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source: trunk/GSASIIplot.py @ 335

Last change on this file since 335 was 335, checked in by vondreele, 12 years ago
Add delete Pawley list; scratch "leBail" from things mods to texture display stuff refactor instrument parameters GUI as sizer based - no grid table some mods to peak fit output
Property svn:keywords set to `Date Author Revision URL Id`
File size: 105.0 KB

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1	#GSASII plotting routines
2	########### SVN repository information ###################
3	# $Date: 2011-07-07 18:53:57 +0000 (Thu, 07 Jul 2011) $
4	# $Author: vondreele $
5	# $Revision: 335 $
6	# $URL: trunk/GSASIIplot.py $
7	# $Id: GSASIIplot.py 335 2011-07-07 18:53:57Z vondreele $
8	########### SVN repository information ###################
9	import math
10	import time
11	import copy
12	import os.path
13	import numpy as np
14	import numpy.linalg as nl
15	import wx
16	import wx.aui
17	import wx.glcanvas
18	import matplotlib as mpl
19	import mpl_toolkits.mplot3d.axes3d as mp3d
20	import GSASIIpath
21	import GSASIIgrid as G2gd
22	import GSASIIimage as G2img
23	import GSASIIpwd as G2pwd
24	import GSASIIIO as G2IO
25	import GSASIIpwdGUI as G2pdG
26	import GSASIIimgGUI as G2imG
27	import GSASIIphsGUI as G2phG
28	import GSASIIlattice as G2lat
29	import GSASIIspc as G2spc
30	import pytexture as ptx
31	from OpenGL.GL import *
32	from OpenGL.GLU import *
33	from OpenGL.GLUT import *
34	from OpenGL.GLE import *
35	from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
36	from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
37
38	# useful degree trig functions
39	sind = lambda x: math.sin(x*math.pi/180.)
40	cosd = lambda x: math.cos(x*math.pi/180.)
41	tand = lambda x: math.tan(x*math.pi/180.)
42	asind = lambda x: 180.*math.asin(x)/math.pi
43	acosd = lambda x: 180.*math.acos(x)/math.pi
44	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
45	atand = lambda x: 180.*math.atan(x)/math.pi
46	# numpy versions
47	npsind = lambda x: np.sin(x*np.pi/180.)
48	npcosd = lambda x: np.cos(x*np.pi/180.)
49	npacosd = lambda x: 180.*np.arccos(x)/np.pi
50	npasind = lambda x: 180.*np.arcsin(x)/np.pi
51	npatand = lambda x: 180.*np.arctan(x)/np.pi
52	npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi
53
54	class G2PlotMpl(wx.Panel):
55	def __init__(self,parent,id=-1,dpi=None,**kwargs):
56	wx.Panel.__init__(self,parent,id=id,**kwargs)
57	mpl.rcParams['legend.fontsize'] = 8
58	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
59	self.canvas = Canvas(self,-1,self.figure)
60	self.toolbar = Toolbar(self.canvas)
61
62	self.toolbar.Realize()
63
64	sizer=wx.BoxSizer(wx.VERTICAL)
65	sizer.Add(self.canvas,1,wx.EXPAND)
66	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
67	self.SetSizer(sizer)
68
69	class G2PlotOgl(wx.Panel):
70	def __init__(self,parent,id=-1,dpi=None,**kwargs):
71	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
72	self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs)
73	self.camera = {}
74	sizer=wx.BoxSizer(wx.VERTICAL)
75	sizer.Add(self.canvas,1,wx.EXPAND)
76	self.SetSizer(sizer)
77
78	class G2Plot3D(wx.Panel):
79	def __init__(self,parent,id=-1,dpi=None,**kwargs):
80	wx.Panel.__init__(self,parent,id=id,**kwargs)
81	self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
82	self.canvas = Canvas(self,-1,self.figure)
83	self.toolbar = Toolbar(self.canvas)
84
85	self.toolbar.Realize()
86
87	sizer=wx.BoxSizer(wx.VERTICAL)
88	sizer.Add(self.canvas,1,wx.EXPAND)
89	sizer.Add(self.toolbar,0,wx.LEFT\|wx.EXPAND)
90	self.SetSizer(sizer)
91
92	class G2PlotNoteBook(wx.Panel):
93	def __init__(self,parent,id=-1):
94	wx.Panel.__init__(self,parent,id=id)
95	#so one can't delete a plot page!!
96	self.nb = wx.aui.AuiNotebook(self, \
97	style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB)
98	sizer = wx.BoxSizer()
99	sizer.Add(self.nb,1,wx.EXPAND)
100	self.SetSizer(sizer)
101	self.status = parent.CreateStatusBar()
102	self.status.SetFieldsCount(2)
103	self.status.SetStatusWidths([150,-1])
104	self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
105
106	self.plotList = []
107
108	def addMpl(self,name=""):
109	page = G2PlotMpl(self.nb)
110	self.nb.AddPage(page,name)
111
112	self.plotList.append(name)
113
114	return page.figure
115
116	def add3D(self,name=""):
117	page = G2Plot3D(self.nb)
118	self.nb.AddPage(page,name)
119
120	self.plotList.append(name)
121
122	return page.figure
123
124	def addOgl(self,name=""):
125	page = G2PlotOgl(self.nb)
126	self.nb.AddPage(page,name)
127
128	self.plotList.append(name)
129
130	return page.figure
131
132	def Delete(self,name):
133	try:
134	item = self.plotList.index(name)
135	del self.plotList[item]
136	self.nb.DeletePage(item)
137	except ValueError: #no plot of this name - do nothing
138	return
139
140	def clear(self):
141	while self.nb.GetPageCount():
142	self.nb.DeletePage(0)
143	self.plotList = []
144	self.status.DestroyChildren()
145
146	def Rename(self,oldName,newName):
147	try:
148	item = self.plotList.index(oldName)
149	self.plotList[item] = newName
150	self.nb.SetPageText(item,newName)
151	except ValueError: #no plot of this name - do nothing
152	return
153
154	def OnPageChanged(self,event):
155	if self.plotList:
156	self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
157	self.status.DestroyChildren() #get rid of special stuff on status bar
158
159	def PlotSngl(self,newPlot=False):
160	'''Single crystal structure factor plotting package - displays zone of reflections as rings proportional
161	to F, F**2, etc. as requested
162	'''
163	from matplotlib.patches import Circle
164	global HKL,HKLF
165
166	def OnSCMotion(event):
167	xpos = event.xdata
168	if xpos:
169	xpos = round(xpos) #avoid out of frame mouse position
170	ypos = round(event.ydata)
171	zpos = Data['Layer']
172	if '100' in Data['Zone']:
173	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
174	elif '010' in Data['Zone']:
175	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
176	elif '001' in Data['Zone']:
177	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
178	Page.canvas.SetToolTipString(HKLtxt)
179	self.G2plotNB.status.SetFields(['HKL = '+HKLtxt,''])
180
181	def OnSCPick(event):
182	zpos = Data['Layer']
183	pos = event.artist.center
184	if '100' in Data['Zone']:
185	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
186	hkl = np.array([zpos,pos[0],pos[1]])
187	elif '010' in Data['Zone']:
188	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
189	hkl = np.array([pos[0],zpos,pos[1]])
190	elif '001' in Data['Zone']:
191	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
192	hkl = np.array([pos[0],pos[1],zpos])
193	h,k,l = hkl
194	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
195	if len(hklf):
196	Fosq,sig,Fcsq = hklf[0]
197	HKLtxt = '(%3d,%3d,%3d %.2f %.3f %.2f %.2f)'%(h,k,l,Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
198	self.G2plotNB.status.SetFields(['','HKL, Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt])
199
200	def OnSCKeyPress(event):
201	print event.key
202
203	try:
204	plotNum = self.G2plotNB.plotList.index('Structure Factors')
205	Page = self.G2plotNB.nb.GetPage(plotNum)
206	if not newPlot:
207	Plot = Page.figure.gca() #get previous powder plot & get limits
208	xylim = Plot.get_xlim(),Plot.get_ylim()
209	Page.figure.clf()
210	Plot = Page.figure.gca() #get a fresh plot after clf()
211	except ValueError:
212	Plot = self.G2plotNB.addMpl('Structure Factors').gca()
213	plotNum = self.G2plotNB.plotList.index('Structure Factors')
214	Page = self.G2plotNB.nb.GetPage(plotNum)
215	# Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
216	Page.canvas.mpl_connect('pick_event', OnSCPick)
217	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
218	Page.SetFocus()
219
220	Plot.set_aspect(aspect='equal')
221	HKLref = self.PatternTree.GetItemPyData(self.Sngl)
222	Data = self.PatternTree.GetItemPyData( \
223	G2gd.GetPatternTreeItemId(self,self.Sngl, 'HKL Plot Controls'))
224	Type = Data['Type']
225	scale = Data['Scale']
226	HKLmax = Data['HKLmax']
227	HKLmin = Data['HKLmin']
228	FosqMax = Data['FoMax']
229	FoMax = math.sqrt(FosqMax)
230	ifFc = Data['ifFc']
231	xlabel = ['k, h=','h, k=','h, l=']
232	ylabel = ['l','l','k']
233	zones = ['100','010','001']
234	pzone = [[1,2],[0,2],[0,1]]
235	izone = zones.index(Data['Zone'])
236	Plot.set_title(self.PatternTree.GetItemText(self.Sngl)[5:])
237	HKL = []
238	HKLF = []
239	for H,Fosq,sig,Fcsq,x,x,x in HKLref:
240	HKL.append(H)
241	HKLF.append([Fosq,sig,Fcsq])
242	if H[izone] == Data['Layer']:
243	B = 0
244	if Type == 'Fosq':
245	A = scale*Fosq/FosqMax
246	B = scale*Fcsq/FosqMax
247	C = abs(A-B)
248	elif Type == 'Fo':
249	A = scale*math.sqrt(max(0,Fosq))/FoMax
250	B = scale*math.sqrt(max(0,Fcsq))/FoMax
251	C = abs(A-B)
252	elif Type == '\|DFsq\|/sig':
253	A = abs(Fosq-Fcsq)/(scale*sig)
254	elif Type == '\|DFsq\|>sig':
255	A = abs(Fosq-Fcsq)/(scale*sig)
256	if A < 1.0: A = 0
257	elif Type == '\|DFsq\|>3sig':
258	A = abs(Fosq-Fcsq)/(scale*sig)
259	if A < 3.0: A = 0
260	xy = (H[pzone[izone][0]],H[pzone[izone][1]])
261	if A > 0.0:
262	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=3))
263	if B:
264	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
265	radius = C
266	if radius > 0:
267	if A > B:
268	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
269	else:
270	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
271	HKL = np.array(HKL,dtype=np.int)
272	HKLF = np.array(HKLF)
273	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
274	Plot.set_ylabel(ylabel[izone],fontsize=12)
275	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
276	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
277	if not newPlot:
278	Page.toolbar.push_current()
279	Plot.set_xlim(xylim[0])
280	Plot.set_ylim(xylim[1])
281	xylim = []
282	Page.toolbar.push_current()
283	Page.toolbar.draw()
284	else:
285	Page.canvas.draw()
286
287	def PlotPatterns(self,newPlot=False):
288	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
289	2-theta or q (future TOF). Can display multiple patterns as "waterfall plots" or contour plots. Log I
290	plotting available.
