where(AM>0,np.log(AM),0)
3730	Imin,Imax = [np.amin(A),np.amax(A)]
3731	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
3732	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
3733	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
3734	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
3735
3736	Plot.plot(xcent,ycent,'x')
3737	#G2frame.PatternTree.GetItemText(item)
3738	if Data['showLines']:
3739	LRAzim = Data['LRazimuth'] #NB: integers
3740	Nazm = Data['outAzimuths']
3741	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
3742	AzmthOff = Data['azmthOff']
3743	IOtth = Data['IOtth']
3744	wave = Data['wavelength']
3745	dspI = wave/(2.0*sind(IOtth[0]/2.0))
3746	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
3747	dspO = wave/(2.0*sind(IOtth[1]/2.0))
3748	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
3749	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
3750	if ellI:
3751	xyI = []
3752	for azm in Azm:
3753	xy = G2img.GetDetectorXY(dspI,azm,Data)
3754	if np.any(xy):
3755	xyI.append(xy)
3756	if len(xyI):
3757	xyI = np.array(xyI)
3758	arcxI,arcyI = xyI.T
3759	Plot.plot(arcxI,arcyI,picker=3)
3760	if ellO:
3761	xyO = []
3762	for azm in Azm:
3763	xy = G2img.GetDetectorXY(dspO,azm,Data)
3764	if np.any(xy):
3765	xyO.append(xy)
3766	if len(xyO):
3767	xyO = np.array(xyO)
3768	arcxO,arcyO = xyO.T
3769	Plot.plot(arcxO,arcyO,picker=3)
3770	if ellO and ellI:
3771	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
3772	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
3773	for i in range(Nazm):
3774	cake = LRAzim[0]+i*delAzm-AzmthOff
3775	if Data['centerAzm']:
3776	cake += delAzm/2.
3777	ind = np.searchsorted(Azm,cake)
3778	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
3779
3780	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
3781	for xring,yring in Data['ring']:
3782	Plot.plot(xring,yring,'r+',picker=3)
3783	if Data['setRings']:
3784	N = 0
3785	for ring in Data['rings']:
3786	xring,yring = np.array(ring).T[:2]
3787	Plot.plot(xring,yring,'.',color=colors[N%6])
3788	N += 1
3789	for ellipse in Data['ellipses']: #what about hyperbola?
3790	cent,phi,[width,height],col = ellipse
3791	if width > 0: #ellipses
3792	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
3793	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
3794	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
3795	for N,ring in enumerate(StrSta['d-zero']):
3796	xring,yring = ring['ImxyObs']
3797	Plot.plot(xring,yring,colors[N%6]+'.')
3798	#masks - mask lines numbered after integration limit lines
3799	spots = Masks['Points']
3800	rings = Masks['Rings']
3801	arcs = Masks['Arcs']
3802	polygons = Masks['Polygons']
3803	if 'Frames' not in Masks:
3804	Masks['Frames'] = []
3805	frame = Masks['Frames']
3806	for spot in spots:
3807	if spot:
3808	x,y,d = spot
3809	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
3810	G2frame.ringList = []
3811	for iring,ring in enumerate(rings):
3812	if ring:
3813	tth,thick = ring
3814	wave = Data['wavelength']
3815	xy1 = []
3816	xy2 = []
3817	Azm = np.linspace(0,362,181)
3818	for azm in Azm:
3819	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
3820	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
3821	x1,y1 = np.array(xy1).T
3822	x2,y2 = np.array(xy2).T
3823	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
3824	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
3825	G2frame.arcList = []
3826	for iarc,arc in enumerate(arcs):
3827	if arc:
3828	tth,azm,thick = arc
3829	wave = Data['wavelength']
3830	xy1 = []
3831	xy2 = []
3832	aR = azm[0],azm[1],azm[1]-azm[0]
3833	if azm[1]-azm[0] > 180:
3834	aR[2] /= 2
3835	Azm = np.linspace(aR[0],aR[1],aR[2])
3836	for azm in Azm:
3837	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
3838	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
3839	x1,y1 = np.array(xy1).T
3840	x2,y2 = np.array(xy2).T
3841	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
3842	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
3843	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
3844	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
3845	G2frame.polyList = []
3846	for ipoly,polygon in enumerate(polygons):
3847	if polygon:
3848	x,y = np.hsplit(np.array(polygon),2)
3849	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
3850	Plot.plot(x,y,'r')
3851	G2frame.frameList = []
3852	if frame:
3853	x,y = np.hsplit(np.array(frame),2)
3854	G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0])
3855	Plot.plot(x,y,'g')
3856	if newImage:
