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source: trunk/GSASIIplot.py @ 1978

Last change on this file since 1978 was 1978, checked in by vondreele, 10 years ago
fix to update reflections in HKLplot remove ZigZag? from incommensurate list add pylab to G2math if in debug mode revisions to modulations anticipating Crenel & Sawtooth fixes to SS structure factor calcs. Some success.
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[762]	1	# -- coding: utf-8 --
[939]	2	'''
	3	GSASIIplot: plotting routines
	4	===============================
	5
	6	'''
[762]	7	########### SVN repository information ###################
	8	# $Date: 2015-09-24 21:34:39 +0000 (Thu, 24 Sep 2015) $
	9	# $Author: vondreele $
	10	# $Revision: 1978 $
	11	# $URL: trunk/GSASIIplot.py $
	12	# $Id: GSASIIplot.py 1978 2015-09-24 21:34:39Z vondreele $
	13	########### SVN repository information ###################
	14	import math
	15	import time
	16	import copy
[834]	17	import sys
[762]	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: 1978 $")
	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
[1657]	39	import GSASIIctrls as G2G
[762]	40	import pytexture as ptx
	41	from OpenGL.GL import *
	42	from OpenGL.GLU import *
	43	from OpenGL.GLE import *
[985]	44	import gltext
[762]	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.)
[798]	60	nptand = lambda x: np.tan(x*np.pi/180.)
[762]	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
[1625]	65	GkDelta = unichr(0x0394)
[762]	66
	67	class G2PlotMpl(wx.Panel):
[1889]	68	'Creates a Matplotlib 2-D plot in the GSAS-II graphics window'
[762]	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):
[1889]	84	'Creates an OpenGL plot in the GSAS-II graphics window'
[762]	85	def __init__(self,parent,id=-1,dpi=None,**kwargs):
	86	self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs)
[1379]	87	if 'win' in sys.platform: #Windows (& Mac) already double buffered
[834]	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)
[1379]	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
[762]	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):
[1889]	105	'Creates a 3D Matplotlib plot in the GSAS-II graphics window'
[762]	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):
[1889]	120	'create a tabbed window for GSAS-II graphics'
[762]	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)
[1004]	133	self.nb.Bind(wx.EVT_KEY_UP,self.OnNotebookKey)
[762]	134
	135	self.plotList = []
	136
[1004]	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:
[1077]	146	Page = self.nb.GetPage(self.nb.GetSelection())
	147	except ValueError: # occurs with no plot tabs
	148	return
	149	try:
[1004]	150	Page.canvas.SetFocus()
	151	wx.PostEvent(Page.canvas,event)
	152	except AttributeError:
	153	pass
	154
[762]	155	def addMpl(self,name=""):
[939]	156	'Add a tabbed page with a matplotlib plot'
[762]	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=""):
[939]	165	'Add a tabbed page with a 3D plot'
[762]	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=""):
[939]	174	'Add a tabbed page with an openGL plot'
[762]	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):
[939]	183	'delete a tabbed page'
[762]	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):
[939]	192	'clear all pages from plot window'
[762]	193	while self.nb.GetPageCount():
	194	self.nb.DeletePage(0)
	195	self.plotList = []
	196	self.status.DestroyChildren()
	197
	198	def Rename(self,oldName,newName):
[939]	199	'rename a tab'
[762]	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
[939]	207	def OnPageChanged(self,event):
	208	'respond to someone pressing a tab on the plot window'
[762]	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):
[1583]	214	'Override the matplotlib toolbar so we can add more icons'
[762]	215	ON_MPL_HELP = wx.NewId()
[796]	216	ON_MPL_KEY = wx.NewId()
[1583]	217	arrows = {}
	218	for direc in ('left','right','up','down','Expand X',
[1585]	219	'Shrink X','Expand Y','Shrink Y'):
[1583]	220	arrows[direc] = wx.NewId()
[762]	221	def __init__(self,plotCanvas):
[1583]	222	'''Adds additional icons to toolbar'''
[762]	223	Toolbar.__init__(self,plotCanvas)
[1583]	224	self.plotCanvas = plotCanvas
[1635]	225	POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6 # remove one button, nos. start at 1!
[1894]	226	self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN) #doesn't work in miniconda
[1585]	227	self.parent = self.GetParent()
[832]	228	key = os.path.join(os.path.split(__file__)[0],'key.ico')
[796]	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)
[762]	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)
[1583]	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)
[1585]	240	for direc in ('Expand X','Shrink X','Expand Y','Shrink Y'):
[1583]	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.
[1585]	269	xmin += delta
[1583]	270	xmax -= delta
	271	elif event.Id == self.arrows['Expand Y']:
	272	delta = (ymax-ymin)/10.
[1585]	273	ymin += delta
[1583]	274	ymax -= delta
	275	elif event.Id == self.arrows['Shrink X']:
	276	delta = (xmax-xmin)/10.
[1585]	277	xmin -= delta
[1583]	278	xmax += delta
	279	elif event.Id == self.arrows['Shrink Y']:
	280	delta = (ymax-ymin)/10.
[1585]	281	ymin -= delta
[1583]	282	ymax += delta
	283	else:
	284	# should not happen!
	285	GSASIIpath.IPyBreak()
[1585]	286	self.parent.toolbar.push_current()
[1583]	287	ax.axis((xmin,xmax,ymin,ymax))
	288	#print xmin,xmax,ymin,ymax
	289	self.plotCanvas.figure.canvas.draw()
[1585]	290	self.parent.toolbar.draw()
	291	# self.parent.toolbar.push_current()
[1583]	292
[762]	293	def OnHelp(self,event):
[1583]	294	'Respond to press of help button on plot toolbar'
[762]	295	Page = self.GetParent().GetParent()
	296	pageNo = Page.GetSelection()
	297	bookmark = Page.GetPageText(pageNo)
	298	bookmark = bookmark.strip(')').replace('(','_')
[1657]	299	G2G.ShowHelp(bookmark,self.TopLevelParent)
[796]	300	def OnKey(self,event):
[1583]	301	'''Provide user with list of keystrokes defined for plot as well as an
	302	alternate way to access the same functionality
	303	'''
[796]	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()
[978]	312
[762]	313	################################################################################
	314	##### PlotSngl
	315	################################################################################
	316
[1286]	317	def PlotSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=''):
[1442]	318	'''Structure factor plotting package - displays zone of reflections as rings proportional
[762]	319	to F, F**2, etc. as requested
	320	'''
[1134]	321	from matplotlib.patches import Circle,CirclePolygon
[1978]	322	HKLref = hklRef
	323	global HKL,HKLF,HKLref
[1288]	324
[1286]	325	def OnSCKeyPress(event):
	326	i = zones.index(Data['Zone'])
[1285]	327	newPlot = False
[1442]	328	pwdrChoice = {'f':'Fo','s':'Fosq','u':'Unit Fc'}
[1441]	329	hklfChoice = {'1':'\|DFsq\|>sig','3':'\|DFsq\|>3sig','w':'\|DFsq\|/sig','f':'Fo','s':'Fosq','i':'Unit Fc'}
[1285]	330	if event.key == 'h':
	331	Data['Zone'] = '100'
[1288]	332	newPlot = True
[1285]	333	elif event.key == 'k':
	334	Data['Zone'] = '010'
[1288]	335	newPlot = True
[1285]	336	elif event.key == 'l':
	337	Data['Zone'] = '001'
[1288]	338	newPlot = True
[1442]	339	elif event.key == 'i':
[1285]	340	Data['Scale'] *= 1.1
	341	elif event.key == 'd':
	342	Data['Scale'] /= 1.1
[1694]	343	elif event.key in ['+','=']:
[1286]	344	Data['Layer'] = min(Data['Layer']+1,HKLmax[i])
[1285]	345	elif event.key == '-':
[1286]	346	Data['Layer'] = max(Data['Layer']-1,HKLmin[i])
[1285]	347	elif event.key == '0':
	348	Data['Layer'] = 0
[1441]	349	Data['Scale'] = 1.0
	350	elif event.key in hklfChoice and 'HKLF' in Name:
	351	Data['Type'] = hklfChoice[event.key]
[1288]	352	newPlot = True
[1441]	353	elif event.key in pwdrChoice and 'PWDR' in Name:
	354	Data['Type'] = pwdrChoice[event.key]
	355	newPlot = True
[1978]	356	PlotSngl(G2frame,newPlot,Data,HKLref,Title)
[1285]	357
[762]	358	def OnSCMotion(event):
	359	xpos = event.xdata
	360	if xpos:
	361	xpos = round(xpos) #avoid out of frame mouse position
	362	ypos = round(event.ydata)
	363	zpos = Data['Layer']
	364	if '100' in Data['Zone']:
	365	HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos)
	366	elif '010' in Data['Zone']:
	367	HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos)
	368	elif '001' in Data['Zone']:
	369	HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos)
	370	Page.canvas.SetToolTipString(HKLtxt)
[1286]	371	G2frame.G2plotNB.status.SetStatusText('HKL = '+HKLtxt,0)
	372	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
[762]	373
[1288]	374	def OnSCPress(event):
[762]	375	zpos = Data['Layer']
[1288]	376	xpos = event.xdata
	377	if xpos:
	378	pos = int(round(event.xdata)),int(round(event.ydata))
	379	if '100' in Data['Zone']:
	380	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1]))
	381	hkl = np.array([zpos,pos[0],pos[1]])
	382	elif '010' in Data['Zone']:
	383	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1]))
	384	hkl = np.array([pos[0],zpos,pos[1]])
	385	elif '001' in Data['Zone']:
	386	Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos))
	387	hkl = np.array([pos[0],pos[1],zpos])
	388	h,k,l = hkl
	389	hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))]
	390	if len(hklf):
	391	Fosq,sig,Fcsq = hklf[0]
	392	HKLtxt = '( %.2f %.3f %.2f %.2f)'%(Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig))
	393	G2frame.G2plotNB.status.SetStatusText('Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt,1)
[762]	394
[1288]	395	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
	396	if not Title:
	397	Title = Name
[762]	398	try:
[1286]	399	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
	400	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[762]	401	if not newPlot:
	402	Plot = Page.figure.gca() #get previous powder plot & get limits
	403	xylim = Plot.get_xlim(),Plot.get_ylim()
	404	Page.figure.clf()
	405	Plot = Page.figure.gca() #get a fresh plot after clf()
	406	except ValueError:
[1286]	407	Plot = G2frame.G2plotNB.addMpl('Structure Factors').gca()
	408	plotNum = G2frame.G2plotNB.plotList.index('Structure Factors')
	409	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[1288]	410	Page.canvas.mpl_connect('button_press_event', OnSCPress)
[762]	411	Page.canvas.mpl_connect('motion_notify_event', OnSCMotion)
[1286]	412	Page.canvas.mpl_connect('key_press_event', OnSCKeyPress)
	413	Page.keyPress = OnSCKeyPress
[1442]	414	Page.Choice = (' key press','i: increase scale','d: decrease scale',
[1441]	415	'h: select 100 zone','k: select 010 zone','l: select 001 zone',
[1442]	416	'f: select Fo','s: select Fosq','u: select unit Fc',
[1441]	417	'+: increase index','-: decrease index','0: zero layer',)
[1288]	418	if 'HKLF' in Name:
[1441]	419	Page.Choice += ('w: select \|DFsq\|/sig','1: select \|DFsq\|>sig','3: select \|DFsq\|>3sig',)
[762]	420	Page.SetFocus()
	421
[1286]	422	G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1)
[762]	423	Plot.set_aspect(aspect='equal')
[1285]	424
[762]	425	Type = Data['Type']
	426	scale = Data['Scale']
	427	HKLmax = Data['HKLmax']
	428	HKLmin = Data['HKLmin']
	429	FosqMax = Data['FoMax']
[1506]	430	Super = Data['Super']
	431	SuperVec = []
[1599]	432	if Super:
	433	SuperVec = np.array(Data['SuperVec'][0])
[762]	434	FoMax = math.sqrt(FosqMax)
	435	xlabel = ['k, h=','h, k=','h, l=']
	436	ylabel = ['l','l','k']
	437	zones = ['100','010','001']
	438	pzone = [[1,2],[0,2],[0,1]]
	439	izone = zones.index(Data['Zone'])
[1441]	440	Plot.set_title(Data['Type']+' for '+Title)
[762]	441	HKL = []
	442	HKLF = []
[1134]	443	time0 = time.time()
[1978]	444	for refl in HKLref:
[1506]	445	H = refl[:3]
[1286]	446	if 'HKLF' in Name:
[1504]	447	Fosq,sig,Fcsq = refl[5+Super:8+Super]
[1285]	448	else:
[1504]	449	Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super]
[1599]	450	if Super:
	451	HKL.append(H+SuperVec*refl[3])
	452	else:
	453	HKL.append(H)
[762]	454	HKLF.append([Fosq,sig,Fcsq])
	455	if H[izone] == Data['Layer']:
[837]	456	A = 0
[762]	457	B = 0
	458	if Type == 'Fosq':
	459	A = scale*Fosq/FosqMax
	460	B = scale*Fcsq/FosqMax
	461	C = abs(A-B)
	462	elif Type == 'Fo':
	463	A = scale*math.sqrt(max(0,Fosq))/FoMax
	464	B = scale*math.sqrt(max(0,Fcsq))/FoMax
	465	C = abs(A-B)
[1441]	466	elif Type == 'Unit Fc':
	467	A = scale/2
	468	B = scale/2
	469	C = 0.0
	470	if Fcsq and Fosq > 0:
	471	A *= min(1.0,Fosq/Fcsq)
	472	C = abs(A-B)
[762]	473	elif Type == '\|DFsq\|/sig':
[837]	474	if sig > 0.:
[1288]	475	A = (Fosq-Fcsq)/(3*sig)
[837]	476	B = 0
[762]	477	elif Type == '\|DFsq\|>sig':
[837]	478	if sig > 0.:
[1288]	479	A = (Fosq-Fcsq)/(3*sig)
[840]	480	if abs(A) < 1.0: A = 0
[837]	481	B = 0
[762]	482	elif Type == '\|DFsq\|>3sig':
[837]	483	if sig > 0.:
[1288]	484	A = (Fosq-Fcsq)/(3*sig)
[840]	485	if abs(A) < 3.0: A = 0
[1599]	486	B = 0
	487	if Super:
	488	h = H+SuperVec*refl[3]
	489	else:
	490	h = H
[1506]	491	xy = (h[pzone[izone][0]],h[pzone[izone][1]])
[840]	492	if Type in ['\|DFsq\|/sig','\|DFsq\|>sig','\|DFsq\|>3sig']:
	493	if A > 0.0:
[1288]	494	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
[840]	495	else:
[1288]	496	Plot.add_artist(Circle(xy,radius=-A,ec='r',fc='w'))
[840]	497	else:
[843]	498	if A > 0.0 and A > B:
[1288]	499	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
[840]	500	if B:
	501	Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w'))
[843]	502	if A < B:
[1288]	503	Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w'))
[840]	504	radius = C
	505	if radius > 0:
	506	if A > B:
	507	Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g'))
	508	else:
	509	Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r'))
[1134]	510	# print 'plot time: %.3f'%(time.time()-time0)
[1506]	511	HKL = np.array(HKL)
[762]	512	HKLF = np.array(HKLF)
	513	Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12)
	514	Plot.set_ylabel(ylabel[izone],fontsize=12)
[1286]	515	if not newPlot:
	516	Page.toolbar.push_current()
	517	Plot.set_xlim(xylim[0])
	518	Plot.set_ylim(xylim[1])
[837]	519	# xylim = []
[1286]	520	Page.toolbar.push_current()
	521	Page.toolbar.draw()
	522	else:
	523	Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]]))
	524	Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]]))
	525	Page.canvas.draw()
[1442]	526
	527	################################################################################
	528	##### Plot3DSngl
	529	################################################################################
	530
[1643]	531	def Plot3DSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=False):
[1442]	532	'''3D Structure factor plotting package - displays reflections as rings proportional
	533	to F, F**2, etc. as requested as 3D array
	534	'''
	535
[1598]	536	global ifBox
	537	ifBox = False
[1442]	538	def OnKeyBox(event):
	539	mode = cb.GetValue()
	540	if mode in ['jpeg','bmp','tiff',]:
	541	try:
	542	import Image as Im
	543	except ImportError:
	544	try:
	545	from PIL import Image as Im
	546	except ImportError:
	547	print "PIL/pillow Image module not present. Cannot save images without this"
	548	raise Exception("PIL/pillow Image module not found")
[1643]	549	try:
	550	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
	551	except NameError: #for when generalData doesn't exist!
	552	Fname = os.path.join(Mydir,'unknown'+'.'+mode)
	553	print Fname+' saved'
[1442]	554	size = Page.canvas.GetSize()
	555	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
	556	if mode in ['jpeg',]:
	557	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
[1608]	558	im = Im.new("RGBA", (size[0],size[1]))
[1442]	559	else:
	560	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
[1608]	561	im = Im.new("RGB", (size[0],size[1]))
[1442]	562	im.fromstring(Pix)
	563	im.save(Fname,mode)
	564	cb.SetValue(' save as/key:')
	565	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
	566	else:
	567	event.key = cb.GetValue()[0]
	568	cb.SetValue(' save as/key:')
	569	wx.CallAfter(OnKey,event)
	570	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
	571
	572	def OnKey(event): #on key UP!!