291	'''
292	global HKL
293
294	def OnPick(event):
295	if self.itemPicked is not None: return
296	PatternId = self.PatternId
297	try:
298	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
299	except TypeError:
300	return
301	Parms = dict(zip(Names,Values))
302	try:
303	wave = Parms['Lam']
304	except KeyError:
305	wave = Parms['Lam1']
306	PickId = self.PickId
307	pick = event.artist
308	mouse = event.mouseevent
309	xpos = pick.get_xdata()
310	ypos = pick.get_ydata()
311	ind = event.ind
312	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
313	if self.PatternTree.GetItemText(PickId) == 'Peak List':
314	if ind.all() != [0]: #picked a data point
315	if 'C' in Parms['Type']: #CW data - TOF later in an elif
316	ins = [Parms[x] for x in ['U','V','W','X','Y']]
317	if self.qPlot: #qplot - convert back to 2-theta
318	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
319	sig = ins[0]tand(xy[0]/2.0)2+ins[1]tand(xy[0]/2.0)+ins[2]
320	gam = ins[3]/cosd(xy[0]/2.0)+ins[4]*tand(xy[0]/2.0)
321	data = self.PatternTree.GetItemPyData(self.PickId)
322	XY = [xy[0],0, xy[1],1, sig,0, gam,0] #default refine intensity 1st
323	data.append(XY)
324	G2pdG.UpdatePeakGrid(self,data)
325	PlotPatterns(self)
326	else: #picked a peak list line
327	self.itemPicked = pick
328	elif self.PatternTree.GetItemText(PickId) == 'Limits':
329	if ind.all() != [0]: #picked a data point
330	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
331	data = self.PatternTree.GetItemPyData(LimitId)
332	if 'C' in Parms['Type']: #CW data - TOF later in an elif
333	if self.qPlot: #qplot - convert back to 2-theta
334	xy[0] = 2.0asind(xy[0]wave/(4*math.pi))
335	if mouse.button==1:
336	data[1][0] = min(xy[0],data[1][1])
337	if mouse.button==3:
338	data[1][1] = max(xy[0],data[1][0])
339	self.PatternTree.SetItemPyData(LimitId,data)
340	G2pdG.UpdateLimitsGrid(self,data)
341	PlotPatterns(self)
342	else: #picked a limit line
343	self.itemPicked = pick
344
345	def OnPlotKeyPress(event):
346	newPlot = False
347	if event.key == 'w':
348	if self.Weight:
349	self.Weight = False
350	else:
351	self.Weight = True
352	print 'plot weighting:',self.Weight
353	elif event.key == 'n':
354	if self.Contour:
355	pass
356	else:
357	if self.logPlot:
358	self.logPlot = False
359	else:
360	self.Offset[0] = 0
361	self.logPlot = True
362	elif event.key == 'u':
363	if self.Contour:
364	self.Cmax = min(1.0,self.Cmax*1.2)
365	elif self.logPlot:
366	pass
367	elif self.Offset[0] < 100.:
368	self.Offset[0] += 1.
369	elif event.key == 'd':
370	if self.Contour:
371	self.Cmax = max(0.0,self.Cmax*0.8)
372	elif self.logPlot:
373	pass
374	elif self.Offset[0] > 0.:
375	self.Offset[0] -= 1.
376	elif event.key == 'l':
377	self.Offset[1] -= 1.
378	elif event.key == 'r':
379	self.Offset[1] += 1.
380	elif event.key == 'o':
381	self.Offset = [0,0]
382	elif event.key == 'c':
383	newPlot = True
384	if self.Contour:
385	self.Contour = False
386	else:
387	self.Contour = True
388	self.SinglePlot = False
389	self.Offset = [0.,0.]
390	elif event.key == 'q':
391	newPlot = True
392	if self.qPlot:
393	self.qPlot = False
394	else:
395	self.qPlot = True
396	elif event.key == 's':
397	if self.Contour:
398	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
399	choice.sort()
400	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
401	if dlg.ShowModal() == wx.ID_OK:
402	sel = dlg.GetSelection()
403	self.ContourColor = choice[sel]
404	else:
405	self.ContourColor = 'Paired'
406	dlg.Destroy()
407	else:
408	if self.SinglePlot:
409	self.SinglePlot = False
410	else:
411	self.SinglePlot = True
412	elif event.key == '+':
413	if self.PickId:
414	self.PickId = False
415	elif event.key == 'i': #for smoothing contour plot
416	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
417	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
418	'mitchell','sinc','lanczos']
419	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
420	if dlg.ShowModal() == wx.ID_OK:
421	sel = dlg.GetSelection()
422	self.Interpolate = choice[sel]
423	else:
424	self.Interpolate = 'nearest'
425	dlg.Destroy()
426
427	PlotPatterns(self,newPlot=newPlot)
428
429	def OnKeyBox(event):
430	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('Powder Patterns'):
431	event.key = cb.GetValue()[0]
432	cb.SetValue(' key press')
433	OnPlotKeyPress(event)
434
435	def OnMotion(event):
436	xpos = event.xdata
437	if xpos: #avoid out of frame mouse position
438	ypos = event.ydata
439	Page.canvas.SetCursor(wx.CROSS_CURSOR)
440	try:
441	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
442	Parms = dict(zip(Names,Values))
443	try:
444	wave = Parms['Lam']
445	except KeyError:
446	wave = Parms['Lam1']
447	if self.qPlot:
448	xpos = 2.0asind(xposwave/(4*math.pi))
449	dsp = 0.0
450	if abs(xpos) > 0.: #avoid possible singularity at beam center
451	dsp = wave/(2.*sind(abs(xpos)/2.0))
452	if self.Contour:
453	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f pattern ID =%5d'%(xpos,dsp,int(ypos)),1)
454	else:
455	self.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f Intensity =%9.1f'%(xpos,dsp,ypos),1)
456	if self.itemPicked:
457	Page.canvas.SetToolTipString('%9.3f'%(xpos))
458	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
459	found = []
460	if len(HKL):
461	view = Page.toolbar._views.forward()[0][:2]
462	wid = view[1]-view[0]
463	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
464	if len(found):
465	h,k,l = found[0][:3]
466	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
467	else:
468	Page.canvas.SetToolTipString('')
469
470	except TypeError:
471	self.G2plotNB.status.SetStatusText('Select PWDR powder pattern first',1)
472
473	def OnRelease(event):
474	if self.itemPicked is None: return
475	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1::2]
476	Parms = dict(zip(Names,Values))
477	try:
478	wave = Parms['Lam']
479	except KeyError:
480	wave = Parms['Lam1']
481	xpos = event.xdata
482	if xpos: #avoid out of frame mouse position
483	lines = []
484	for line in self.Lines: lines.append(line.get_xdata()[0])
485	lineNo = lines.index(self.itemPicked.get_xdata()[0])
486	if lineNo in [0,1]:
487	LimitId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Limits')
488	data = self.PatternTree.GetItemPyData(LimitId)
489	# print 'limits',xpos
490	if self.qPlot:
491	data[1][lineNo] = 2.0asind(wavexpos/(4*math.pi))
492	else:
493	data[1][lineNo] = xpos
494	self.PatternTree.SetItemPyData(LimitId,data)
495	if self.PatternTree.GetItemText(self.PickId) == 'Limits':
496	G2pdG.UpdateLimitsGrid(self,data)
497	else:
498	PeakId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List')
499	data = self.PatternTree.GetItemPyData(PeakId)
500	# print 'peaks',xpos
501	if event.button == 3:
502	del data[lineNo-2]
503	else:
504	if self.qPlot:
505	data[lineNo-2][0] = 2.0asind(wavexpos/(4*math.pi))
506	else:
507	data[lineNo-2][0] = xpos
508	self.PatternTree.SetItemPyData(PeakId,data)
509	G2pdG.UpdatePeakGrid(self,data)
510	PlotPatterns(self)
511	self.itemPicked = None
512
513	xylim = []
514	try:
515	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
516	Page = self.G2plotNB.nb.GetPage(plotNum)
517	if not newPlot:
518	Plot = Page.figure.gca() #get previous powder plot & get limits
519	xylim = Plot.get_xlim(),Plot.get_ylim()
520	Page.figure.clf()
521	Plot = Page.figure.gca() #get a fresh plot after clf()
522	except ValueError:
523	newPlot = True
524	self.Cmax = 1.0
525	Plot = self.G2plotNB.addMpl('Powder Patterns').gca()
526	plotNum = self.G2plotNB.plotList.index('Powder Patterns')
527	Page = self.G2plotNB.nb.GetPage(plotNum)
528	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
529	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
530	Page.canvas.mpl_connect('pick_event', OnPick)
531	Page.canvas.mpl_connect('button_release_event', OnRelease)
532	Page.SetFocus()
533	self.G2plotNB.status.DestroyChildren()
534	if self.Contour:
535	Choice = (' key press','d: lower contour max','u: raise contour max',
536	'i: interpolation method','s: color scheme','c: contour off')
537	else:
538	if self.logPlot:
539	Choice = (' key press','n: log(I) off','l: offset left','r: offset right',
540	'c: contour on','q: toggle q plot','s: toggle single plot','+: no selection')
541	else:
542	Choice = (' key press','l: offset left','r: offset right','d: offset down',
543	'u: offset up','o: reset offset','n: log(I) on','c: contour on',
544	'q: toggle q plot','s: toggle single plot','+: no selection')
545	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
546	choices=Choice)
547	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
548	cb.SetValue(' key press')
549
550	PickId = self.PickId
551	PatternId = self.PatternId
552	colors=['b','g','r','c','m','k']
553	Lines = []
554	if self.SinglePlot:
555	Pattern = self.PatternTree.GetItemPyData(PatternId)
556	Pattern.append(self.PatternTree.GetItemText(PatternId))
557	PlotList = [Pattern,]
558	ParmList = [self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
559	self.PatternId, 'Instrument Parameters'))[1],]
560	else:
561	PlotList = []
562	ParmList = []
563	item, cookie = self.PatternTree.GetFirstChild(self.root)
564	while item:
565	if 'PWDR' in self.PatternTree.GetItemText(item):
566	Pattern = self.PatternTree.GetItemPyData(item)
567	if len(Pattern) < 3: # put name on end if needed
568	Pattern.append(self.PatternTree.GetItemText(item))
569	PlotList.append(Pattern)
570	ParmList.append(self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,
571	item,'Instrument Parameters'))[1])
572	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
573	Ymax = 1.0
574	lenX = 0
575	HKL = np.array(self.HKL)
576	for Pattern in PlotList:
577	xye = Pattern[1]
578	Ymax = max(Ymax,max(xye[1]))
579	offset = self.Offset[0]*Ymax/100.0
580	Title = 'Powder Patterns: '+os.path.split(self.GSASprojectfile)[1]
581	if self.logPlot:
582	Title = 'log('+Title+')'
583	Plot.set_title(Title)
584	if self.qPlot:
585	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
586	else:
587	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
588	Plot.set_ylabel('Intensity',fontsize=12)
589	if self.Contour:
590	ContourZ = []
591	ContourY = []
592	Nseq = 0
593	for N,Pattern in enumerate(PlotList):
594	Parms = ParmList[N]
595	ifpicked = False
596	LimitId = 0
597	xye = np.array(Pattern[1])
598	if PickId:
599	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
600	LimitId = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
601	if self.qPlot:
602	Id = G2gd.GetPatternTreeItemId(self,self.root, Pattern[2])
603	X = 4np.pinpsind(xye[0]/2.0)/Parms[1]
604	else:
605	X = xye[0]
606	if not lenX:
607	lenX = len(X)
608	Y = xye[1]+offset*N
609	if LimitId:
610	limits = np.array(self.PatternTree.GetItemPyData(LimitId))
611	if self.qPlot:
612	limits = 4np.pinpsind(limits/2.0)/Parms[1]
613	Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))
614	Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
615	if self.Contour:
616
617	if lenX == len(X):
618	ContourY.append(N)
619	ContourZ.append(Y)
620	ContourX = X
621	Nseq += 1
622	Plot.set_ylabel('Data sequence',fontsize=12)
623	else:
624	X += self.Offset[1].005N
625	if ifpicked:
626	Z = xye[3]+offset*N
627	W = xye[4]+offset*N
628	D = xye[5]+offsetN-Ymax.02
629	if self.Weight:
630	W2 = np.sqrt(xye[2])
631	D = W2-Ymax.02
632	if self.logPlot:
633	Plot.semilogy(X,Y,colors[N%6]+'+',picker=3.,clip_on=False,nonposy='mask')
634	Plot.semilogy(X,Z,colors[(N+1)%6],picker=False,nonposy='mask')
635	Plot.semilogy(X,W,colors[(N+2)%6],picker=False,nonposy='mask')
636	else:
637	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
638	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
639	Plot.plot(X,W,colors[(N+2)%6],picker=False)
640	Plot.plot(X,D,colors[(N+3)%6],picker=False)
641	Plot.axhline(0.,color=wx.BLACK)
642	Page.canvas.SetToolTipString('')
643	if self.PatternTree.GetItemText(PickId) == 'Peak List':
644	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
645	Page.canvas.SetToolTipString(tip)
646	data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List'))
647	for item in data:
648	if self.qPlot:
649	Lines.append(Plot.axvline(4math.pisind(item[0]/2.)/Parms[1],color=colors[N%6],picker=2.))
650	else:
651	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
652	if self.PatternTree.GetItemText(PickId) == 'Limits':
653	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
654	Page.canvas.SetToolTipString(tip)
655	data = self.LimitsTable.GetData()
656	else:
657	if self.logPlot:
658	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='clip')
659	else:
660	Plot.plot(X,Y,colors[N%6],picker=False)
661	if PickId and self.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
662	Values,Names = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1::2]
663	Parms = dict(zip(Names,Values))
664	try:
665	wave = Parms['Lam']
666	except KeyError:
667	wave = Parms['Lam1']
668	peaks = np.array((self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))))
669	for peak in peaks:
670	if self.qPlot:
671	Plot.axvline(4np.pisind(peak[0]/2.0)/wave,color='b')
672	else:
673	Plot.axvline(peak[0],color='b')
674	for hkl in self.HKL:
675	if self.qPlot:
676	Plot.axvline(4np.pisind(hkl[5]/2.0)/wave,color='r',dashes=(5,5))
677	else:
678	Plot.axvline(hkl[5],color='r',dashes=(5,5))
679	if self.Contour:
680	acolor = mpl.cm.get_cmap(self.ContourColor)
681	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
682	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
683	Page.figure.colorbar(Img)
684	else:
685	self.Lines = Lines
686	if not newPlot:
687	Page.toolbar.push_current()
688	Plot.set_xlim(xylim[0])
689	Plot.set_ylim(xylim[1])
690	xylim = []
691	Page.toolbar.push_current()
692	Page.toolbar.draw()
693	else:
694	Page.canvas.draw()
695	self.Pwdr = True
696
697	def PlotISFG(self,newPlot=False,type=''):
698	''' PLotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
699	or multiple plots with waterfall and contour plots as options
700	'''
701	if not type:
702	type = self.G2plotNB.plotList[self.G2plotNB.nb.GetSelection()]
703	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
704	return
705	superMinusOne = unichr(0xaf)+unichr(0xb9)
706
707	def OnPlotKeyPress(event):
708	newPlot = False
709	if event.key == 'u':
710	if self.Contour:
711	self.Cmax = min(1.0,self.Cmax*1.2)
712	elif self.Offset[0] < 100.:
713	self.Offset[0] += 1.
714	elif event.key == 'd':
715	if self.Contour:
716	self.Cmax = max(0.0,self.Cmax*0.8)
717	elif self.Offset[0] > 0.:
718	self.Offset[0] -= 1.
719	elif event.key == 'l':
720	self.Offset[1] -= 1.
721	elif event.key == 'r':
722	self.Offset[1] += 1.
723	elif event.key == 'o':
724	self.Offset = [0,0]
725	elif event.key == 'c':
726	newPlot = True
727	if self.Contour:
728	self.Contour = False
729	else:
730	self.Contour = True
731	self.SinglePlot = False
732	self.Offset = [0.,0.]
733	elif event.key == 's':
734	if self.Contour:
735	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
736	choice.sort()
737	dlg = wx.SingleChoiceDialog(self,'Select','Color scheme',choice)
738	if dlg.ShowModal() == wx.ID_OK:
739	sel = dlg.GetSelection()
740	self.ContourColor = choice[sel]
741	else:
742	self.ContourColor = 'Paired'
743	dlg.Destroy()
744	else:
745	if self.SinglePlot:
746	self.SinglePlot = False
747	else:
748	self.SinglePlot = True
749	elif event.key == 'i': #for smoothing contour plot
750	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
751	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
752	'mitchell','sinc','lanczos']
753	dlg = wx.SingleChoiceDialog(self,'Select','Interpolation',choice)
754	if dlg.ShowModal() == wx.ID_OK:
755	sel = dlg.GetSelection()
756	self.Interpolate = choice[sel]
757	else:
758	self.Interpolate = 'nearest'
759	dlg.Destroy()
760	elif event.key == 't' and not self.Contour:
761	if self.Legend:
762	self.Legend = False
763	else:
764	self.Legend = True
765
766
767	PlotISFG(self,newPlot=newPlot,type=type)
768
769	def OnKeyBox(event):
770	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index(type):
771	event.key = cb.GetValue()[0]
772	cb.SetValue(' key press')
773	OnPlotKeyPress(event)
774
775	def OnMotion(event):
776	xpos = event.xdata
777	if xpos: #avoid out of frame mouse position
778	ypos = event.ydata
779	Page.canvas.SetCursor(wx.CROSS_CURSOR)
780	try:
781	if self.Contour:
782	self.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
783	else:
784	self.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
785	except TypeError:
786	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
787
788	xylim = []
789	try:
790	plotNum = self.G2plotNB.plotList.index(type)
791	Page = self.G2plotNB.nb.GetPage(plotNum)
792	if not newPlot:
793	Plot = Page.figure.gca() #get previous plot & get limits
794	xylim = Plot.get_xlim(),Plot.get_ylim()
795	Page.figure.clf()
796	Plot = Page.figure.gca()
797	except ValueError:
798	newPlot = True
799	self.Cmax = 1.0
800	Plot = self.G2plotNB.addMpl(type).gca()
801	plotNum = self.G2plotNB.plotList.index(type)
802	Page = self.G2plotNB.nb.GetPage(plotNum)
803	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
804	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
805
806	Page.SetFocus()
807	self.G2plotNB.status.DestroyChildren()
808	if self.Contour:
809	Choice = (' key press','d: lower contour max','u: raise contour max',
810	'i: interpolation method','s: color scheme','c: contour off')
811	else:
812	Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
813	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
814	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
815	choices=Choice)
816	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
817	cb.SetValue(' key press')
818	PatternId = self.PatternId
819	PickId = self.PickId
820	Plot.set_title(type)
821	if type == 'G(R)':
822	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
823	else:
824	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
825	Plot.set_ylabel(r''+type,fontsize=14)
826	colors=['b','g','r','c','m','k']
827	name = self.PatternTree.GetItemText(PatternId)[4:]
828	Pattern = []
829	if self.SinglePlot:
830	name = self.PatternTree.GetItemText(PatternId)
831	name = type+name[4:]
832	Id = G2gd.GetPatternTreeItemId(self,PatternId,name)
833	Pattern = self.PatternTree.GetItemPyData(Id)
834	if Pattern:
835	Pattern.append(name)
836	PlotList = [Pattern,]
837	else:
838	PlotList = []
839	item, cookie = self.PatternTree.GetFirstChild(self.root)
840	while item:
841	if 'PDF' in self.PatternTree.GetItemText(item):
842	name = type+self.PatternTree.GetItemText(item)[4:]
843	Id = G2gd.GetPatternTreeItemId(self,item,name)
844	Pattern = self.PatternTree.GetItemPyData(Id)
845	if Pattern:
846	Pattern.append(name)
847	PlotList.append(Pattern)
848	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
849	PDFdata = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'PDF Controls'))
850	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
851	Xb = [0.,10.]
852	Yb = [0.,-40.np.pinumbDen]
853	Ymax = 1.0
854	lenX = 0
855	for Pattern in PlotList:
856	xye = Pattern[1]
857	Ymax = max(Ymax,max(xye[1]))
858	offset = self.Offset[0]*Ymax/100.0
859	if self.Contour:
860	ContourZ = []
861	ContourY = []
862	Nseq = 0
863	for N,Pattern in enumerate(PlotList):
864	xye = Pattern[1]
865	if PickId:
866	ifpicked = Pattern[2] == self.PatternTree.GetItemText(PatternId)
867	X = xye[0]
868	if not lenX:
869	lenX = len(X)
870	Y = xye[1]+offset*N
871	if self.Contour:
872	if lenX == len(X):
873	ContourY.append(N)
874	ContourZ.append(Y)
875	ContourX = X
876	Nseq += 1
877	Plot.set_ylabel('Data sequence',fontsize=12)
878	else:
879	X = xye[0]+self.Offset[1].005N
880	if ifpicked:
881	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
882	Page.canvas.SetToolTipString('')
883	else:
884	if self.Legend:
885	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
886	else:
887	Plot.plot(X,Y,colors[N%6],picker=False)
888	if type == 'G(R)':
889	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
890	elif type == 'F(Q)':
891	Plot.axhline(0.,color=wx.BLACK)
892	elif type == 'S(Q)':
893	Plot.axhline(1.,color=wx.BLACK)
894	if self.Contour:
895	acolor = mpl.cm.get_cmap(self.ContourColor)
896	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*self.Cmax,interpolation=self.Interpolate,
897	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
898	Page.figure.colorbar(Img)
899	elif self.Legend:
900	Plot.legend(loc='best')
901	if not newPlot:
902	Page.toolbar.push_current()
903	Plot.set_xlim(xylim[0])
904	Plot.set_ylim(xylim[1])
905	xylim = []
906	Page.toolbar.push_current()
907	Page.toolbar.draw()
908	else:
909	Page.canvas.draw()
910
911	def PlotXY(self,XY,newPlot=False,type=''):
912	'''simple plot of xy data, used for diagnostic purposes
913	'''
914	def OnMotion(event):
915	xpos = event.xdata
916	if xpos: #avoid out of frame mouse position
917	ypos = event.ydata
918	Page.canvas.SetCursor(wx.CROSS_CURSOR)
919	try:
920	self.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,type,ypos),1)
921	except TypeError:
922	self.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
923
924	try:
925	plotNum = self.G2plotNB.plotList.index(type)
926	Page = self.G2plotNB.nb.GetPage(plotNum)
927	if not newPlot:
928	Plot = Page.figure.gca()
929	xylim = Plot.get_xlim(),Plot.get_ylim()
930	Page.figure.clf()
931	Plot = Page.figure.gca()
932	except ValueError:
933	newPlot = True
934	Plot = self.G2plotNB.addMpl(type).gca()
935	plotNum = self.G2plotNB.plotList.index(type)
936	Page = self.G2plotNB.nb.GetPage(plotNum)
937	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
938
939	Page.SetFocus()
940	self.G2plotNB.status.DestroyChildren()
941	Plot.set_title(type)
942	Plot.set_xlabel(r'X',fontsize=14)
943	Plot.set_ylabel(r''+type,fontsize=14)
944	colors=['b','g','r','c','m','k']
945	Ymax = 1.0
946	lenX = 0
947	X,Y = XY[:2]
948	Ymax = max(Ymax,max(Y))
949	Plot.plot(X,Y,'k',picker=False)
950	if not newPlot:
951	Page.toolbar.push_current()
952	Plot.set_xlim(xylim[0])
953	Plot.set_ylim(xylim[1])
954	xylim = []
955	Page.toolbar.push_current()
956	Page.toolbar.draw()
957	else:
958	Page.canvas.draw()
959
960	def PlotPowderLines(self):
961	''' plotting of powder lines (i.e. no powder pattern) as sticks
962	'''
963	global HKL
964
965	def OnMotion(event):
966	xpos = event.xdata
967	if xpos: #avoid out of frame mouse position
968	Page.canvas.SetCursor(wx.CROSS_CURSOR)
969	self.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
970	if self.PickId and self.PatternTree.GetItemText(self.PickId) in ['Index Peak List','Unit Cells List']:
971	found = []
972	if len(HKL):
973	view = Page.toolbar._views.forward()[0][:2]
974	wid = view[1]-view[0]
975	found = HKL[np.where(np.fabs(HKL.T[5]-xpos) < 0.002*wid)]
976	if len(found):
977	h,k,l = found[0][:3]
978	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
979	else:
980	Page.canvas.SetToolTipString('')
981
982	try:
983	plotNum = self.G2plotNB.plotList.index('Powder Lines')
984	Page = self.G2plotNB.nb.GetPage(plotNum)
985	Page.figure.clf()
986	Plot = Page.figure.gca()
987	except ValueError:
988	Plot = self.G2plotNB.addMpl('Powder Lines').gca()
989	plotNum = self.G2plotNB.plotList.index('Powder Lines')
990	Page = self.G2plotNB.nb.GetPage(plotNum)
991	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
992
993	Page.SetFocus()
994	Plot.set_title('Powder Pattern Lines')
995	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
996	PickId = self.PickId
997	PatternId = self.PatternId
998	peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
999	for peak in peaks:
1000	Plot.axvline(peak[0],color='b')
1001	HKL = np.array(self.HKL)
1002	for hkl in self.HKL:
1003	Plot.axvline(hkl[5],color='r',dashes=(5,5))
1004	xmin = peaks[0][0]
1005	xmax = peaks[-1][0]
1006	delt = xmax-xmin
1007	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
1008	Plot.set_xlim(xlim)
1009	Page.canvas.draw()
1010	Page.toolbar.push_current()
1011
1012	def PlotPeakWidths(self):
1013	''' Plotting of instrument broadening terms as function of 2-theta (future TOF)
1014	Seen when "Instrument Parameters" chosen from powder pattern data tree
1015	'''
1016	PatternId = self.PatternId
1017	limitID = G2gd.GetPatternTreeItemId(self,PatternId, 'Limits')
1018	if limitID:
1019	limits = self.PatternTree.GetItemPyData(limitID)
1020	else:
1021	return
1022	instParms = self.PatternTree.GetItemPyData( \
1023	G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
1024	if instParms[0][0] in ['PXC','PNC']:
1025	lam = instParms[1][1]
1026	if len(instParms[1]) == 13:
1027	GU,GV,GW,LX,LY = instParms[0][6:11]
1028	else:
1029	GU,GV,GW,LX,LY = instParms[0][4:9]
1030	peakID = G2gd.GetPatternTreeItemId(self,PatternId, 'Peak List')
1031	if peakID:
1032	peaks = self.PatternTree.GetItemPyData(peakID)
1033	else:
1034	peaks = []
1035
1036	try:
1037	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1038	Page = self.G2plotNB.nb.GetPage(plotNum)
1039	Page.figure.clf()
1040	Plot = Page.figure.gca()
1041	except ValueError:
1042	Plot = self.G2plotNB.addMpl('Peak Widths').gca()
1043	plotNum = self.G2plotNB.plotList.index('Peak Widths')
1044	Page = self.G2plotNB.nb.GetPage(plotNum)
1045	Page.SetFocus()
1046
1047	Page.canvas.SetToolTipString('')
1048	colors=['b','g','r','c','m','k']
1049	Xmin,Xmax = limits[1]
1050	Xmin = min(0.5,max(Xmin,1))
1051	Xmin /= 2
1052	Xmax /= 2
1053	nPts = 100
1054	delt = (Xmax-Xmin)/nPts
1055	thetas = []
1056	for i in range(nPts):
1057	thetas.append(Xmin+i*delt)
1058	X = []
1059	Y = []
1060	Z = []
1061	W = []
1062	V = []
1063	sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
1064	gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
1065	gamFW = lambda s,g: math.exp(math.log(s*5+2.69269s*4g+2.42843s3g*2+4.47163s*2g*3+0.07842sg4+g*5)/5.)