3857	colorBar = Page.figure.colorbar(Img)
3858	Plot.set_xlim(xlim)
3859	Plot.set_ylim(ylim)
3860	if Data['invert_x']:
3861	Plot.invert_xaxis()
3862	if Data['invert_y']:
3863	Plot.invert_yaxis()
3864	if not newPlot and xylim:
3865	Page.toolbar.push_current()
3866	Plot.set_xlim(xylim[0])
3867	Plot.set_ylim(xylim[1])
3868	xylim = []
3869	Page.toolbar.push_current()
3870	Page.toolbar.draw()
3871	# patch for wx 2.9 on Mac, to force a redraw
3872	i,j= wx.__version__.split('.')[0:2]
3873	if int(i)+int(j)/10. > 2.8 and 'wxOSX' in wx.PlatformInfo:
3874	Page.canvas.draw()
3875	else:
3876	Page.canvas.draw()
3877	finally:
3878	wx.EndBusyCursor()
3879
3880	################################################################################
3881	##### PlotIntegration
3882	################################################################################
3883
3884	def PlotIntegration(G2frame,newPlot=False,event=None):
3885	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
3886	'''
3887
3888	def OnMotion(event):
3889	Page.canvas.SetToolTipString('')
3890	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3891	azm = event.ydata
3892	tth = event.xdata
3893	if azm and tth:
3894	G2frame.G2plotNB.status.SetFields(\
3895	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3896
3897	try:
3898	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
3899	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3900	if not newPlot:
3901	Plot = Page.figure.gca() #get previous plot & get limits
3902	xylim = Plot.get_xlim(),Plot.get_ylim()
3903	Page.figure.clf()
3904	Plot = Page.figure.gca() #get a fresh plot after clf()
3905
3906	except ValueError:
3907	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
3908	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
3909	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3910	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3911	Page.views = False
3912	view = False
3913	Page.Choice = None
3914	if not event:
3915	Page.SetFocus()
3916
3917	Data = G2frame.PatternTree.GetItemPyData(
3918	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3919	image = G2frame.Integrate[0]
3920	xsc = G2frame.Integrate[1]
3921	ysc = G2frame.Integrate[2]
3922	Imin,Imax = Data['range'][1]
3923	acolor = mpl.cm.get_cmap(Data['color'])
3924	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3925	Plot.set_ylabel('azimuth',fontsize=12)
3926	Plot.set_xlabel('2-theta',fontsize=12)
3927	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
3928	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
3929	colorBar = Page.figure.colorbar(Img)
3930	# if Data['ellipses']:
3931	# for ellipse in Data['ellipses']:
3932	# x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
3933	# tth,azm = G2img.GetTthAzm(x,y,Data)
3934	## azm = np.where(azm < 0.,azm+360,azm)
3935	# Plot.plot(tth,azm,'b,')
3936	if not newPlot:
3937	Page.toolbar.push_current()
3938	Plot.set_xlim(xylim[0])
3939	Plot.set_ylim(xylim[1])
3940	xylim = []
3941	Page.toolbar.push_current()
3942	Page.toolbar.draw()
3943	else:
3944	Page.canvas.draw()
3945
3946	################################################################################
3947	##### PlotTRImage
3948	################################################################################
3949
3950	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
3951	'''a test plot routine - not normally used
3952	'''
3953
3954	def OnMotion(event):
3955	Page.canvas.SetToolTipString('')
3956	Page.canvas.SetCursor(wx.CROSS_CURSOR)
3957	azm = event.xdata
3958	tth = event.ydata
3959	if azm and tth:
3960	G2frame.G2plotNB.status.SetFields(\
3961	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
3962
3963	try:
3964	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3965	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3966	if not newPlot:
3967	Plot = Page.figure.gca() #get previous plot & get limits
3968	xylim = Plot.get_xlim(),Plot.get_ylim()
3969	Page.figure.clf()
3970	Plot = Page.figure.gca() #get a fresh plot after clf()
3971
3972	except ValueError:
3973	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
3974	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
3975	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
3976	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
3977	Page.views = False
3978	view = False
3979	Page.Choice = None
3980	Page.SetFocus()
3981
3982	Data = G2frame.PatternTree.GetItemPyData(
3983	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
3984	Imin,Imax = Data['range'][1]
3985	step = (Imax-Imin)/5.