[1598]	573	global ifBox
[1442]	574	Choice = {'F':'Fo','S':'Fosq','U':'Unit','D':'dFsq','W':'dFsq/sig'}
[1969]	575	viewChoice = {'L':[[0,0,1],[1,0,0],[0,1,0]],'K':[[0,1,0],[0,0,1],[1,0,0]],'H':[[1,0,0],[0,0,1],[0,1,0]]}
[1442]	576	try:
	577	keyCode = event.GetKeyCode()
	578	if keyCode > 255:
	579	keyCode = 0
	580	key = chr(keyCode)
	581	except AttributeError: #if from OnKeyBox above
	582	key = str(event.key).upper()
[1966]	583	if key in ['C','H','K','L']:
	584	if key == 'C':
	585	Data['Zone'] = False
	586	key = 'L'
[1969]	587	Data['viewKey'] = key
[1442]	588	drawingData['viewPoint'][0] = drawingData['default']
[1969]	589	drawingData['viewDir'] = np.array(viewChoice[key][0])
	590	drawingData['viewUp'] = np.array(viewChoice[key][1])
[1442]	591	drawingData['oldxy'] = []
[1969]	592	if Data['Zone']:
	593	if key == 'L':
	594	Q = [-1,0,0,0]
	595	else:
	596	V0 = np.array(viewChoice[key][0])
	597	V1 = np.array(viewChoice[key][1])
	598	V0 = np.inner(Amat,V0)
	599	V1 = np.inner(Amat,V1)
	600	V0 /= nl.norm(V0)
	601	V1 /= nl.norm(V1)
	602	A = np.arccos(np.sum(V1*V0))
	603	Q = G2mth.AV2Q(-A,viewChoice[key][2])
[1976]	604	G2frame.G2plotNB.status.SetStatusText('zone = %s'%(str(viewChoice[key][0])),1)
[1969]	605	else:
	606	V0 = np.array(viewChoice[key][0])
	607	V = np.inner(Bmat,V0)
	608	V /= np.sqrt(np.sum(V**2))
	609	V *= np.array([0,0,1])
	610	A = np.arccos(np.sum(V*V0))
	611	Q = G2mth.AV2Q(-A,viewChoice[key][2])
[1967]	612	drawingData['Quaternion'] = Q
[1966]	613	elif key in 'Z':
	614	Data['Zone'] = not Data['Zone']
[1598]	615	elif key in 'B':
	616	ifBox = not ifBox
[1694]	617	elif key in ['+','=']:
[1442]	618	Data['Scale'] *= 1.25
	619	elif key == '-':
	620	Data['Scale'] /= 1.25
[1969]	621	elif key == 'P':
	622	vec = viewChoice[Data['viewKey']][0]
	623	drawingData['viewPoint'][0] -= vec
	624	elif key == 'N':
	625	vec = viewChoice[Data['viewKey']][0]
	626	drawingData['viewPoint'][0] += vec
[1442]	627	elif key == '0':
[1656]	628	drawingData['viewPoint'][0] = [0,0,0]
[1442]	629	Data['Scale'] = 1.0
	630	elif key == 'I':
	631	Data['Iscale'] = not Data['Iscale']
	632	elif key in Choice:
[1466]	633	Data['Type'] = Choice[key]
[1442]	634	Draw('key')
	635
	636	Name = G2frame.PatternTree.GetItemText(G2frame.PatternId)
[1909]	637	if Title and Title in G2frame.GetPhaseData(): #NB: save image as e.g. jpeg will fail if False; MyDir is unknown
[1442]	638	generalData = G2frame.GetPhaseData()[Title]['General']
	639	cell = generalData['Cell'][1:7]
[1607]	640	Mydir = generalData['Mydir']
[1442]	641	else:
[1909]	642	Title = 'Unknown'
[1442]	643	cell = [10,10,10,90,90,90]
[1607]	644	Mydir = G2frame.dirname
[1442]	645	drawingData = Data['Drawing']
[1506]	646	Super = Data['Super']
	647	SuperVec = []
[1598]	648	if Super:
	649	SuperVec = np.array(Data['SuperVec'][0])
[1442]	650	defaultViewPt = copy.copy(drawingData['viewPoint'])
	651	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
	652	Gmat,gmat = G2lat.cell2Gmat(cell)
	653	invcell = G2lat.Gmat2cell(Gmat)
	654	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	655	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	656	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Bmat,[0,0,1]))
	657	Wt = np.array([255,255,255])
	658	Rd = np.array([255,0,0])
	659	Gr = np.array([0,255,0])
	660	wxGreen = wx.Colour(0,255,0)
	661	Bl = np.array([0,0,255])
	662	Or = np.array([255,128,0])
	663	wxOrange = wx.Colour(255,128,0)
	664	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]])
	665	uEdges = np.array([
[1598]	666	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
	667	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
	668	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
	669	uColors = [Rd,Gr,Bl, Wt,Wt,Wt, Wt,Wt,Wt, Wt,Wt,Wt]
[1442]	670	def FillHKLRC():
	671	R = np.zeros(len(hklRef))
	672	C = []
	673	HKL = []
	674	RC = []
	675	for i,refl in enumerate(hklRef):
[1506]	676	H = refl[:3]
[1442]	677	if 'HKLF' in Name:
[1504]	678	Fosq,sig,Fcsq = refl[5+Super:8+Super]
[1786]	679	if refl[3+Super] < 0:
	680	Fosq,sig,Fcsq = [0,1,0]
[1442]	681	else:
[1504]	682	Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super]
[1598]	683	if Super:
	684	HKL.append(H+SuperVec*refl[3])
	685	else:
	686	HKL.append(H)
[1442]	687	if Data['Type'] == 'Unit':
	688	R[i] = 0.1
	689	C.append(Gr)
	690	elif Data['Type'] == 'Fosq':
	691	if Fosq > 0:
	692	R[i] = Fosq
	693	C.append(Gr)
	694	else:
	695	R[i] = -Fosq
	696	C.append(Rd)
	697	elif Data['Type'] == 'Fo':
	698	if Fosq > 0:
	699	R[i] = np.sqrt(Fosq)
	700	C.append(Gr)
	701	else:
	702	R[i] = np.sqrt(-Fosq)
	703	C.append(Rd)
	704	elif Data['Type'] == 'dFsq/sig':
	705	dFsig = (Fosq-Fcsq)/sig
	706	if dFsig > 0:
	707	R[i] = dFsig
	708	C.append(Gr)
	709	else:
	710	R[i] = -dFsig
	711	C.append(Rd)
	712	elif Data['Type'] == 'dFsq':
	713	dF = Fosq-Fcsq
	714	if dF > 0:
	715	R[i] = dF
	716	C.append(Gr)
	717	else:
	718	R[i] = -dF
	719	C.append(Rd)
	720	R /= np.max(R)
	721	R *= Data['Scale']
[1506]	722	R = np.where(R<1.e-5,1.e-5,R)
[1442]	723	if Data['Iscale']:
	724	R = np.where(R<=1.,R,1.)
	725	C = np.array(C)
	726	C = (C.T*R).T
[1506]	727	R = np.ones_like(R)*0.05
[1442]	728	return HKL,zip(list(R),C)
	729
[1786]	730	def GetTruePosition(xy):
	731	View = glGetIntegerv(GL_VIEWPORT)
	732	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
	733	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
	734	Zmax = 1.
[1787]	735	xy = [int(xy[0]),int(View[3]-xy[1])]
[1786]	736	for i,ref in enumerate(hklRef):
[1787]	737	h,k,l = ref[:3]
[1786]	738	X,Y,Z = gluProject(h,k,l,Model,Proj,View)
	739	XY = [int(X),int(Y)]
[1787]	740	if np.allclose(xy,XY,atol=10) and Z < Zmax:
[1786]	741	Zmax = Z
[1787]	742	return [int(h),int(k),int(l)]
[1786]	743
[1442]	744	def SetTranslation(newxy):
	745	#first get translation vector in screen coords.