1066	gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
1067	for theta in thetas:
1068	X.append(4.0math.pisind(theta)/lam) #q
1069	s = sig(theta,GU,GV,GW)
1070	g = gam(theta,LX,LY)
1071	G = gamFW(g,s)
1072	H = gamFW2(g,s)
1073	Y.append(s/tand(theta))
1074	Z.append(g/tand(theta))
1075	W.append(G/tand(theta))
1076	V.append(H/tand(theta))
1077	Plot.set_title('Instrument and sample peak widths')
1078	Plot.set_ylabel(r'$\Delta q/q, \Delta d/d$',fontsize=14)
1079	Plot.set_xlabel(r'$q, \AA^{-1}$',fontsize=14)
1080	Plot.plot(X,Y,color='r',label='Gaussian')
1081	Plot.plot(X,Z,color='g',label='Lorentzian')
1082	Plot.plot(X,W,color='b',label='G+L')
1083	Plot.plot(X,V,color='k',label='G+L2')
1084	X = []
1085	Y = []
1086	Z = []
1087	W = []
1088	V = []
1089	for peak in peaks:
1090	X.append(4.0math.pisind(peak[0]/2.0)/lam)
1091	try:
1092	s = 1.17741math.sqrt(peak[4])math.pi/18000.
1093	except ValueError:
1094	s = 0.01
1095	g = peak[6]*math.pi/18000.
1096	G = gamFW(g,s)
1097	H = gamFW2(g,s)
1098	Y.append(s/tand(peak[0]/2.))
1099	Z.append(g/tand(peak[0]/2.))
1100	W.append(G/tand(peak[0]/2.))
1101	V.append(H/tand(peak[0]/2.))
1102	Plot.plot(X,Y,'+',color='r',label='G peak')
1103	Plot.plot(X,Z,'+',color='g',label='L peak')
1104	Plot.plot(X,W,'+',color='b',label='G+L peak')
1105	Plot.plot(X,V,'+',color='k',label='G+L2 peak')
1106	Plot.legend(loc='best')
1107	Page.canvas.draw()
1108
1109	def PlotStrain(self,data):
1110	'''Plot 3D microstrain figure. In this instance data is for a phase
1111	'''
1112	PatternId = self.PatternId
1113	generalData = data['General']
1114	SGData = generalData['SGData']
1115	MuStrKeys = G2spc.MustrainNames(SGData)
1116	cell = generalData['Cell'][1:]
1117	A,B = G2lat.cell2AB(cell[:6])
1118	Vol = cell[6]
1119	useList = data['Histograms']
1120	for item in useList:
1121	if useList[item]['Show']:
1122	break
1123	else:
1124	self.G2plotNB.Delete('Microstrain')
1125	return #nothing to show!!
1126
1127	numPlots = len(useList)
1128
1129	try:
1130	plotNum = self.G2plotNB.plotList.index('Microstrain')
1131	Page = self.G2plotNB.nb.GetPage(plotNum)
1132	Page.figure.clf()
1133	Plot = mp3d.Axes3D(Page.figure)
1134	if not Page.IsShown():
1135	Page.Show()
1136	except ValueError:
1137	Plot = mp3d.Axes3D(self.G2plotNB.add3D('Microstrain'))
1138	plotNum = self.G2plotNB.plotList.index('Microstrain')
1139	Page = self.G2plotNB.nb.GetPage(plotNum)
1140	Page.SetFocus()
1141	self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
1142
1143	for item in useList:
1144	if useList[item]['Show']:
1145	muStrain = useList[item]['Mustrain']
1146	PHI = np.linspace(0.,360.,30,True)
1147	PSI = np.linspace(0.,180.,30,True)
1148	X = np.outer(npsind(PHI),npsind(PSI))
1149	Y = np.outer(npcosd(PHI),npsind(PSI))
1150	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
1151	if muStrain[0] == 'isotropic':
1152	muiso = muStrain[1][0]*math.pi/0.018 #centidegrees to radians!
1153	X *= muiso
1154	Y *= muiso
1155	Z *= muiso
1156
1157	elif muStrain[0] == 'uniaxial':
1158	def uniaxMustrain(xyz,muiso,muaniso,axes):
1159	cp = abs(np.dot(xyz,axes))
1160	S = muiso+muaniso*cp
1161	return Sxyzmath.pi/0.018 #centidegrees to radians!
1162	muiso,muaniso = muStrain[1][:2]
1163	axes = np.inner(A,np.array(muStrain[3]))
1164	axes /= nl.norm(axes)
1165	Shkl = np.array(muStrain[1])
1166	Shape = X.shape[0]
1167	XYZ = np.dstack((X,Y,Z))
1168	XYZ = np.nan_to_num(np.apply_along_axis(uniaxMustrain,2,XYZ,muiso,muaniso,axes))
1169	X,Y,Z = np.dsplit(XYZ,3)
1170	X = X[:,:,0]
1171	Y = Y[:,:,0]
1172	Z = Z[:,:,0]
1173
1174	elif muStrain[0] == 'generalized':
1175	def genMustrain(xyz,SGData,A,Shkl):
1176	uvw = np.inner(A.T,xyz)
1177	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
1178	sum = np.sqrt(np.sum(np.multiply(Shkl,Strm)))*math.pi/0.018 #centidegrees to radians!
1179	return sum*xyz
1180	Shkl = np.array(muStrain[4])
1181	if np.any(Shkl):
1182	Shape = X.shape[0]
1183	XYZ = np.dstack((X,Y,Z))
1184	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
1185	X,Y,Z = np.dsplit(XYZ,3)
1186	X = X[:,:,0]
1187	Y = Y[:,:,0]
1188	Z = Z[:,:,0]
1189
1190	if np.any(X) and np.any(Y) and np.any(Z):
1191	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g')
1192
1193	Plot.set_xlabel('X')
1194	Plot.set_ylabel('Y')
1195	Plot.set_zlabel('Z')
1196	Page.canvas.draw()
1197
1198	def PlotTexture(self,data,newPlot=False,Start=False):
1199	'''Pole figure, inverse pole figure(?), 3D pole distribution and 3D inverse pole distribution(?)
1200	plotting; Need way to select
1201	pole figure or pole distribution to be displayed - do in key enter menu
1202	dict generalData contains all phase info needed which is in data
1203	'''
1204
1205	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1206	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
1207	PatternId = self.PatternId
1208	generalData = data['General']
1209	SGData = generalData['SGData']
1210	textureData = generalData['SH Texture']
1211	if not textureData['Order']:
1212	self.G2plotNB.Delete('Texture')
1213	return #no plot!!