3986	V = np.arange(Imin,Imax,step)
3987	acolor = mpl.cm.get_cmap(Data['color'])
3988	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
3989	Plot.set_xlabel('azimuth',fontsize=12)
3990	Plot.set_ylabel('2-theta',fontsize=12)
3991	Plot.contour(tax,tay,taz,V,cmap=acolor)
3992	if Data['showLines']:
3993	IOtth = Data['IOtth']
3994	if Data['fullIntegrate']:
3995	LRAzim = [-180,180]
3996	else:
3997	LRAzim = Data['LRazimuth'] #NB: integers
3998	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
3999	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
4000	if not Data['fullIntegrate']:
4001	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
4002	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
4003	if Data['setRings']:
4004	rings = np.concatenate((Data['rings']),axis=0)
4005	for xring,yring,dsp in rings:
4006	x,y = G2img.GetTthAzm(xring,yring,Data)
4007	Plot.plot(y,x,'r+')
4008	if Data['ellipses']:
4009	for ellipse in Data['ellipses']:
4010	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
4011	x,y = np.hsplit(ring,2)
4012	tth,azm = G2img.GetTthAzm(x,y,Data)
4013	Plot.plot(azm,tth,'b,')
4014	if not newPlot:
4015	Page.toolbar.push_current()
4016	Plot.set_xlim(xylim[0])
4017	Plot.set_ylim(xylim[1])
4018	xylim = []
4019	Page.toolbar.push_current()
4020	Page.toolbar.draw()
4021	else:
4022	Page.canvas.draw()
4023
4024	################################################################################
4025	##### PlotStructure
4026	################################################################################
4027
4028	def PlotStructure(G2frame,data,firstCall=False):
4029	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
4030	thermal motion ellipsoids and polyhedra
4031	'''
4032
4033	def FindPeaksBonds(XYZ):
4034	rFact = data['Drawing'].get('radiusFactor',0.85) #data['Drawing'] could be empty!
4035	Bonds = [[] for x in XYZ]
4036	for i,xyz in enumerate(XYZ):
4037	Dx = XYZ-xyz
4038	dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
4039	IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2))
4040	for j in IndB[0]:
4041	Bonds[i].append(Dx[j]/2.)
4042	Bonds[j].append(-Dx[j]/2.)
4043	return Bonds
4044
4045	# PlotStructure initialization here
4046	ForthirdPI = 4.0*math.pi/3.0
4047	generalData = data['General']
4048	cell = generalData['Cell'][1:7]
4049	Vol = generalData['Cell'][7:8][0]
4050	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
4051	Gmat,gmat = G2lat.cell2Gmat(cell)
4052	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4053	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
4054	SGData = generalData['SGData']
4055	if generalData['Type'] in ['modulated','magnetic']:
4056	SSGData = generalData['SSGData']
4057	Mydir = generalData['Mydir']
4058	atomData = data['Atoms']
4059	mapPeaks = []
4060	drawingData = data['Drawing']
4061	if not drawingData:
4062	return #nothing setup, nothing to draw
4063	if 'Map Peaks' in data:
4064	mapPeaks = np.array(data['Map Peaks'])
4065	peakMax = 100.