	746	oldxy = drawingData['oldxy']
	747	if not len(oldxy): oldxy = list(newxy)
	748	dxy = newxy-oldxy
	749	drawingData['oldxy'] = list(newxy)
	750	V = np.array([-dxy[0],dxy[1],0.])
	751	#then transform to rotated crystal coordinates & apply to view point
	752	Q = drawingData['Quaternion']
	753	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
	754	Tx,Ty,Tz = drawingData['viewPoint'][0]
	755	Tx += V[0]*0.1
	756	Ty += V[1]*0.1
	757	Tz += V[2]*0.1
	758	drawingData['viewPoint'][0] = Tx,Ty,Tz
	759
	760	def SetRotation(newxy):
	761	'Perform a rotation in x-y space due to a left-mouse drag'
	762	#first get rotation vector in screen coords. & angle increment
	763	oldxy = drawingData['oldxy']
	764	if not len(oldxy): oldxy = list(newxy)
	765	dxy = newxy-oldxy
	766	drawingData['oldxy'] = list(newxy)
	767	V = np.array([dxy[1],dxy[0],0.])
	768	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
	769	if not A: return # nothing changed, nothing to do
	770	# next transform vector back to xtal coordinates via inverse quaternion
	771	# & make new quaternion
	772	Q = drawingData['Quaternion']
	773	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
	774	DQ = G2mth.AVdeg2Q(A,V)
	775	Q = G2mth.prodQQ(Q,DQ)
	776	drawingData['Quaternion'] = Q
	777	# finally get new view vector - last row of rotation matrix
	778	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
	779	VD /= np.sqrt(np.sum(VD**2))
	780	drawingData['viewDir'] = VD
	781
	782	def SetRotationZ(newxy):
	783	#first get rotation vector (= view vector) in screen coords. & angle increment
	784	View = glGetIntegerv(GL_VIEWPORT)
	785	cent = [View[2]/2,View[3]/2]
	786	oldxy = drawingData['oldxy']
	787	if not len(oldxy): oldxy = list(newxy)
	788	dxy = newxy-oldxy
	789	drawingData['oldxy'] = list(newxy)
	790	V = drawingData['viewDir']
	791	A = [0,0]
	792	A[0] = dxy[1]*.25
	793	A[1] = dxy[0]*.25
	794	if newxy[0] > cent[0]:
	795	A[0] *= -1
	796	if newxy[1] < cent[1]:
	797	A[1] *= -1
	798	# next transform vector back to xtal coordinates & make new quaternion
	799	Q = drawingData['Quaternion']
	800	V = np.inner(Amat,V)
	801	Qx = G2mth.AVdeg2Q(A[0],V)
	802	Qy = G2mth.AVdeg2Q(A[1],V)
	803	Q = G2mth.prodQQ(Q,Qx)
	804	Q = G2mth.prodQQ(Q,Qy)
	805	drawingData['Quaternion'] = Q
	806
	807	def OnMouseDown(event):
	808	xy = event.GetPosition()
	809	drawingData['oldxy'] = list(xy)
	810
	811	def OnMouseMove(event):
	812	if event.ShiftDown(): #don't want any inadvertant moves when picking
	813	return
	814	newxy = event.GetPosition()
	815
	816	if event.Dragging():
	817	if event.LeftIsDown():
	818	SetRotation(newxy)
	819	Q = drawingData['Quaternion']
	820	elif event.RightIsDown():
	821	SetTranslation(newxy)
	822	Tx,Ty,Tz = drawingData['viewPoint'][0]
	823	elif event.MiddleIsDown():
	824	SetRotationZ(newxy)
	825	Q = drawingData['Quaternion']
	826	Draw('move')
[1787]	827	else:
	828	hkl = GetTruePosition(newxy)
	829	if hkl:
	830	h,k,l = hkl
[1969]	831	Page.canvas.SetToolTipString('%d,%d,%d'%(h,k,l))
	832	G2frame.G2plotNB.status.SetStatusText('hkl = %d,%d,%d'%(h,k,l),1)
[1442]	833
	834	def OnMouseWheel(event):
	835	if event.ShiftDown():
	836	return
	837	drawingData['cameraPos'] += event.GetWheelRotation()/120.
	838	drawingData['cameraPos'] = max(0.1,min(20.00,drawingData['cameraPos']))
	839	Draw('wheel')
	840
	841	def SetBackground():
	842	R,G,B,A = Page.camera['backColor']
	843	glClearColor(R,G,B,A)
	844	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
	845
	846	def SetLights():
	847	glEnable(GL_DEPTH_TEST)
	848	glShadeModel(GL_SMOOTH)
	849	glEnable(GL_LIGHTING)
	850	glEnable(GL_LIGHT0)
	851	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
	852	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
	853	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
	854
[1598]	855	def RenderBox(x,y,z):
[1442]	856	xyz = np.array([x,y,z])
	857	glEnable(GL_COLOR_MATERIAL)
	858	glLineWidth(1)
	859	glPushMatrix()
	860	glTranslate(x,y,z)
[1598]	861	glColor4ubv([0,0,0,0])
[1442]	862	glBegin(GL_LINES)
	863	for line,color in zip(uEdges,uColors):
	864	glColor3ubv(color)
[1598]	865	glVertex3fv(line[0])
	866	glVertex3fv(line[1])
	867	glEnd()
	868	glPopMatrix()
	869	glColor4ubv([0,0,0,0])
	870	glDisable(GL_COLOR_MATERIAL)
	871
	872	def RenderUnitVectors(x,y,z):
	873	xyz = np.array([x,y,z])
	874	glEnable(GL_COLOR_MATERIAL)
	875	glLineWidth(1)
	876	glPushMatrix()
	877	glTranslate(x,y,z)
	878	glBegin(GL_LINES)
	879	for line,color in zip(uEdges,uColors)[:3]:
	880	glColor3ubv(color)
[1969]	881	glVertex3fv([0,0,0])
	882	# glVertex3fv(-line[1])
[1442]	883	glVertex3fv(line[1])
	884	glEnd()
	885	glPopMatrix()
	886	glColor4ubv([0,0,0,0])
	887	glDisable(GL_COLOR_MATERIAL)
	888
	889	def RenderDots(XYZ,RC):
	890	glEnable(GL_COLOR_MATERIAL)
	891	XYZ = np.array(XYZ)
	892	glPushMatrix()
	893	for xyz,rc in zip(XYZ,RC):
	894	x,y,z = xyz
	895	r,c = rc
[1969]	896	glColor3ubv(c)
[1442]	897	glPointSize(r*50)
	898	glBegin(GL_POINTS)
	899	glVertex3fv(xyz)
	900	glEnd()
	901	glPopMatrix()
	902	glColor4ubv([0,0,0,0])
	903	glDisable(GL_COLOR_MATERIAL)
	904
	905	def Draw(caller=''):
	906	#useful debug?
	907	# if caller:
	908	# print caller
	909	# end of useful debug
	910	G2frame.G2plotNB.status.SetStatusText('Plot type = %s for %s'%(Data['Type'],Name),1)
	911	VS = np.array(Page.canvas.GetSize())
	912	aspect = float(VS[0])/float(VS[1])
	913	cPos = drawingData['cameraPos']
	914	Zclip = drawingData['Zclip']*cPos/20.
[1966]	915	if Data['Zone']:
	916	Zclip = 0.1
[1442]	917	Q = drawingData['Quaternion']
[1976]	918	Tx,Ty,Tz = drawingData['viewPoint'][0][:3]
[1442]	919	G,g = G2lat.cell2Gmat(cell)
	920	GS = G
	921	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
	922	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
	923	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
	924
	925	HKL,RC = FillHKLRC()
	926
	927	SetBackground()
	928	glInitNames()
	929	glPushName(0)
	930
	931	glMatrixMode(GL_PROJECTION)
	932	glLoadIdentity()
	933	glViewport(0,0,VS[0],VS[1])
	934	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
[1967]	935	gluLookAt(0,0,cPos,0,0,0,0,1,0)
[1442]	936	SetLights()
	937
	938	glMatrixMode(GL_MODELVIEW)
	939	glLoadIdentity()
	940	matRot = G2mth.Q2Mat(Q)
	941	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	942	glMultMatrixf(matRot.T)
	943	glMultMatrixf(B4mat.T)
	944	glTranslate(-Tx,-Ty,-Tz)
	945	x,y,z = drawingData['viewPoint'][0]
[1598]	946	if ifBox:
	947	RenderBox(x,y,z)
	948	else:
	949	RenderUnitVectors(x,y,z)
[1442]	950	RenderUnitVectors(0,0,0)
	951	RenderDots(HKL,RC)
	952	time0 = time.time()
	953	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
	954	Page.canvas.SwapBuffers()
	955
	956	# PlotStructure execution starts here (N.B. initialization above)
	957	try:
	958	plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors')
	959	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	960	except ValueError:
	961	Plot = G2frame.G2plotNB.addOgl('3D Structure Factors')
	962	plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors')
	963	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	964	Page.views = False
	965	view = False
	966	altDown = False
	967	Font = Page.GetFont()
	968	Page.SetFocus()
	969	Page.Choice = None
[1966]	970	choice = [' save as/key:','jpeg','tiff','bmp','h: view down h','k: view down k','l: view down l',
	971	'z: zero zone toggle','c: reset to default','b: toggle box ','+: increase scale','-: decrease scale',
	972	'f: Fobs','s: Fobs**2','u: unit','d: Fo-Fc','w: DF/sig','i: toggle intensity scaling']
[1442]	973	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
	974	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
	975	cb.SetValue(' save as/key:')
	976	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
	977	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
	978	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
	979	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
	980	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
	981	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
	982	# Page.canvas.Bind(wx.EVT_SIZE, OnSize)
	983	Page.camera['position'] = drawingData['cameraPos']
	984	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
	985	Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255.