1214	SHData = generalData['SH Texture']
1215	SHCoef = SHData['SH Coeff'][1]
1216	cell = generalData['Cell'][1:7]
1217	Amat,Bmat = G2lat.cell2AB(cell)
1218	sq2 = 1.0/math.sqrt(2.0)
1219
1220	def rp2xyz(r,p):
1221	z = npcosd(r)
1222	xy = np.sqrt(1.-z**2)
1223	return xynpsind(p),xynpcosd(p),z
1224
1225	def OnMotion(event):
1226	SHData = data['General']['SH Texture']
1227	if event.xdata and event.ydata: #avoid out of frame errors
1228	xpos = event.xdata
1229	ypos = event.ydata
1230	if 'Inverse' in SHData['PlotType']:
1231	r = xpos2+ypos2
1232	if r <= 1.0:
1233	if 'equal' in self.Projection:
1234	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
1235	else:
1236	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
1237	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
1238	xyz = np.inner(Amat.T,np.array([rp2xyz(r,p)]))
1239	y,x,z = list(xyz/np.max(np.abs(xyz)))
1240
1241	self.G2plotNB.status.SetFields(['',
1242	'psi =%9.3f, beta =%9.3f, MRD =%9.3f xyz=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
1243
1244	elif 'Axial' in SHData['PlotType']:
1245	pass
1246
1247	else: #ordinary pole figure
1248	z = xpos2+ypos2
1249	if z <= 1.0:
1250	z = np.sqrt(z)
1251	if 'equal' in self.Projection:
1252	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
1253	else:
1254	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
1255	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
1256	self.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
1257
1258	try:
1259	plotNum = self.G2plotNB.plotList.index('Texture')
1260	Page = self.G2plotNB.nb.GetPage(plotNum)
1261	Page.figure.clf()
1262	Plot = Page.figure.gca()
1263	if not Page.IsShown():
1264	Page.Show()
1265	except ValueError:
1266	Plot = self.G2plotNB.addMpl('Texture').gca()
1267	plotNum = self.G2plotNB.plotList.index('Texture')
1268	Page = self.G2plotNB.nb.GetPage(plotNum)
1269	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1270
1271	Page.SetFocus()
1272	self.G2plotNB.status.SetFields(['',''])
1273	PH = np.array(SHData['PFhkl'])
1274	phi,beta = G2lat.CrsAng(PH,cell,SGData)
1275	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
1276	PX = np.array(SHData['PFxyz'])
1277	gam = atan2d(PX[0],PX[1])
1278	xy = math.sqrt(PX[0]2+PX[1]2)
1279	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
1280	psi = asind(xy/xyz)
1281	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
1282	if 'Axial' in SHData['PlotType']:
1283	X = np.linspace(0,90.0,26)
1284	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
1285	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
1286	Plot.legend(loc='best')
1287	Plot.set_title('Axial distribution for HKL='+str(SHData['PFhkl']))
1288	Plot.set_xlabel(r'$\psi$',fontsize=16)
1289	Plot.set_ylabel('MRD',fontsize=14)
1290
1291	else:
1292	npts = 201
1293	if 'Inverse' in SHData['PlotType']:
1294	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1295	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1296	if 'equal' in self.Projection:
1297	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1298	else:
1299	R = np.where(R <= 1.,2.*npatand(R),0.0)
1300	Z = np.zeros_like(R)
1301	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
1302	Z = np.reshape(Z,(npts,npts))
1303	CS = Plot.contour(Y,X,Z,aspect='equal')
1304	Plot.clabel(CS,fontsize=9,inline=1)
1305	Img = Plot.imshow(Z.T,aspect='equal',cmap=self.ContourColor,extent=[-1,1,-1,1])
1306	if newPlot:
1307	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1308	newPlot = False
1309	Plot.set_title('Inverse pole figure for XYZ='+str(SHData['PFxyz']))
1310	Plot.set_xlabel(self.Projection.capitalize()+' projection')
1311
1312	else:
1313	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
1314	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
1315	if 'equal' in self.Projection:
1316	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
1317	else:
1318	R = np.where(R <= 1.,2.*npatand(R),0.0)
1319	Z = np.zeros_like(R)
1320	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
1321	Z = np.reshape(Z,(npts,npts))
1322	CS = Plot.contour(Y,X,Z,aspect='equal')
1323	Plot.clabel(CS,fontsize=9,inline=1)
1324	Img = Plot.imshow(Z.T,aspect='equal',cmap=self.ContourColor,extent=[-1,1,-1,1])
1325	if newPlot:
1326	# Page.figure.colorbar(Img) #colorbar fails - crashes gsasii
1327	newPlot = False
1328	Plot.set_title('Pole figure for HKL='+str(SHData['PFhkl']))
1329	Plot.set_xlabel(self.Projection.capitalize()+' projection')
1330	Page.canvas.draw()
1331
1332
1333	def PlotExposedImage(self,newPlot=False,event=None):
1334	'''General access module for 2D image plotting
1335	'''
1336	plotNo = self.G2plotNB.nb.GetSelection()
1337	if self.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
1338	PlotImage(self,newPlot,event,newImage=True)
1339	elif self.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
1340	PlotIntegration(self,newPlot,event)
1341
1342	def PlotImage(self,newPlot=False,event=None,newImage=True):
1343	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
1344	masks, etc.
1345	'''
1346	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
1347	import numpy.ma as ma
1348	Dsp = lambda tth,wave: wave/(2.*sind(tth/2.))
1349	global Data,Masks
1350	colors=['b','g','r','c','m','k']
1351	Data = self.PatternTree.GetItemPyData(
1352	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1353	Masks = self.PatternTree.GetItemPyData(
1354	G2gd.GetPatternTreeItemId(self,self.Image, 'Masks'))
1355
1356	def OnImMotion(event):
1357	Page.canvas.SetToolTipString('')
1358	sizexy = Data['size']
1359	if event.xdata and event.ydata: #avoid out of frame errors
1360	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1361	item = self.itemPicked
1362	pixelSize = Data['pixelSize']
1363	scalex = 1000./pixelSize[0]
1364	scaley = 1000./pixelSize[1]
1365	if item and self.PatternTree.GetItemText(self.PickId) == 'Image Controls':
1366	if 'Text' in str(item):
1367	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
1368	else:
1369	xcent,ycent = Data['center']
1370	xpos = event.xdata-xcent
1371	ypos = event.ydata-ycent
1372	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
1373	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
1374	Page.canvas.SetToolTipString('%6d deg'%(azm))
1375	elif 'line1' in str(item) or 'line2' in str(item):
1376	Page.canvas.SetToolTipString('%8.3fdeg'%(tth))
1377	else:
1378	xpos = event.xdata
1379	ypos = event.ydata
1380	xpix = xpos*scalex
1381	ypix = ypos*scaley
1382	Int = 0
1383	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
1384	Int = self.ImageZ[ypix][xpix]
1385	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1386	Q = 2.*math.pi/dsp
1387	if self.setPoly:
1388	self.G2plotNB.status.SetFields(['','Polygon mask pick - LB next point, RB close polygon'])
1389	else:
1390	self.G2plotNB.status.SetFields(\
1391	['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)])
1392
1393	def OnImPlotKeyPress(event):
1394	try:
1395	PickName = self.PatternTree.GetItemText(self.PickId)
1396	except TypeError:
1397	return
1398	if PickName == 'Masks':
1399	Xpos = event.xdata
1400	if not Xpos: #got point out of frame
1401	return
1402	Ypos = event.ydata
1403	if event.key == 's':
1404	Masks['Points'].append([Xpos,Ypos,1.])
1405	elif event.key == 'r':
1406	tth = G2img.GetTth(Xpos,Ypos,Data)
1407	Masks['Rings'].append([tth,0.1])
1408	elif event.key == 'a':
1409	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
1410	azm = int(azm)
1411	Masks['Arcs'].append([tth,[azm-5,azm+5],0.1])
1412	elif event.key == 'p':
1413	self.setPoly = True
1414	Masks['Polygons'].append([])
1415	self.G2plotNB.status.SetFields(['','Polygon mask active - LB pick next point, RB close polygon'])
1416	G2imG.UpdateMasks(self,Masks)
1417	elif PickName == 'Image Controls':
1418	if event.key == 'c':
1419	Xpos = event.xdata
1420	if not Xpos: #got point out of frame
1421	return
1422	Ypos = event.ydata
1423	dlg = wx.MessageDialog(self,'Are you sure you want to change the center?',
1424	'Center change',style=wx.OK\|wx.CANCEL)
1425	try:
1426	if dlg.ShowModal() == wx.ID_OK:
1427	print 'move center to: ',Xpos,Ypos
1428	Data['center'] = [Xpos,Ypos]
1429	G2imG.UpdateImageControls(self,Data,Masks)
1430	finally:
1431	dlg.Destroy()
1432	elif event.key == 'l':
1433	if self.logPlot:
1434	self.logPlot = False
1435	else:
1436	self.logPlot = True
1437	PlotImage(self,newImage=True)
1438
1439	def OnKeyBox(event):
1440	if self.G2plotNB.nb.GetSelection() == self.G2plotNB.plotList.index('2D Powder Image'):
1441	event.key = cb.GetValue()[0]
1442	cb.SetValue(' key press')
1443	if event.key in 'l':
1444	OnImPlotKeyPress(event)
1445
1446	def OnImPick(event):
1447	if self.PatternTree.GetItemText(self.PickId) not in ['Image Controls','Masks']:
1448	return
1449	if self.setPoly:
1450	polygon = Masks['Polygons'][-1]
1451	xpos,ypos = event.mouseevent.xdata,event.mouseevent.ydata
1452	if xpos and ypos: #point inside image
1453	if len(polygon) > 2 and event.mouseevent.button == 3:
1454	x0,y0 = polygon[0]
1455	polygon.append([x0,y0])
1456	self.setPoly = False
1457	self.G2plotNB.status.SetFields(['','Polygon closed - RB drag a vertex to change shape'])
1458	else:
1459	self.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(xpos,ypos)])
1460	polygon.append([xpos,ypos])
1461	G2imG.UpdateMasks(self,Masks)
1462	else:
1463	if self.itemPicked is not None: return
1464	self.itemPicked = event.artist
1465	self.mousePicked = event.mouseevent
1466
1467	def OnImRelease(event):
1468	try:
1469	PickName = self.PatternTree.GetItemText(self.PickId)
1470	except TypeError:
1471	return
1472	if PickName not in ['Image Controls','Masks']:
1473	return
1474	pixelSize = Data['pixelSize']
1475	scalex = 1000./pixelSize[0]
1476	scaley = 1000./pixelSize[1]
1477	pixLimit = Data['pixLimit']
1478	if self.itemPicked is None and PickName == 'Image Controls':
1479	# sizexy = Data['size']
1480	Xpos = event.xdata
1481	if not (Xpos and self.ifGetRing): #got point out of frame
1482	return
1483	Ypos = event.ydata
1484	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
1485	if event.button == 1:
1486	Xpix = Xpos*scalex
1487	Ypix = Ypos*scaley
1488	xpos,ypos,I,J = G2img.ImageLocalMax(self.ImageZ,pixLimit,Xpix,Ypix)
1489	if I and J:
1490	xpos += .5 #shift to pixel center
1491	ypos += .5
1492	xpos /= scalex #convert to mm
1493	ypos /= scaley
1494	Data['ring'].append([xpos,ypos])
1495	elif event.button == 3:
1496	self.dataFrame.GetStatusBar().SetStatusText('Calibrating...')
1497	if G2img.ImageCalibrate(self,Data):
1498	self.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check')
1499	print 'Calibration successful'
1500	else:
1501	self.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose')
1502	print 'Calibration failed'
1503	self.ifGetRing = False
1504	G2imG.UpdateImageControls(self,Data,Masks)
1505	return
1506	PlotImage(self,newImage=False)
1507	return
1508	else:
1509	xpos = event.xdata
1510	if xpos: #avoid out of frame mouse position
1511	ypos = event.ydata
1512	if self.ifGetRing: #delete a calibration ring pick
1513	xypos = [xpos,ypos]
1514	rings = Data['ring']
1515	for ring in rings:
1516	if np.allclose(ring,xypos,.01,0):
1517	rings.remove(ring)
1518	else:
1519	tth,azm,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
1520	itemPicked = str(self.itemPicked)
1521	if 'Line2D' in itemPicked and PickName == 'Image Controls':
1522	if 'line1' in itemPicked:
1523	Data['IOtth'][0] = max(tth,0.001)
1524	elif 'line2' in itemPicked:
1525	Data['IOtth'][1] = tth
1526	elif 'line3' in itemPicked:
1527	Data['LRazimuth'][0] = int(azm)
1528	if Data['fullIntegrate']:
1529	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
1530	elif 'line4' in itemPicked and not Data['fullIntegrate']:
1531	Data['LRazimuth'][1] = int(azm)
1532
1533	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
1534	Data['LRazimuth'][0] -= 360
1535
1536	azLim = np.array(Data['LRazimuth'])
1537	if np.any(azLim>360):
1538	azLim -= 360
1539	Data['LRazimuth'] = list(azLim)
1540
1541	if Data['IOtth'][0] > Data['IOtth'][1]:
1542	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
1543
1544	self.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
1545	self.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
1546	self.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
1547	self.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
1548	elif 'Circle' in itemPicked and PickName == 'Masks':
1549	spots = Masks['Points']
1550	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
1551	newPos = np.array([float(newPos[0]),float(newPos[1])])
1552	for spot in spots:
1553	if np.allclose(np.array([spot[:2]]),newPos):
1554	spot[:2] = xpos,ypos
1555	G2imG.UpdateMasks(self,Masks)
1556	elif 'Line2D' in itemPicked and PickName == 'Masks':
1557	Obj = self.itemPicked.findobj()
1558	rings = Masks['Rings']
1559	arcs = Masks['Arcs']
1560	polygons = Masks['Polygons']
1561	for ring in self.ringList:
1562	if Obj == ring[0]:
1563	rN = ring[1]
1564	if ring[2] == 'o':
1565	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)-rings[rN][1]/2.
1566	else:
1567	rings[rN][0] = G2img.GetTth(xpos,ypos,Data)+rings[rN][1]/2.