4066	if len(mapPeaks):
4067	peakMax = np.max(mapPeaks.T[0])
4068	resRBData = data['RBModels'].get('Residue',[])
4069	vecRBData = data['RBModels'].get('Vector',[])
4070	rbAtmDict = {}
4071	for rbObj in resRBData+vecRBData:
4072	exclList = ['X' for i in range(len(rbObj['Ids']))]
4073	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
4074	testRBObj = data.get('testRBObj',{})
4075	rbObj = testRBObj.get('rbObj',{})
4076	MCSA = data.get('MCSA',{})
4077	mcsaModels = MCSA.get('Models',[])
4078	if len(mcsaModels) > 1:
4079	XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA)
4080	mcsaXYZ = []
4081	mcsaTypes = []
4082	neqv = 0
4083	for xyz,atyp in zip(XYZs,Types):
4084	equiv = G2spc.GenAtom(xyz,SGData,All=True,Move=False)
4085	neqv = max(neqv,len(equiv))
4086	for item in equiv:
4087	mcsaXYZ.append(item[0])
4088	mcsaTypes.append(atyp)
4089	mcsaXYZ = np.array(mcsaXYZ)
4090	mcsaTypes = np.array(mcsaTypes)
4091	nuniq = mcsaXYZ.shape[0]/neqv
4092	mcsaXYZ = np.reshape(mcsaXYZ,(nuniq,neqv,3))
4093	mcsaTypes = np.reshape(mcsaTypes,(nuniq,neqv))
4094	cent = np.fix(np.sum(mcsaXYZ+2.,axis=0)/nuniq)-2
4095	cent[0] = [0,0,0] #make sure 1st one isn't moved
4096	mcsaXYZ = np.swapaxes(mcsaXYZ,0,1)-cent[:,np.newaxis,:]
4097	mcsaTypes = np.swapaxes(mcsaTypes,0,1)
4098	mcsaXYZ = np.reshape(mcsaXYZ,(nuniq*neqv,3))
4099	mcsaTypes = np.reshape(mcsaTypes,(nuniq*neqv))
4100	mcsaBonds = FindPeaksBonds(mcsaXYZ)
4101	drawAtoms = drawingData.get('Atoms',[])
4102	mapData = {}
4103	flipData = {}
4104	rhoXYZ = []
4105	showBonds = False
4106	if 'Map' in generalData:
4107	mapData = generalData['Map']
4108	showBonds = mapData.get('Show bonds',False)
4109	if 'Flip' in generalData:
4110	flipData = generalData['Flip']
4111	Wt = np.array([255,255,255])
4112	Rd = np.array([255,0,0])
4113	Gr = np.array([0,255,0])
4114	wxGreen = wx.Colour(0,255,0)
4115	Bl = np.array([0,0,255])
4116	Or = np.array([255,128,0])
4117	wxOrange = wx.Colour(255,128,0)
4118	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]])
4119	uEdges = np.array([
4120	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
4121	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
4122	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
4123	mD = 0.1
4124	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
4125	mapPeakVecs = np.inner(mV,Bmat)
4126
4127	backColor = np.array(list(drawingData['backColor'])+[0,])
4128	Bc = np.array(list(drawingData['backColor']))
4129	uColors = [Rd,Gr,Bl,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc]
4130	altDown = False
4131	shiftDown = False
4132	ctrlDown = False
4133	G2frame.tau = 0.
4134
4135	def OnKeyBox(event):
4136	mode = cb.GetValue()
4137	if mode in ['jpeg','bmp','tiff',]:
4138	try:
4139	import Image as Im
4140	except ImportError:
4141	try:
4142	from PIL import Image as Im
4143	except ImportError:
4144	print "PIL/pillow Image module not present. Cannot save images without this"
4145	raise Exception("PIL/pillow Image module not found")
4146	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
4147	size = Page.canvas.GetSize()
4148	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
4149	if mode in ['jpeg',]:
4150	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
4151	im = Im.new("RGBA", (size[0],size[1]))
4152	else:
4153	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
4154	im = Im.new("RGB", (size[0],size[1]))
4155	im.fromstring(Pix)
4156	im.save(Fname,mode)
4157	cb.SetValue(' save as/key:')
4158	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
4159	else:
4160	event.key = cb.GetValue()[0]
4161	cb.SetValue(' save as/key:')
4162	wx.CallAfter(OnKey,event)
4163	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
4164
4165	def OnKey(event): #on key UP!!