[1656]	986	Page.controls = Data
[1442]	987	try:
	988	Page.canvas.SetCurrent()
	989	except:
	990	pass
	991	Draw('main')
	992	# if firstCall: Draw('main') # draw twice the first time that graphics are displayed
	993
[762]	994
	995	################################################################################
	996	##### PlotPatterns
	997	################################################################################
	998
[1199]	999	def PlotPatterns(G2frame,newPlot=False,plotType='PWDR'):
[762]	1000	'''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs
[796]	1001	2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I
[762]	1002	plotting available.
	1003	'''
[1017]	1004	global exclLines
[1382]	1005	global DifLine
	1006	global Ymax
[1199]	1007	plottype = plotType
[1672]	1008	#patch
	1009	data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
	1010	if 'Offset' not in data[0] and plotType in ['PWDR','SASD']: #plot offset data
	1011	data[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,
[1715]	1012	'refDelt':0.01,})
[1672]	1013	G2frame.PatternTree.SetItemPyData(G2frame.PickId,data)
	1014	#end patch
[762]	1015	def OnPlotKeyPress(event):
[1401]	1016	try: #one way to check if key stroke will work on plot
	1017	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
	1018	except TypeError:
	1019	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1)
	1020	return
[762]	1021	newPlot = False
[1341]	1022	if event.key == 'w':
[1339]	1023	G2frame.Weight = not G2frame.Weight
[1341]	1024	if not G2frame.Weight and 'PWDR' in plottype:
[762]	1025	G2frame.SinglePlot = True
	1026	newPlot = True
[1205]	1027	elif event.key == 'e' and 'SASD' in plottype:
	1028	G2frame.ErrorBars = not G2frame.ErrorBars
[1300]	1029	elif event.key == 'b':
[1205]	1030	G2frame.SubBack = not G2frame.SubBack
	1031	if not G2frame.SubBack:
[792]	1032	G2frame.SinglePlot = True
[762]	1033	elif event.key == 'n':
	1034	if G2frame.Contour:
	1035	pass
	1036	else:
[1205]	1037	G2frame.logPlot = not G2frame.logPlot
	1038	if not G2frame.logPlot:
[1672]	1039	Pattern[0]['Offset'][0] = 0
[762]	1040	newPlot = True
[1368]	1041	elif event.key == 's' and 'PWDR' in plottype:
	1042	if G2frame.Contour:
	1043	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
	1044	choice.sort()
	1045	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
	1046	if dlg.ShowModal() == wx.ID_OK:
	1047	sel = dlg.GetSelection()
	1048	G2frame.ContourColor = choice[sel]
	1049	else:
	1050	G2frame.ContourColor = 'Paired'
	1051	dlg.Destroy()
	1052	elif G2frame.SinglePlot:
[1715]	1053	G2frame.plotStyle['sqrtPlot'] = not G2frame.plotStyle['sqrtPlot']
	1054	if G2frame.plotStyle['sqrtPlot']:
[1672]	1055	Pattern[0]['delOffset'] = .002
	1056	Pattern[0]['refOffset'] = -1.0
	1057	Pattern[0]['refDelt'] = .001
[1368]	1058	else:
[1672]	1059	Pattern[0]['delOffset'] = .02
	1060	Pattern[0]['refOffset'] = -1.0
	1061	Pattern[0]['refDelt'] = .01
[1368]	1062	newPlot = True
[1366]	1063	elif event.key == 'u' and (G2frame.Contour or not G2frame.SinglePlot):
[762]	1064	if G2frame.Contour:
	1065	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
[1672]	1066	elif Pattern[0]['Offset'][0] < 100.:
	1067	Pattern[0]['Offset'][0] += 1.
[1369]	1068	elif event.key == 'd' and (G2frame.Contour or not G2frame.SinglePlot):
[762]	1069	if G2frame.Contour:
	1070	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
[1672]	1071	elif Pattern[0]['Offset'][0] > 0.:
	1072	Pattern[0]['Offset'][0] -= 1.
[1366]	1073	elif event.key == 'l' and not G2frame.SinglePlot:
[1672]	1074	Pattern[0]['Offset'][1] -= 1.
[1366]	1075	elif event.key == 'r' and not G2frame.SinglePlot:
[1672]	1076	Pattern[0]['Offset'][1] += 1.
[1366]	1077	elif event.key == 'o' and not G2frame.SinglePlot:
[1205]	1078	G2frame.Cmax = 1.0
[1672]	1079	Pattern[0]['Offset'] = [0,0]
[1300]	1080	elif event.key == 'c' and 'PWDR' in plottype:
[762]	1081	newPlot = True
[1205]	1082	if not G2frame.Contour:
[762]	1083	G2frame.SinglePlot = False
[1672]	1084	Pattern[0]['Offset'] = [0.,0.]
[1341]	1085	else:
	1086	G2frame.SinglePlot = True
	1087	G2frame.Contour = not G2frame.Contour
[1205]	1088	elif event.key == 'q':
	1089	if 'PWDR' in plottype:
	1090	newPlot = True
[1715]	1091	G2frame.plotStyle['qPlot'] = not G2frame.plotStyle['qPlot']
	1092	G2frame.plotStyle['dPlot'] = False
[1205]	1093	elif 'SASD' in plottype:
	1094	newPlot = True
[1715]	1095	G2frame.plotStyle['sqPlot'] = not G2frame.plotStyle['sqPlot']
[1462]	1096	elif event.key == 't' and 'PWDR' in plottype:
[1715]	1097	G2frame.plotStyle['dPlot'] = not G2frame.plotStyle['dPlot']
	1098	G2frame.plotStyle['qPlot'] = False
[1462]	1099	newPlot = True
[1366]	1100	elif event.key == 'm':
[1715]	1101	G2frame.plotStyle['sqrtPlot'] = False
[1368]	1102	G2frame.SinglePlot = not G2frame.SinglePlot
[762]	1103	newPlot = True
[1694]	1104	elif event.key in ['+','=']:
[762]	1105	if G2frame.PickId:
	1106	G2frame.PickId = False
[1205]	1107	elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot
[762]	1108	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
	1109	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
	1110	'mitchell','sinc','lanczos']
	1111	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
	1112	if dlg.ShowModal() == wx.ID_OK:
	1113	sel = dlg.GetSelection()
	1114	G2frame.Interpolate = choice[sel]
	1115	else:
	1116	G2frame.Interpolate = 'nearest'
	1117	dlg.Destroy()
[1583]	1118	else:
[1652]	1119	# print 'no binding for key',event.key
[1583]	1120	#GSASIIpath.IPyBreak()
	1121	return
[1204]	1122	wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype)
[762]	1123
	1124	def OnMotion(event):
	1125	xpos = event.xdata
	1126	if xpos: #avoid out of frame mouse position
	1127	ypos = event.ydata
	1128	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	1129	try:
[796]	1130	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
[1715]	1131	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
[1475]	1132	q = xpos
	1133	dsp = 2.*np.pi/q
	1134	try:
	1135	xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos)
	1136	except ValueError: #avoid bad value in asin beyond upper limit
	1137	pass
	1138	elif 'SASD' in plottype:
	1139	q = xpos
	1140	dsp = 2.*np.pi/q
[1715]	1141	elif G2frame.plotStyle['dPlot']:
[1475]	1142	dsp = xpos
	1143	q = 2.*np.pi/dsp
	1144	xpos = G2lat.Dsp2pos(Parms,xpos)
[1519]	1145	elif G2frame.Contour and 'T' in Parms['Type'][0]:
	1146	xpos = X[xpos]
	1147	dsp = G2lat.Pos2dsp(Parms,xpos)
	1148	q = 2.*np.pi/dsp
[1475]	1149	else:
	1150	dsp = G2lat.Pos2dsp(Parms,xpos)
	1151	q = 2.*np.pi/dsp
	1152	if G2frame.Contour: #PWDR only
	1153	if 'C' in Parms['Type'][0]:
	1154	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
[792]	1155	else:
[1475]	1156	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
	1157	else:
	1158	if 'C' in Parms['Type'][0]:
[1204]	1159	if 'PWDR' in plottype:
[1715]	1160	if G2frame.plotStyle['sqrtPlot']:
[1370]	1161	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
	1162	else:
	1163	G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
[1204]	1164	elif 'SASD' in plottype:
[1475]	1165	G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1)
[1463]	1166	else:
[1715]	1167	if G2frame.plotStyle['sqrtPlot']:
[1475]	1168	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
[1370]	1169	else:
[1475]	1170	G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
[762]	1171	if G2frame.itemPicked:
[1237]	1172	Page.canvas.SetToolTipString('%9.5f'%(xpos))
[762]	1173	if G2frame.PickId:
	1174	found = []
[1582]	1175	pickIdText = G2frame.PatternTree.GetItemText(G2frame.PickId)
	1176	if pickIdText in ['Index Peak List','Unit Cells List','Reflection Lists'] or \
[1592]	1177	'PWDR' in pickIdText:
[1582]	1178	indx = -1
	1179	if pickIdText in ['Index Peak List','Unit Cells List',]:
	1180	indx = -2
[1933]	1181	if len(G2frame.HKL):
[762]	1182	view = Page.toolbar._views.forward()[0][:2]
	1183	wid = view[1]-view[0]
[1933]	1184	found = G2frame.HKL[np.where(np.fabs(G2frame.HKL.T[indx]-xpos) < 0.002*wid)]
[762]	1185	if len(found):
[1571]	1186	if len(found[0]) > 6: #SS reflections
	1187	h,k,l,m = found[0][:4]
	1188	Page.canvas.SetToolTipString('%d,%d,%d,%d'%(int(h),int(k),int(l),int(m)))
	1189	else:
	1190	h,k,l = found[0][:3]
	1191	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
[762]	1192	else:
	1193	Page.canvas.SetToolTipString('')
	1194
	1195	except TypeError:
[1401]	1196	G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1)
[1237]	1197
	1198	def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots
	1199	olderr = np.seterr(invalid='ignore')
[762]	1200
	1201	def OnPick(event):
[1889]	1202	'''Respond to an item being picked. This usually means that the item
	1203	will be dragged with the mouse.