1568	for arc in self.arcList:
1569	if Obj == arc[0]:
1570	aN = arc[1]
1571	if arc[2] == 'o':
1572	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)-arcs[aN][2]/2
1573	elif arc[2] == 'i':
1574	arcs[aN][0] = G2img.GetTth(xpos,ypos,Data)+arcs[aN][2]/2
1575	elif arc[2] == 'l':
1576	arcs[aN][1][0] = int(G2img.GetAzm(xpos,ypos,Data))
1577	else:
1578	arcs[aN][1][1] = int(G2img.GetAzm(xpos,ypos,Data))
1579	for poly in self.polyList:
1580	if Obj == poly[0]:
1581	ind = self.itemPicked.contains(self.mousePicked)[1]['ind'][0]
1582	oldPos = np.array([self.mousePicked.xdata,self.mousePicked.ydata])
1583	pN = poly[1]
1584	for i,xy in enumerate(polygons[pN]):
1585	if np.allclose(np.array([xy]),oldPos,atol=1.0):
1586	polygons[pN][i] = xpos,ypos
1587	G2imG.UpdateMasks(self,Masks)
1588	# else: #keep for future debugging
1589	# print str(self.itemPicked),event.xdata,event.ydata,event.button
1590	PlotImage(self,newImage=True)
1591	self.itemPicked = None
1592
1593	try:
1594	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1595	Page = self.G2plotNB.nb.GetPage(plotNum)
1596	if not newPlot:
1597	Plot = Page.figure.gca() #get previous powder plot & get limits
1598	xylim = Plot.get_xlim(),Plot.get_ylim()
1599	if newImage:
1600	Page.figure.clf()
1601	Plot = Page.figure.gca() #get a fresh plot after clf()
1602
1603	except ValueError:
1604	Plot = self.G2plotNB.addMpl('2D Powder Image').gca()
1605	plotNum = self.G2plotNB.plotList.index('2D Powder Image')
1606	Page = self.G2plotNB.nb.GetPage(plotNum)
1607	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
1608	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
1609	Page.canvas.mpl_connect('pick_event', OnImPick)
1610	Page.canvas.mpl_connect('button_release_event', OnImRelease)
1611	xylim = []
1612	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
1613	Page.SetFocus()
1614	Title = self.PatternTree.GetItemText(self.Image)[4:]
1615	self.G2plotNB.status.DestroyChildren()
1616	if self.logPlot:
1617	Title = 'log('+Title+')'
1618	Plot.set_title(Title)
1619	try:
1620	if self.PatternTree.GetItemText(self.PickId) in ['Image Controls',]:
1621	if self.logPlot:
1622	Choice = (' key press','l: log(I) off')
1623	else:
1624	Choice = (' key press','l: log(I) on')
1625	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
1626	choices=Choice)
1627	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
1628	cb.SetValue(' key press')
1629	except TypeError:
1630	pass
1631	size,imagefile = self.PatternTree.GetItemPyData(self.Image)
1632	if imagefile != self.oldImagefile:
1633	imagefile = G2IO.CheckImageFile(self,imagefile)
1634	if not imagefile:
1635	self.G2plotNB.Delete('2D Powder Image')
1636	return
1637	self.PatternTree.SetItemPyData(self.Image,[size,imagefile])
1638	self.ImageZ = G2IO.GetImageData(self,imagefile,imageOnly=True)
1639	# print self.ImageZ.shape,self.ImageZ.size,Data['size'] #might be useful debugging line
1640	self.oldImagefile = imagefile
1641
1642	imScale = 1
1643	if len(self.ImageZ) > 1024:
1644	imScale = len(self.ImageZ)/1024
1645	sizexy = Data['size']
1646	pixelSize = Data['pixelSize']
1647	scalex = 1000./pixelSize[0]
1648	scaley = 1000./pixelSize[1]
1649	Xmax = sizexy[0]*pixelSize[0]/1000.
1650	Ymax = sizexy[1]*pixelSize[1]/1000.
1651	xlim = (0,Xmax)
1652	ylim = (Ymax,0)
1653	Imin,Imax = Data['range'][1]
1654	acolor = mpl.cm.get_cmap(Data['color'])
1655	xcent,ycent = Data['center']
1656	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
1657	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
1658	#do threshold mask - "real" mask - others are just bondaries
1659	Zlim = Masks['Thresholds'][1]
1660	wx.BeginBusyCursor()
1661	try:
1662
1663	if newImage:
1664	MA = ma.masked_greater(ma.masked_less(self.ImageZ,Zlim[0]),Zlim[1])
1665	MaskA = ma.getmaskarray(MA)
1666	A = G2img.ImageCompress(MA,imScale)
1667	AM = G2img.ImageCompress(MaskA,imScale)
1668	if self.logPlot:
1669	A = np.log(A)
1670	AM = np.log(AM)
1671	Imin,Imax = [np.amin(A),np.amax(A)]
1672	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
1673	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
1674	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
1675	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
1676	if self.setPoly:
1677	Img.set_picker(True)
1678
1679	Plot.plot(xcent,ycent,'x')
1680	if Data['showLines']:
1681	LRAzim = Data['LRazimuth'] #NB: integers
1682	Nazm = Data['outAzimuths']
1683	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
1684	AzmthOff = Data['azmthOff']
1685	IOtth = Data['IOtth']
1686	wave = Data['wavelength']
1687	dspI = wave/(2.0*sind(IOtth[0]/2.0))
1688	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
1689	dspO = wave/(2.0*sind(IOtth[1]/2.0))
1690	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
1691	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
1692	if ellI:
1693	xyI = []
1694	for azm in Azm:
1695	xyI.append(G2img.GetDetectorXY(dspI,azm-90.,Data))
1696	xyI = np.array(xyI)
1697	arcxI,arcyI = xyI.T
1698	Plot.plot(arcxI,arcyI,picker=3)
1699	if ellO:
1700	xyO = []
1701	for azm in Azm:
1702	xyO.append(G2img.GetDetectorXY(dspO,azm-90.,Data))
1703	xyO = np.array(xyO)
1704	arcxO,arcyO = xyO.T
1705	Plot.plot(arcxO,arcyO,picker=3)
1706	if ellO and ellI:
1707	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
1708	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
1709	for i in range(Nazm):
1710	cake = LRAzim[0]+i*delAzm
1711	ind = np.searchsorted(Azm,cake)
1712	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
1713
1714	for xring,yring in Data['ring']:
1715	Plot.plot(xring,yring,'r+',picker=3)
1716	if Data['setRings']:
1717	# rings = np.concatenate((Data['rings']),axis=0)
1718	N = 0
1719	for ring in Data['rings']:
1720	xring,yring = np.array(ring).T[:2]
1721	Plot.plot(xring,yring,'+',color=colors[N%6])
1722	N += 1
1723	for ellipse in Data['ellipses']:
1724	cent,phi,[width,height],col = ellipse
1725	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
1726	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
1727	#masks - mask lines numbered after integration limit lines
1728	spots = Masks['Points']
1729	rings = Masks['Rings']
1730	arcs = Masks['Arcs']
1731	polygons = Masks['Polygons']
1732	for x,y,d in spots:
1733	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
1734	self.ringList = []
1735	for iring,(tth,thick) in enumerate(rings):
1736	wave = Data['wavelength']
1737	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data))),2)
1738	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth-thick/2.,wave),Data))),2)
1739	self.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
1740	self.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
1741	self.arcList = []
1742	for iarc,(tth,azm,thick) in enumerate(arcs):
1743	wave = Data['wavelength']
1744	x1,y1 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(tth+thick/2.,wave),Data),azm)),2)
1745	x2,y2 = np.hsplit(np.array(G2img.makeIdealRing(G2img.GetEllipse(Dsp(max(0.01,tth-thick/2.),wave),Data),azm)),2)
1746	self.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
1747	self.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
1748	self.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
1749	self.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
1750	self.polyList = []
1751	for ipoly,polygon in enumerate(polygons):
1752	x,y = np.hsplit(np.array(polygon),2)
1753	self.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
1754	Plot.plot(x,y,'r')
1755	if newImage:
1756	colorBar = Page.figure.colorbar(Img)
1757	Plot.set_xlim(xlim)
1758	Plot.set_ylim(ylim)
1759	if not newPlot and xylim:
1760	Page.toolbar.push_current()
1761	Plot.set_xlim(xylim[0])
1762	Plot.set_ylim(xylim[1])
1763	xylim = []
1764	Page.toolbar.push_current()
1765	Page.toolbar.draw()
1766	else:
1767	Page.canvas.draw()
1768	finally:
1769	wx.EndBusyCursor()
1770
1771	def PlotIntegration(self,newPlot=False,event=None):
1772	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
1773	'''
1774
1775	def OnMotion(event):
1776	Page.canvas.SetToolTipString('')
1777	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1778	azm = event.ydata
1779	tth = event.xdata
1780	if azm and tth:
1781	self.G2plotNB.status.SetFields(\
1782	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1783
1784	try:
1785	plotNum = self.G2plotNB.plotList.index('2D Integration')
1786	Page = self.G2plotNB.nb.GetPage(plotNum)
1787	if not newPlot:
1788	Plot = Page.figure.gca() #get previous plot & get limits
1789	xylim = Plot.get_xlim(),Plot.get_ylim()
1790	Page.figure.clf()
1791	Plot = Page.figure.gca() #get a fresh plot after clf()
1792
1793	except ValueError:
1794	Plot = self.G2plotNB.addMpl('2D Integration').gca()
1795	plotNum = self.G2plotNB.plotList.index('2D Integration')
1796	Page = self.G2plotNB.nb.GetPage(plotNum)
1797	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1798	Page.views = False
1799	view = False
1800	if not event:
1801	Page.SetFocus()
1802
1803	Data = self.PatternTree.GetItemPyData(
1804	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1805	image = self.Integrate[0]
1806	xsc = self.Integrate[1]
1807	ysc = self.Integrate[2]
1808	Imin,Imax = Data['range'][1]
1809	acolor = mpl.cm.get_cmap(Data['color'])
1810	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1811	Plot.set_ylabel('azimuth',fontsize=12)
1812	Plot.set_xlabel('2-theta',fontsize=12)
1813	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
1814	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
1815	colorBar = Page.figure.colorbar(Img)
1816	if Data['setRings'] and Data['rings']:
1817	rings = np.concatenate((Data['rings']),axis=0)
1818	for xring,yring,dsp in rings:
1819	x,y = G2img.GetTthAzm(xring,yring,Data)
1820	Plot.plot(x,y,'r+')
1821	if Data['ellipses']:
1822	for ellipse in Data['ellipses']:
1823	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1824	x,y = np.hsplit(ring,2)
1825	tth,azm = G2img.GetTthAzm(x,y,Data)
1826	azm = np.where(azm < 0.,azm+360,azm)
1827	Plot.plot(tth,azm,'b,')
1828	if not newPlot:
1829	Page.toolbar.push_current()
1830	Plot.set_xlim(xylim[0])
1831	Plot.set_ylim(xylim[1])
1832	xylim = []
1833	Page.toolbar.push_current()
1834	Page.toolbar.draw()
1835	else:
1836	Page.canvas.draw()
1837
1838	def PlotTRImage(self,tax,tay,taz,newPlot=False):
1839	'''a test plot routine - not normally used
1840	'''
1841
1842	def OnMotion(event):
1843	Page.canvas.SetToolTipString('')
1844	Page.canvas.SetCursor(wx.CROSS_CURSOR)
1845	azm = event.xdata
1846	tth = event.ydata
1847	if azm and tth:
1848	self.G2plotNB.status.SetFields(\
1849	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
1850
1851	try:
1852	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1853	Page = self.G2plotNB.nb.GetPage(plotNum)
1854	if not newPlot:
1855	Plot = Page.figure.gca() #get previous plot & get limits
1856	xylim = Plot.get_xlim(),Plot.get_ylim()
1857	Page.figure.clf()
1858	Plot = Page.figure.gca() #get a fresh plot after clf()
1859
1860	except ValueError:
1861	Plot = self.G2plotNB.addMpl('2D Transformed Powder Image').gca()
1862	plotNum = self.G2plotNB.plotList.index('2D Transformed Powder Image')
1863	Page = self.G2plotNB.nb.GetPage(plotNum)
1864	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
1865	Page.views = False
1866	view = False
1867	Page.SetFocus()
1868
1869	Data = self.PatternTree.GetItemPyData(
1870	G2gd.GetPatternTreeItemId(self,self.Image, 'Image Controls'))
1871	Imin,Imax = Data['range'][1]
1872	step = (Imax-Imin)/5.