4166	try:
4167	keyCode = event.GetKeyCode()
4168	if keyCode > 255:
4169	keyCode = 0
4170	key = chr(keyCode)
4171	except AttributeError: #if from OnKeyBox above
4172	key = str(event.key).upper()
4173	indx = drawingData['selectedAtoms']
4174	cx,ct = drawingData['atomPtrs'][:2]
4175	if key in ['C']:
4176	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
4177	drawingData['viewDir'] = [0,0,1]
4178	drawingData['oldxy'] = []
4179	V0 = np.array([0,0,1])
4180	V = np.inner(Amat,V0)
4181	V /= np.sqrt(np.sum(V**2))
4182	A = np.arccos(np.sum(V*V0))
4183	Q = G2mth.AV2Q(A,[0,1,0])
4184	drawingData['Quaternion'] = Q
4185	SetViewPointText(drawingData['viewPoint'][0])
4186	SetViewDirText(drawingData['viewDir'])
4187	Q = drawingData['Quaternion']
4188	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
4189	elif key in ['N']:
4190	drawAtoms = drawingData['Atoms']
4191	if not len(drawAtoms): #no atoms
4192	return
4193	pI = drawingData['viewPoint'][1]
4194	if not len(pI):
4195	pI = [0,0]
4196	if indx:
4197	pI[0] = indx[pI[1]]
4198	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4199	pI[1] += 1
4200	if pI[1] >= len(indx):
4201	pI[1] = 0
4202	else:
4203	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4204	pI[0] += 1
4205	if pI[0] >= len(drawAtoms):
4206	pI[0] = 0
4207	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
4208	SetViewPointText(drawingData['viewPoint'][0])
4209	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
4210
4211	elif key in ['P']:
4212	drawAtoms = drawingData['Atoms']
4213	if not len(drawAtoms): #no atoms
4214	return
4215	pI = drawingData['viewPoint'][1]
4216	if not len(pI):
4217	pI = [0,0]
4218	if indx:
4219	pI[0] = indx[pI[1]]
4220	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4221	pI[1] -= 1
4222	if pI[1] < 0:
4223	pI[1] = len(indx)-1
4224	else:
4225	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
4226	pI[0] -= 1
4227	if pI[0] < 0:
4228	pI[0] = len(drawAtoms)-1
4229	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
4230	SetViewPointText(drawingData['viewPoint'][0])
4231	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
4232	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
4233	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
4234	SetMapRoll(dirDict[key])
4235	if 'rho' in generalData.get('4DmapData',{}):
4236	Set4DMapRoll(dirDict[key])
4237	SetPeakRoll(dirDict[key])
4238	SetMapPeaksText(mapPeaks)
4239	elif key in ['+','-','=','0'] and generalData['Type'] in ['modulated','magnetic']:
4240	if key == '0':
4241	G2frame.tau = 0.
4242	elif key in ['+','=']:
4243	G2frame.tau += 0.05
4244	elif key == '-':
4245	G2frame.tau -= 0.05
4246	G2frame.tau %= 1. #force 0-1 range
4247	Draw('key')
4248
4249	def GetTruePosition(xy,Add=False):
4250	View = glGetIntegerv(GL_VIEWPORT)
4251	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
4252	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
4253	Zmax = 1.
4254	if Add:
4255	Indx = GetSelectedAtoms()
4256	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
4257	for i,peak in enumerate(mapPeaks):
4258	x,y,z = peak[1:4]
4259	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
4260	XY = [int(X),int(View[3]-Y)]
4261	if np.allclose(xy,XY,atol=10) and Z < Zmax:
4262	Zmax = Z
4263	try:
4264	Indx.remove(i)
4265	ClearSelectedAtoms()
4266	for id in Indx:
4267	SetSelectedAtoms(id,Add)
4268	except:
4269	SetSelectedAtoms(i,Add)
4270	else:
4271	cx = drawingData['atomPtrs'][0]
4272	for i,atom in enumerate(drawAtoms):
4273	x,y,z = atom[cx:cx+3]
4274	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
4275	XY = [int(X),int(View[3]-Y)]
4276	if np.allclose(xy,XY,atol=10) and Z < Zmax:
4277	Zmax = Z
4278	try:
4279	Indx.remove(i)
4280	ClearSelectedAtoms()
4281	for id in Indx:
4282	SetSelectedAtoms(id,Add)
4283	except:
4284	SetSelectedAtoms(i,Add)
4285
4286	def OnMouseDown(event):
4287	xy = event.GetPosition()
4288	if event.ShiftDown():
4289	if event.LeftIsDown():
4290	GetTruePosition(xy)
4291	elif event.RightIsDown():
4292	GetTruePosition(xy,True)
4293	else:
4294	drawingData['oldxy'] = list(xy)
4295
4296	def OnMouseMove(event):
4297	if event.ShiftDown(): #don't want any inadvertant moves when picking
4298	return
4299	newxy = event.GetPosition()
4300
4301	if event.Dragging():
4302	if event.AltDown() and rbObj:
4303	if event.LeftIsDown():
4304	SetRBRotation(newxy)
4305	Q = rbObj['Orient'][0]
4306	