	1204	'''
	1205	def OnDragMarker(event):
	1206	'''Respond to dragging of a plot Marker
	1207	'''
	1208	Page.canvas.restore_region(savedplot)
	1209	G2frame.itemPicked.set_data([event.xdata], [event.ydata])
	1210	Page.figure.gca().draw_artist(G2frame.itemPicked)
	1211	Page.canvas.blit(Page.figure.gca().bbox)
	1212	def OnDragLine(event):
	1213	'''Respond to dragging of a plot line
	1214	'''
	1215	Page.canvas.restore_region(savedplot)
	1216	coords = G2frame.itemPicked.get_data()
	1217	coords[0][0] = coords[0][1] = event.xdata
	1218	coords = G2frame.itemPicked.set_data(coords)
	1219	Page.figure.gca().draw_artist(G2frame.itemPicked)
	1220	Page.canvas.blit(Page.figure.gca().bbox)
	1221
[762]	1222	if G2frame.itemPicked is not None: return
	1223	PatternId = G2frame.PatternId
	1224	try:
[796]	1225	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
[762]	1226	except TypeError:
	1227	return
	1228	PickId = G2frame.PickId
	1229	pick = event.artist
[1237]	1230	mouse = event.mouseevent
[762]	1231	xpos = pick.get_xdata()
	1232	ypos = pick.get_ydata()
	1233	ind = event.ind
	1234	xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0])
[1889]	1235	# convert from plot units
	1236	if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta
	1237	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
	1238	elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta
	1239	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
	1240	if G2frame.plotStyle['sqrtPlot']:
	1241	xy[1] = xy[1]**2
[762]	1242	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
[1343]	1243	if ind.all() != [0] and ObsLine[0].get_label() in str(pick): #picked a data point
[792]	1244	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
[1190]	1245	XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
[1445]	1246	data['peaks'].append(XY)
	1247	data['sigDict'] = {} #now invalid
[762]	1248	G2pdG.UpdatePeakGrid(G2frame,data)
[1199]	1249	PlotPatterns(G2frame,plotType=plottype)
[762]	1250	else: #picked a peak list line
	1251	G2frame.itemPicked = pick
	1252	elif G2frame.PatternTree.GetItemText(PickId) == 'Limits':
	1253	if ind.all() != [0]: #picked a data point
	1254	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
	1255	data = G2frame.PatternTree.GetItemPyData(LimitId)
[1715]	1256	if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta
[1475]	1257	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
[1715]	1258	elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta
[1475]	1259	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
[1017]	1260	if G2frame.ifGetExclude:
	1261	excl = [0,0]
	1262	excl[0] = max(data[1][0],min(xy[0],data[1][1]))
	1263	excl[1] = excl[0]+0.1
	1264	data.append(excl)
	1265	G2frame.ifGetExclude = False
	1266	else:
	1267	if mouse.button==1:
	1268	data[1][0] = min(xy[0],data[1][1])
	1269	if mouse.button==3:
	1270	data[1][1] = max(xy[0],data[1][0])
[762]	1271	G2frame.PatternTree.SetItemPyData(LimitId,data)
[1221]	1272	G2pdG.UpdateLimitsGrid(G2frame,data,plottype)
[1199]	1273	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
[762]	1274	else: #picked a limit line
[1889]	1275	# prepare to animate move of line
[762]	1276	G2frame.itemPicked = pick
[1889]	1277	pick.set_linestyle(':') # set line as dotted
	1278	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	1279	Plot = Page.figure.gca()
	1280	Page.canvas.draw() # refresh without dotted line & save bitmap
	1281	savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox)
	1282	G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragLine)
	1283	pick.set_linestyle('--') # back to dashed
	1284
[1237]	1285	elif G2frame.PatternTree.GetItemText(PickId) == 'Models':
	1286	if ind.all() != [0]: #picked a data point
	1287	LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
	1288	data = G2frame.PatternTree.GetItemPyData(LimitId)
	1289	if mouse.button==1:
	1290	data[1][0] = min(xy[0],data[1][1])
	1291	if mouse.button==3:
	1292	data[1][1] = max(xy[0],data[1][0])
	1293	G2frame.PatternTree.SetItemPyData(LimitId,data)
	1294	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
	1295	else: #picked a limit line
	1296	G2frame.itemPicked = pick
[1889]	1297	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or
	1298	'PWDR' in G2frame.PatternTree.GetItemText(PickId)
	1299	):
[762]	1300	G2frame.itemPicked = pick
	1301	pick = str(pick)
[1889]	1302	elif G2frame.PatternTree.GetItemText(PickId) == 'Background':
[1894]	1303	# selected a fixed background point. Can move it or delete it.
[1889]	1304	for mode,id in G2frame.dataFrame.wxID_BackPts.iteritems(): # what menu is selected?
	1305	if G2frame.dataFrame.BackMenu.FindItemById(id).IsChecked():
	1306	break
	1307	# mode will be 'Add' or 'Move' or 'Del'
	1308	if pick.get_marker() == 'D':
	1309	# find the closest point
	1310	backDict = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Background'))[1]
	1311	d2 = [(x-xy[0])2+(y-xy[1])2 for x,y in backDict['FixedPoints']]
	1312	G2frame.fixPtMarker = d2.index(min(d2))
	1313	if mode == 'Move':
	1314	# animate move of FixedBkg marker
	1315	G2frame.itemPicked = pick
	1316	pick.set_marker('\|') # change the point appearance
	1317	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	1318	Plot = Page.figure.gca()
	1319	Page.canvas.draw() # refresh with changed point & save bitmap
	1320	savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox)
	1321	G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragMarker)
	1322	pick.set_marker('D') # put it back
	1323	elif mode == 'Del':
	1324	del backDict['FixedPoints'][G2frame.fixPtMarker]
	1325	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
	1326	return
	1327	def OnRelease(event): # mouse release from item pick or background pt add/move/del
	1328	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
	1329	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	1330	if G2frame.cid is not None: # if there is a drag connection, delete it
	1331	Page.canvas.mpl_disconnect(G2frame.cid)
	1332	G2frame.cid = None
	1333	PickId = G2frame.PickId # points to item in tree
	1334	if G2frame.PatternTree.GetItemText(PickId) == 'Background' and event.xdata:
[1894]	1335	if Page.toolbar._active: # prevent ops. if a toolbar zoom button pressed
	1336	return
[1889]	1337	# Background page, deal with fixed background points
	1338	if G2frame.SubBack or G2frame.Weight or G2frame.Contour or not G2frame.SinglePlot:
	1339	return
	1340	backDict = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Background'))[1]
	1341	if 'FixedPoints' not in backDict: backDict['FixedPoints'] = []
	1342	try:
	1343	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
	1344	except TypeError:
	1345	return
	1346	# unit conversions
	1347	xy = [event.xdata,event.ydata]
	1348	if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta
	1349	xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
	1350	elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta
	1351	xy[0] = G2lat.Dsp2pos(Parms,xy[0])
	1352	if G2frame.plotStyle['sqrtPlot']:
	1353	xy[1] = xy[1]**2
	1354	for mode,id in G2frame.dataFrame.wxID_BackPts.iteritems(): # what menu item is selected?