1873	V = np.arange(Imin,Imax,step)
1874	acolor = mpl.cm.get_cmap(Data['color'])
1875	Plot.set_title(self.PatternTree.GetItemText(self.Image)[4:])
1876	Plot.set_xlabel('azimuth',fontsize=12)
1877	Plot.set_ylabel('2-theta',fontsize=12)
1878	Plot.contour(tax,tay,taz,V,cmap=acolor)
1879	if Data['showLines']:
1880	IOtth = Data['IOtth']
1881	if Data['fullIntegrate']:
1882	LRAzim = [-180,180]
1883	else:
1884	LRAzim = Data['LRazimuth'] #NB: integers
1885	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
1886	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
1887	if not Data['fullIntegrate']:
1888	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
1889	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
1890	if Data['setRings']:
1891	rings = np.concatenate((Data['rings']),axis=0)
1892	for xring,yring,dsp in rings:
1893	x,y = G2img.GetTthAzm(xring,yring,Data)
1894	Plot.plot(y,x,'r+')
1895	if Data['ellipses']:
1896	for ellipse in Data['ellipses']:
1897	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
1898	x,y = np.hsplit(ring,2)
1899	tth,azm = G2img.GetTthAzm(x,y,Data)
1900	Plot.plot(azm,tth,'b,')
1901	if not newPlot:
1902	Page.toolbar.push_current()
1903	Plot.set_xlim(xylim[0])
1904	Plot.set_ylim(xylim[1])
1905	xylim = []
1906	Page.toolbar.push_current()
1907	Page.toolbar.draw()
1908	else:
1909	Page.canvas.draw()
1910
1911	def PlotStructure(self,data):
1912	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
1913	thermal motion ellipsoids and polyhedra
1914	'''
1915	generalData = data['General']
1916	cell = generalData['Cell'][1:7]
1917	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
1918	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1919	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
1920	Mydir = generalData['Mydir']
1921	atomData = data['Atoms']
1922	drawingData = data['Drawing']
1923	drawAtoms = drawingData['Atoms']
1924	cx,ct,cs = drawingData['atomPtrs']
1925	Wt = [255,255,255]
1926	Rd = [255,0,0]
1927	Gr = [0,255,0]
1928	Bl = [0,0,255]
1929	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]])
1930	uEdges = np.array([
1931	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
1932	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
1933	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
1934	uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
1935	altDown = False
1936	shiftDown = False
1937	ctrlDown = False
1938
1939	def OnKeyBox(event):
1940	import Image
1941	Draw() #make sure plot is fresh!!
1942	mode = cb.GetValue()
1943	Fname = Mydir+'\\'+generalData['Name']+'.'+mode
1944	size = Page.canvas.GetSize()
1945	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
1946	if mode in ['jpeg',]:
1947	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
1948	im = Image.new("RGBA", (size[0],size[1]))
1949	else:
1950	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
1951	im = Image.new("RGB", (size[0],size[1]))
1952	im.fromstring(Pix)
1953	im.save(Fname,mode)
1954	cb.SetValue(' Save as:')
1955	self.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
1956
1957	def GetTruePosition(xy):
1958	View = glGetIntegerv(GL_VIEWPORT)
1959	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
1960	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
1961	Zmax = 1.
1962	for i,atom in enumerate(drawAtoms):
1963	x,y,z = atom[cx:cx+3]
1964	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
1965	XY = [int(X),int(View[3]-Y)]
1966	if np.allclose(xy,XY,atol=10) and Z < Zmax:
1967	Zmax = Z
1968	SetSelectedAtoms(i)
1969
1970	def OnMouseDown(event):
1971	xy = event.GetPosition()
1972	if event.ShiftDown():
1973	GetTruePosition(xy)
1974	else:
1975	drawingData['Rotation'][3] = xy
1976	Draw()
1977
1978	def OnMouseMove(event):
1979	newxy = event.GetPosition()
1980	page = getSelection()
1981	if event.ControlDown() and drawingData['showABC']:
1982	if event.LeftIsDown():
1983	SetTestRot(newxy)
1984	elif event.RightIsDown():
1985	SetTestPos(newxy)
1986	elif event.MiddleIsDown():
1987	SetTestRotZ(newxy)
1988	x,y,z = drawingData['testPos'][0]
1989	self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
1990
1991
1992	if event.Dragging() and not event.ControlDown():
1993	if event.LeftIsDown():
1994	SetRotation(newxy)
1995	angX,angY,angZ = drawingData['Rotation'][:3]
1996	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f ,%.2f'%(angX,angY,angZ),1)
1997	elif event.RightIsDown():
1998	SetTranslation(newxy)
1999	Tx,Ty,Tz = drawingData['viewPoint'][0]
2000	self.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
2001	elif event.MiddleIsDown():
2002	SetRotationZ(newxy)
2003	angX,angY,angZ = drawingData['Rotation'][:3]
2004	self.G2plotNB.status.SetStatusText('New rotation: %.2f, %.2f, %.2f'%(angX,angY,angZ),1)
2005	Draw()
2006
2007	def OnMouseWheel(event):
2008	drawingData['cameraPos'] += event.GetWheelRotation()/24
2009	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
2010	self.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
2011	page = getSelection()
2012	if page:
2013	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2014	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2015	names = [child.GetName() for child in panel]
2016	panel[names.index('cameraPos')].SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
2017	panel[names.index('cameraSlider')].SetValue(drawingData['cameraPos'])
2018	Draw()
2019
2020	def getSelection():
2021	try:
2022	return self.dataDisplay.GetSelection()
2023	except AttributeError:
2024	print self.dataDisplay.GetLabel()
2025	self.G2plotNB.status.SetStatusText('Select this from Phase data window!')
2026	return 0
2027
2028	def SetViewPointText(VP):
2029	page = getSelection()
2030	if page:
2031	if self.dataDisplay.GetPageText(page) == 'Draw Options':
2032	panel = self.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
2033	names = [child.GetName() for child in panel]
2034	panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
2035
2036	def ClearSelectedAtoms():
2037	page = getSelection()
2038	if page:
2039	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2040	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
2041	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2042	self.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
2043
2044	def SetSelectedAtoms(ind):
2045	page = getSelection()
2046	if page:
2047	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2048	self.dataDisplay.GetPage(page).SelectRow(ind) #this is the Atoms grid in Draw Atoms
2049	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2050	Id = drawAtoms[ind][-2]
2051	for i,atom in enumerate(atomData):
2052	if atom[-1] == Id:
2053	self.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
2054
2055	def GetSelectedAtoms():
2056	page = getSelection()
2057	Ind = []
2058	if page:
2059	if self.dataDisplay.GetPageText(page) == 'Draw Atoms':
2060	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
2061	elif self.dataDisplay.GetPageText(page) == 'Atoms':
2062	Ind = self.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
2063	return Ind
2064
2065	def OnKey(event): #on key UP!!
2066	keyCode = event.GetKeyCode()
2067	if keyCode > 255:
2068	keyCode = 0
2069	key,xyz = chr(keyCode),event.GetPosition()
2070	indx = drawingData['selectedAtoms']
2071	if key in ['c','C']:
2072	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
2073	drawingData['testPos'] = [[-.1,-.1,-.1],[0.0,0.0,0.0],[0,0]]
2074	drawingData['Rotation'] = [0.0,0.0,0.0,[]]
2075	SetViewPointText(drawingData['viewPoint'][0])
2076	elif key in ['n','N']:
2077	drawAtoms = drawingData['Atoms']
2078	pI = drawingData['viewPoint'][1]
2079	if indx:
2080	pI[0] = indx[pI[1]]
2081	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2082	pI[1] += 1
2083	if pI[1] >= len(indx):
2084	pI[1] = 0
2085	else:
2086	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2087	pI[0] += 1
2088	if pI[0] >= len(drawAtoms):
2089	pI[0] = 0
2090	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2091	SetViewPointText(drawingData['viewPoint'][0])
2092
2093	elif key in ['p','P']:
2094	drawAtoms = drawingData['Atoms']
2095	pI = drawingData['viewPoint'][1]
2096	if indx:
2097	pI[0] = indx[pI[1]]
2098	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2099	pI[1] -= 1
2100	if pI[1] < 0:
2101	pI[1] = len(indx)-1
2102	else:
2103	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
2104	pI[0] -= 1
2105	if pI[0] < 0:
2106	pI[0] = len(drawAtoms)-1
2107	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
2108	SetViewPointText(drawingData['viewPoint'][0])
2109	Draw()
2110
2111	def SetBackground():
2112	R,G,B,A = Page.camera['backColor']
2113	glClearColor(R,G,B,A)
2114	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
2115
2116	def SetLights():
2117	glEnable(GL_DEPTH_TEST)
2118	glShadeModel(GL_SMOOTH)
2119	glEnable(GL_LIGHTING)
2120	glEnable(GL_LIGHT0)
2121	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
2122	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
2123	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
2124
2125	def SetTranslation(newxy):
2126	Tx,Ty,Tz = drawingData['viewPoint'][0]
2127	anglex,angley,anglez,oldxy = drawingData['Rotation']
2128	Rx = G2lat.rotdMat(anglex,0)
2129	Ry = G2lat.rotdMat(angley,1)
2130	Rz = G2lat.rotdMat(anglez,2)
2131	dxy = list(newxy-oldxy)+[0,]
2132	dxy = np.inner(Bmat,np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy))))
2133	Tx -= dxy[0]*0.01
2134	Ty += dxy[1]*0.01
2135	Tz -= dxy[2]*0.01
2136	drawingData['Rotation'][3] = newxy
2137	drawingData['viewPoint'][0] = Tx,Ty,Tz
2138	SetViewPointText([Tx,Ty,Tz])
2139
2140	def SetTestPos(newxy):
2141	Tx,Ty,Tz = drawingData['testPos'][0]
2142	anglex,angley,anglez,oldxy = drawingData['Rotation']
2143	Rx = G2lat.rotdMat(anglex,0)
2144	Ry = G2lat.rotdMat(angley,1)
2145	Rz = G2lat.rotdMat(anglez,2)
2146	dxy = list(newxy-oldxy)+[0,]
2147	dxy = np.inner(Rz,np.inner(Ry,np.inner(Rx,dxy)))
2148	Tx += dxy[0]*0.001
2149	Ty -= dxy[1]*0.001
2150	Tz += dxy[2]*0.001
2151	drawingData['Rotation'][3] = newxy
2152	drawingData['testPos'][0] = Tx,Ty,Tz
2153
2154	def SetTestRot(newxy):
2155	Txyz = np.array(drawingData['testPos'][0])
2156	oldxy = drawingData['testPos'][2]
2157	Ax,Ay,Az = drawingData['testPos'][1]
2158	Vxyz = np.array(drawingData['viewPoint'][0])
2159	Dxyz = np.inner(Amat,Txyz-Vxyz)
2160	dxy = list(newxy-oldxy)+[0,]
2161	Ax += dxy[1]*0.01
2162	Ay += dxy[0]*0.01
2163	Rx = G2lat.rotdMat(Ax,0)
2164	Ry = G2lat.rotdMat(Ay,1)
2165	Dxyz = np.inner(Ry,np.inner(Rx,Dxyz))
2166	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2167	drawingData['testPos'][1] = [Ax,Ay,Az]