	1355	if G2frame.dataFrame.BackMenu.FindItemById(id).IsChecked():
	1356	break
	1357	if mode == 'Add':
	1358	backDict['FixedPoints'].append(xy)
	1359	Plot = Page.figure.gca()
	1360	Plot.plot(event.xdata,event.ydata,'rD',clip_on=False,picker=3.)
	1361	Page.canvas.draw()
	1362	return
	1363	elif G2frame.itemPicked is not None: # end of drag in move
	1364	backDict['FixedPoints'][G2frame.fixPtMarker] = xy
	1365	G2frame.itemPicked = None
	1366	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
	1367	return
[762]	1368
	1369	if G2frame.itemPicked is None: return
[1463]	1370	if str(DifLine[0]) == str(G2frame.itemPicked):
[1672]	1371	data = G2frame.PatternTree.GetItemPyData(PickId)
[1343]	1372	ypos = event.ydata
[1815]	1373	Pattern[0]['delOffset'] = -ypos/Ymax
[1343]	1374	G2frame.itemPicked = None
[1889]	1375	wx.CallAfter(PlotPatterns,G2frame,plotType=plottype)
[1343]	1376	return
[796]	1377	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
[762]	1378	xpos = event.xdata
	1379	if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos:
	1380	lines = []
	1381	for line in G2frame.Lines:
	1382	lines.append(line.get_xdata()[0])
[1204]	1383	try:
	1384	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
	1385	except ValueError:
	1386	lineNo = -1
[1017]	1387	if lineNo in [0,1] or lineNo in exclLines:
[762]	1388	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
[1743]	1389	limits = G2frame.PatternTree.GetItemPyData(LimitId)
[1017]	1390	id = lineNo/2+1
	1391	id2 = lineNo%2
[1715]	1392	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
[1743]	1393	limits[id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
[1715]	1394	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype:
[1743]	1395	limits[id][id2] = G2lat.Dsp2pos(Parms,xpos)
[762]	1396	else:
[1743]	1397	limits[id][id2] = xpos
	1398	if id > 1 and limits[id][0] > limits[id][1]:
	1399	limits[id].reverse()
	1400	limits[1][0] = min(max(limits[0][0],limits[1][0]),limits[1][1])
	1401	limits[1][1] = max(min(limits[0][1],limits[1][1]),limits[1][0])
[762]	1402	if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits':
[1744]	1403	G2pdG.UpdateLimitsGrid(G2frame,limits,plottype)
[1204]	1404	elif lineNo > 1:
[762]	1405	PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List')
[1743]	1406	peaks = G2frame.PatternTree.GetItemPyData(PeakId)
[762]	1407	if event.button == 3:
[1743]	1408	del peaks['peaks'][lineNo-2]
[762]	1409	else:
[1715]	1410	if G2frame.plotStyle['qPlot']:
[1743]	1411	peaks['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
[1715]	1412	elif G2frame.plotStyle['dPlot']:
[1743]	1413	peaks['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,xpos)
[762]	1414	else:
[1743]	1415	peaks['peaks'][lineNo-2][0] = xpos
	1416	peaks['sigDict'] = {} #no longer valid
	1417	G2pdG.UpdatePeakGrid(G2frame,peaks)
[1237]	1418	elif G2frame.PatternTree.GetItemText(PickId) in ['Models',] and xpos:
	1419	lines = []
	1420	for line in G2frame.Lines:
	1421	lines.append(line.get_xdata()[0])
	1422	try:
	1423	lineNo = lines.index(G2frame.itemPicked.get_xdata()[0])
	1424	except ValueError:
	1425	lineNo = -1
	1426	if lineNo in [0,1]:
	1427	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits')
	1428	data = G2frame.PatternTree.GetItemPyData(LimitId)
	1429	data[1][lineNo] = xpos
	1430	data[1][0] = min(max(data[0][0],data[1][0]),data[1][1])
	1431	data[1][1] = max(min(data[0][1],data[1][1]),data[1][0])
[762]	1432	elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \
	1433	'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos:
[1973]	1434	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists')
	1435	# GSASIIpath.IPyBreak()
	1436	if Id:
	1437	Phases = G2frame.PatternTree.GetItemPyData(Id)
	1438	pick = str(G2frame.itemPicked).split('(')[1].strip(')')
	1439	if 'line' not in pick: #avoid data points, etc.
	1440	data = G2frame.PatternTree.GetItemPyData(PatternId)
	1441	num = Phases.keys().index(pick)
	1442	if num:
	1443	data[0]['refDelt'] = -(event.ydata-Pattern[0]['refOffset'])/(num*Ymax)
	1444	else: #1st row of refl ticks
	1445	data[0]['refOffset'] = event.ydata
[1199]	1446	PlotPatterns(G2frame,plotType=plottype)
[762]	1447	G2frame.itemPicked = None
	1448
[1889]	1449	# beginning PlotPatterns execution
[762]	1450	try:
	1451	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
	1452	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[1907]	1453	Plot = Page.figure.gca() #get previous powder plot & get limits
	1454	G2frame.xylim = Plot.get_xlim(),Plot.get_ylim()
[762]	1455	Page.figure.clf()
	1456	Plot = Page.figure.gca() #get a fresh plot after clf()
	1457	except ValueError:
[1245]	1458	if plottype == 'SASD':
	1459	G2frame.logPlot = True
	1460	G2frame.ErrorBars = True
[762]	1461	newPlot = True
	1462	G2frame.Cmax = 1.0
	1463	Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca()
	1464	plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns')
	1465	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	1466	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
	1467	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	1468	Page.canvas.mpl_connect('pick_event', OnPick)
	1469	Page.canvas.mpl_connect('button_release_event', OnRelease)
[1237]	1470	Page.canvas.mpl_connect('button_press_event',OnPress)
[1281]	1471	if plottype == 'PWDR': # avoids a very nasty clash with KILL_FOCUS in SASD TextCtrl?
	1472	Page.SetFocus()
[762]	1473	G2frame.G2plotNB.status.DestroyChildren()
	1474	if G2frame.Contour:
[1205]	1475	Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
[762]	1476	'i: interpolation method','s: color scheme','c: contour off')
	1477	else:
	1478	if G2frame.logPlot:
[1205]	1479	if 'PWDR' in plottype:
[1366]	1480	if G2frame.SinglePlot:
	1481	Page.Choice = (' key press','n: log(I) off',
[1462]	1482	'c: contour on','q: toggle q plot','t: toggle d-spacing plot',
	1483	'm: toggle multidata plot','w: toggle divide by sig','+: no selection')
[1366]	1484	else:
	1485	Page.Choice = (' key press','n: log(I) off',
	1486	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
[1462]	1487	'c: contour on','q: toggle q plot','t: toggle d-spacing plot',
	1488	'm: toggle multidata plot','w: toggle divide by sig','+: no selection')
[1205]	1489	elif 'SASD' in plottype:
[1366]	1490	if G2frame.SinglePlot:
	1491	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
	1492	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
	1493	else:
	1494	Page.Choice = (' key press','b: toggle subtract background file','n: semilog on',
	1495	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
	1496	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
[762]	1497	else:
[1201]	1498	if 'PWDR' in plottype:
[1366]	1499	if G2frame.SinglePlot:
	1500	Page.Choice = (' key press',
[1368]	1501	'b: toggle subtract background','n: log(I) on','s: toggle sqrt plot','c: contour on',
[1462]	1502	'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot',
	1503	'w: toggle divide by sig','+: no selection')
[1366]	1504	else:
	1505	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down',
	1506	'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on',
[1462]	1507	'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot',
	1508	'w: toggle divide by sig','+: no selection')
[1201]	1509	elif 'SASD' in plottype:
[1366]	1510	if G2frame.SinglePlot:
	1511	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
	1512	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
	1513	else:
	1514	Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars',
	1515	'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset',
	1516	'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection')
[1889]	1517	G2frame.cid = None
[1237]	1518	Page.keyPress = OnPlotKeyPress
[762]	1519	PickId = G2frame.PickId
	1520	PatternId = G2frame.PatternId
	1521	colors=['b','g','r','c','m','k']