2168	drawingData['testPos'][2] = newxy
2169	drawingData['testPos'][0] = Dxyz
2170
2171	def SetTestRotZ(newxy):
2172	Txyz = np.array(drawingData['testPos'][0])
2173	oldxy = drawingData['testPos'][2]
2174	Ax,Ay,Az = drawingData['testPos'][1]
2175	Vxyz = np.array(drawingData['viewPoint'][0])
2176	Dxyz = np.inner(Amat,Txyz-Vxyz)
2177	dxy = list(newxy-oldxy)+[0,]
2178	Az += (dxy[0]+dxy[1])*.01
2179	Rz = G2lat.rotdMat(Az,2)
2180	Dxyz = np.inner(Rz,Dxyz)
2181	Dxyz = np.inner(Bmat,Dxyz)+Vxyz
2182	drawingData['testPos'][1] = [Ax,Ay,Az]
2183	drawingData['testPos'][2] = newxy
2184	drawingData['testPos'][0] = Dxyz
2185
2186	def SetRotation(newxy):
2187	anglex,angley,anglez,oldxy = drawingData['Rotation']
2188	dxy = newxy-oldxy
2189	anglex += dxy[1]*.25
2190	angley += dxy[0]*.25
2191	oldxy = newxy
2192	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2193
2194	def SetRotationZ(newxy):
2195	anglex,angley,anglez,oldxy = drawingData['Rotation']
2196	dxy = newxy-oldxy
2197	anglez += (dxy[0]+dxy[1])*.25
2198	oldxy = newxy
2199	drawingData['Rotation'] = [anglex,angley,anglez,oldxy]
2200
2201	def RenderBox():
2202	glEnable(GL_COLOR_MATERIAL)
2203	glLineWidth(2)
2204	glEnable(GL_BLEND)
2205	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
2206	glEnable(GL_LINE_SMOOTH)
2207	glBegin(GL_LINES)
2208	for line,color in zip(uEdges,uColors):
2209	glColor3ubv(color)
2210	glVertex3fv(line[0])
2211	glVertex3fv(line[1])
2212	glEnd()
2213	glColor4ubv([0,0,0,0])
2214	glDisable(GL_LINE_SMOOTH)
2215	glDisable(GL_BLEND)
2216	glDisable(GL_COLOR_MATERIAL)
2217
2218	def RenderUnitVectors(x,y,z):
2219	xyz = np.array([x,y,z])
2220	glEnable(GL_COLOR_MATERIAL)
2221	glLineWidth(1)
2222	glPushMatrix()
2223	glTranslate(x,y,z)
2224	glScalef(1/cell[0],1/cell[1],1/cell[2])
2225	glBegin(GL_LINES)
2226	for line,color in zip(uEdges,uColors)[:3]:
2227	glColor3ubv(color)
2228	glVertex3fv(line[0])
2229	glVertex3fv(line[1])
2230	glEnd()
2231	glPopMatrix()
2232	glColor4ubv([0,0,0,0])
2233	glDisable(GL_COLOR_MATERIAL)
2234
2235	def RenderSphere(x,y,z,radius,color):
2236	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2237	glPushMatrix()
2238	glTranslate(x,y,z)
2239	glMultMatrixf(B4mat.T)
2240	q = gluNewQuadric()
2241	gluSphere(q,radius,20,10)
2242	glPopMatrix()
2243
2244	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
2245	s1,s2,s3 = E
2246	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2247	glPushMatrix()
2248	glTranslate(x,y,z)
2249	glMultMatrixf(B4mat.T)
2250	glMultMatrixf(R4.T)
2251	glEnable(GL_NORMALIZE)
2252	glScale(s1,s2,s3)
2253	q = gluNewQuadric()
2254	gluSphere(q,ellipseProb,20,10)
2255	glDisable(GL_NORMALIZE)
2256	glPopMatrix()
2257
2258	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
2259	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2260	glPushMatrix()
2261	glTranslate(x,y,z)
2262	glMultMatrixf(B4mat.T)
2263	for bond in Bonds:
2264	glPushMatrix()
2265	Dx = np.inner(Amat,bond)
2266	Z = np.sqrt(np.sum(Dx**2))
2267	azm = atan2d(-Dx[1],-Dx[0])
2268	phi = acosd(Dx[2]/Z)
2269	glRotate(-azm,0,0,1)
2270	glRotate(phi,1,0,0)
2271	q = gluNewQuadric()
2272	gluCylinder(q,radius,radius,Z,slice,2)
2273	glPopMatrix()
2274	glPopMatrix()
2275
2276	def RenderLines(x,y,z,Bonds,color):
2277	xyz = np.array([x,y,z])
2278	glEnable(GL_COLOR_MATERIAL)
2279	glLineWidth(1)
2280	glColor3fv(color)
2281	glPushMatrix()
2282	glBegin(GL_LINES)
2283	for bond in Bonds:
2284	glVertex3fv(xyz)
2285	glVertex3fv(xyz+bond)
2286	glEnd()
2287	glColor4ubv([0,0,0,0])
2288	glPopMatrix()
2289	glDisable(GL_COLOR_MATERIAL)
2290
2291	def RenderPolyhedra(x,y,z,Faces,color):
2292	glPushMatrix()
2293	glTranslate(x,y,z)
2294	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
2295	glShadeModel(GL_SMOOTH)
2296	glMultMatrixf(B4mat.T)
2297	for face,norm in Faces:
2298	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
2299	glFrontFace(GL_CW)
2300	glNormal3fv(norm)
2301	glBegin(GL_TRIANGLES)
2302	for vert in face:
2303	glVertex3fv(vert)
2304	glEnd()
2305	glPopMatrix()
2306
2307	def RenderBackbone(Backbone,BackboneColor,radius):
2308	glPushMatrix()
2309	glMultMatrixf(B4mat.T)
2310	glEnable(GL_COLOR_MATERIAL)
2311	glShadeModel(GL_SMOOTH)
2312	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
2313	glePolyCylinder(Backbone,BackboneColor,radius)
2314	glPopMatrix()
2315	glDisable(GL_COLOR_MATERIAL)
2316
2317	def RenderLabel(x,y,z,label,r):
2318	glPushMatrix()
2319	glTranslate(x,y,z)
2320	glMultMatrixf(B4mat.T)
2321	glDisable(GL_LIGHTING)
2322	glColor3f(0,1.,0)
2323	glRasterPos3f(r,r,r)
2324	for c in list(label):
2325	glutBitmapCharacter(GLUT_BITMAP_8_BY_13,ord(c))
2326	glEnable(GL_LIGHTING)
2327	glPopMatrix()
2328
2329	def Draw():
2330	import numpy.linalg as nl
2331	Ind = GetSelectedAtoms()
2332	VS = np.array(Page.canvas.GetSize())
2333	aspect = float(VS[0])/float(VS[1])
2334	cPos = drawingData['cameraPos']
2335	Zclip = drawingData['Zclip']*cPos/200.
2336	anglex,angley,anglez = drawingData['Rotation'][:3]
2337	Tx,Ty,Tz = drawingData['viewPoint'][0]
2338	cx,ct,cs = drawingData['atomPtrs']
2339	bondR = drawingData['bondRadius']
2340	G,g = G2lat.cell2Gmat(cell)
2341	GS = G
2342	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
2343	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
2344	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
2345	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
2346
2347	SetBackground()
2348	glInitNames()
2349	glPushName(0)
2350
2351	glMatrixMode(GL_PROJECTION)
2352	glLoadIdentity()
2353	glViewport(0,0,VS[0],VS[1])
2354	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
2355	gluLookAt(0,0,cPos,0,0,0,0,1,0)
2356	SetLights()
2357
2358	glMatrixMode(GL_MODELVIEW)
2359	glLoadIdentity()
2360	glRotate(anglez,0,0,1)
2361	glRotate(anglex,cosd(anglez),-sind(anglez),0)
2362	glRotate(angley,sind(anglez),cosd(anglez),0)
2363	glMultMatrixf(A4mat.T)
2364	glTranslate(-Tx,-Ty,-Tz)
2365	if drawingData['unitCellBox']:
2366	RenderBox()
2367	if drawingData['showABC']:
2368	x,y,z = drawingData['testPos'][0]
2369	# if altDown:
2370	# self.G2plotNB.status.SetStatusText('moving test point %.4f,%.4f,%.4f'%(x,y,z),1)
2371	# else:
2372	# self.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)
2373	RenderUnitVectors(x,y,z)
2374	Backbone = []
2375	BackboneColor = []
2376	time0 = time.time()
2377	for iat,atom in enumerate(drawingData['Atoms']):
2378	x,y,z = atom[cx:cx+3]
2379	Bonds = atom[-2]
2380	Faces = atom[-1]
2381	try:
2382	atNum = generalData['AtomTypes'].index(atom[ct])
2383	except ValueError:
2384	atNum = -1
2385	CL = atom[cs+2]
2386	color = np.array(CL)/255.
2387	if iat in Ind:
2388	color = np.array(Gr)/255.
2389	radius = 0.5
2390	if atom[cs] != '':
2391	glLoadName(atom[-3])
2392	if 'balls' in atom[cs]:
2393	vdwScale = drawingData['vdwScale']
2394	ballScale = drawingData['ballScale']
2395	if atNum < 0:
2396	radius = 0.2
2397	elif 'H' == atom[ct]:
2398	if drawingData['showHydrogen']:
2399	if 'vdW' in atom[cs] and atNum >= 0:
2400	radius = vdwScale*generalData['vdWRadii'][atNum]
2401	else:
2402	radius = ballScale*drawingData['sizeH']
2403	else:
2404	radius = 0.0
2405	else:
2406	if 'vdW' in atom[cs]:
2407	radius = vdwScale*generalData['vdWRadii'][atNum]
2408	else:
2409	radius = ballScale*generalData['BondRadii'][atNum]
2410	RenderSphere(x,y,z,radius,color)
2411	if 'sticks' in atom[cs]:
2412	RenderBonds(x,y,z,Bonds,bondR,color)
2413	elif 'ellipsoids' in atom[cs]:
2414	RenderBonds(x,y,z,Bonds,bondR,color)
2415	if atom[cs+3] == 'A':
2416	Uij = atom[cs+5:cs+11]
2417	U = np.multiply(G2spc.Uij2U(Uij),GS)
2418	U = np.inner(Amat,np.inner(U,Amat).T)
2419	E,R = nl.eigh(U)
2420	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
2421	E = np.sqrt(E)
2422	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2423	pass
2424	else:
2425	RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
2426	else:
2427	if atom[ct] == 'H' and not drawingData['showHydrogen']:
2428	pass
2429	else:
2430	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
2431	RenderSphere(x,y,z,radius,color)
2432	elif 'lines' in atom[cs]:
2433	radius = 0.1
2434	RenderLines(x,y,z,Bonds,color)
2435	# RenderBonds(x,y,z,Bonds,0.05,color,6)
2436	elif atom[cs] == 'sticks':
2437	radius = 0.1
2438	RenderBonds(x,y,z,Bonds,bondR,color)
2439	elif atom[cs] == 'polyhedra':
2440	RenderPolyhedra(x,y,z,Faces,color)
2441	elif atom[cs] == 'backbone':
2442	if atom[ct-1].split()[0] in ['C','N']:
2443	Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
2444	BackboneColor.append(list(color))
2445
2446	if atom[cs+1] == 'type':
2447	RenderLabel(x,y,z,atom[ct],radius)
2448	elif atom[cs+1] == 'name':
2449	RenderLabel(x,y,z,atom[ct-1],radius)
2450	elif atom[cs+1] == 'number':
2451	RenderLabel(x,y,z,str(iat+1),radius)
2452	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
2453	RenderLabel(x,y,z,atom[ct-4],radius)
2454	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
2455	RenderLabel(x,y,z,atom[ct-3],radius)
2456	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
2457	RenderLabel(x,y,z,atom[ct-2],radius)
2458	if Backbone:
2459	RenderBackbone(Backbone,BackboneColor,bondR)
2460	# print time.time()-time0
2461	Page.canvas.SwapBuffers()
2462
2463	def OnSize(event):
2464	Draw()
2465
2466	def OnFocus(event):
2467	Draw()
2468
2469	try:
2470	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2471	Page = self.G2plotNB.nb.GetPage(plotNum)
2472	except ValueError:
2473	Plot = self.G2plotNB.addOgl(generalData['Name'])
2474	plotNum = self.G2plotNB.plotList.index(generalData['Name'])
2475	Page = self.G2plotNB.nb.GetPage(plotNum)
2476	Page.views = False
2477	view = False
2478	altDown = False
2479	Page.SetFocus()
2480	cb = wx.ComboBox(self.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,
2481	choices=(' save as:','jpeg','tiff','bmp'))
2482	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
2483	cb.SetValue(' save as:')
2484	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
2485	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
2486	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
2487	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
2488	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
2489	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
2490	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
2491	Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
2492	Page.camera['position'] = drawingData['cameraPos']
2493	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
2494	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
2495	Page.canvas.SetCurrent()
2496	Draw()
2497

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