	1522	Lines = []
[1017]	1523	exclLines = []
[1621]	1524	if G2frame.SinglePlot and PatternId:
[762]	1525	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
	1526	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
	1527	PlotList = [Pattern,]
[796]	1528	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
[792]	1529	G2frame.PatternId, 'Instrument Parameters'))
[1201]	1530	Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
[792]	1531	ParmList = [Parms,]
[1203]	1532	SampleList = [Sample,]
[828]	1533	Title = Pattern[-1]
[762]	1534	else:
[828]	1535	Title = os.path.split(G2frame.GSASprojectfile)[1]
[762]	1536	PlotList = []
	1537	ParmList = []
[1201]	1538	SampleList = []
[762]	1539	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
	1540	while item:
[1201]	1541	if plottype in G2frame.PatternTree.GetItemText(item):
[762]	1542	Pattern = G2frame.PatternTree.GetItemPyData(item)
	1543	if len(Pattern) < 3: # put name on end if needed
	1544	Pattern.append(G2frame.PatternTree.GetItemText(item))
[1774]	1545	if 'Offset' not in Pattern[0]: #plot offset data
	1546	Pattern[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,})
[762]	1547	PlotList.append(Pattern)
	1548	ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
[796]	1549	item,'Instrument Parameters'))[0])
[1201]	1550	SampleList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
	1551	item, 'Sample Parameters')))
[762]	1552	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
	1553	lenX = 0
[1084]	1554	Ymax = None
[762]	1555	for Pattern in PlotList:
	1556	xye = Pattern[1]
[1086]	1557	if xye[1] is None: continue
[1084]	1558	if Ymax is None: Ymax = max(xye[1])
[762]	1559	Ymax = max(Ymax,max(xye[1]))
[1084]	1560	if Ymax is None: return # nothing to plot
[1694]	1561	offsetX = Pattern[0]['Offset'][1]
	1562	offsetY = Pattern[0]['Offset'][0]
[762]	1563	if G2frame.logPlot:
	1564	Title = 'log('+Title+')'
	1565	Plot.set_title(Title)
[1715]	1566	if G2frame.plotStyle['qPlot'] or 'SASD' in plottype and not G2frame.Contour:
[1203]	1567	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=16)
[1715]	1568	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype and not G2frame.Contour:
[1462]	1569	Plot.set_xlabel(r'$d, \AA$',fontsize=16)
[792]	1570	else:
	1571	if 'C' in ParmList[0]['Type'][0]:
[1203]	1572	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=16)
[792]	1573	else:
[1519]	1574	if G2frame.Contour:
	1575	Plot.set_xlabel(r'Channel no.',fontsize=16)
	1576	else:
	1577	Plot.set_xlabel(r'$TOF, \mathsf{\mu}$s',fontsize=16)
[762]	1578	if G2frame.Weight:
[1341]	1579	if 'PWDR' in plottype:
	1580	Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=16)
	1581	elif 'SASD' in plottype:
	1582	Plot.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16)
[762]	1583	else:
[792]	1584	if 'C' in ParmList[0]['Type'][0]:
[1201]	1585	if 'PWDR' in plottype:
[1715]	1586	if G2frame.plotStyle['sqrtPlot']:
[1368]	1587	Plot.set_ylabel(r'$\sqrt{Intensity}$',fontsize=16)
	1588	else:
[1370]	1589	Plot.set_ylabel(r'$Intensity$',fontsize=16)
[1201]	1590	elif 'SASD' in plottype:
[1205]	1591	if G2frame.sqPlot:
[1370]	1592	Plot.set_ylabel(r'$S(Q)=I*Q^{4}$',fontsize=16)
[1205]	1593	else:
[1370]	1594	Plot.set_ylabel(r'$Intensity, cm^{-1}$',fontsize=16)
[792]	1595	else:
[1715]	1596	if G2frame.plotStyle['sqrtPlot']:
[1370]	1597	Plot.set_ylabel(r'$\sqrt{Normalized\ intensity}$',fontsize=16)
	1598	else:
	1599	Plot.set_ylabel(r'$Normalized\ intensity$',fontsize=16)
[762]	1600	if G2frame.Contour:
	1601	ContourZ = []
	1602	ContourY = []
	1603	Nseq = 0
	1604	for N,Pattern in enumerate(PlotList):
	1605	Parms = ParmList[N]
[1201]	1606	Sample = SampleList[N]
[792]	1607	if 'C' in Parms['Type'][0]:
[795]	1608	wave = G2mth.getWave(Parms)
[792]	1609	else:
	1610	difC = Parms['difC'][1]
[762]	1611	ifpicked = False
	1612	LimitId = 0
[1084]	1613	if Pattern[1] is None: continue # skip over uncomputed simulations
[1025]	1614	xye = ma.array(ma.getdata(Pattern[1]))
[1199]	1615	Zero = Parms.get('Zero',[0.,0.])[1]
[1774]	1616	if PickId:
	1617	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
	1618	LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId,'Limits')
	1619	limits = G2frame.PatternTree.GetItemPyData(LimitId)
	1620	excls = limits[2:]
	1621	for excl in excls:
	1622	xye[0] = ma.masked_inside(xye[0],excl[0],excl[1])
[1715]	1623	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
[762]	1624	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
[1475]	1625	X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye[0])
[1715]	1626	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype:
[1462]	1627	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
[1475]	1628	X = G2lat.Pos2dsp(Parms,xye[0])
[762]	1629	else:
[1475]	1630	X = xye[0]
[762]	1631	if not lenX:
[1087]	1632	lenX = len(X)
[1201]	1633	if 'PWDR' in plottype:
[1715]	1634	if G2frame.plotStyle['sqrtPlot']:
[1420]	1635	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
[1368]	1636	Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1]))
[1420]	1637	np.seterr(invalid=olderr['invalid'])
[1368]	1638	else:
[1694]	1639	Y = xye[1]+offsetYNYmax/100.0
[1201]	1640	elif 'SASD' in plottype:
[1300]	1641	B = xye[5]
[1217]	1642	if G2frame.sqPlot:
[1694]	1643	Y = xye[1]Sample['Scale'][0](1.05)*(offsetYN)X*4
[1205]	1644	else:
[1694]	1645	Y = xye[1]Sample['Scale'][0](1.05)*(offsetYN)
[1204]	1646	if LimitId and ifpicked:
[762]	1647	limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
[1475]	1648	lims = limits[1]
[1715]	1649	if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype:
[1475]	1650	lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims)
[1715]	1651	elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype:
[1475]	1652	lims = G2lat.Pos2dsp(Parms,lims)
	1653	Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.))
	1654	Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.))
[1017]	1655	for i,item in enumerate(limits[2:]):
	1656	Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))
	1657	Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.))
	1658	exclLines += [2i+2,2i+3]
[1519]	1659	if G2frame.Contour:
[762]	1660	if lenX == len(X):
	1661	ContourY.append(N)
	1662	ContourZ.append(Y)
[1519]	1663	if 'C' in ParmList[0]['Type'][0]:
	1664	ContourX = X
	1665	else: #'T'OF
	1666	ContourX = range(lenX)
[762]	1667	Nseq += 1
	1668	Plot.set_ylabel('Data sequence',fontsize=12)
	1669	else:
[1205]	1670	if 'SASD' in plottype and G2frame.logPlot:
[1694]	1671	X = (1.01)(offsetXN)
[1205]	1672	else:
[1694]	1673	X += offsetX.005N
[1017]	1674	Xum = ma.getdata(X)
[1349]	1675	DifLine = ['']
[762]	1676	if ifpicked:
[1715]	1677	if G2frame.plotStyle['sqrtPlot']:
[1582]	1678	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
[1368]	1679	Z = np.where(xye[3]>=0.,np.sqrt(xye[3]),-np.sqrt(-xye[3]))
[1582]	1680	np.seterr(invalid=olderr['invalid'])
[1368]	1681	else:
[1694]	1682	Z = xye[3]+offsetYNYmax/100.0
[1339]	1683	if 'PWDR' in plottype:
[1715]	1684	if G2frame.plotStyle['sqrtPlot']:
[1586]	1685	olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
[1368]	1686	W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4]))
[1586]	1687	np.seterr(invalid=olderr['invalid'])
[1672]	1688	D = np.where(xye[5],(Y-Z),0.)-Ymax*Pattern[0]['delOffset']
[1368]	1689	else:
[1694]	1690	W = xye[4]+offsetYNYmax/100.0
[1672]	1691	D = xye[5]-Ymax*Pattern[0]['delOffset'] #powder background
[1201]	1692	elif 'SASD' in plottype:
[1264]	1693	if G2frame.sqPlot:
[1300]	1694	W = xye[4]X*4
[1264]	1695	Z = xye[3]X*4
[1300]	1696	B = BX*4
[1264]	1697	else:
[1300]	1698	W = xye[4]
	1699	if G2frame.SubBack:
	1700	YB = Y-B
	1701	ZB = Z
	1702	else:
	1703	YB = Y
	1704	ZB = Z+B
[1232]	1705	Plot.set_yscale("log",nonposy='mask')
[1341]	1706	if np.any(W>0.):
	1707	Plot.set_ylim(bottom=np.min(np.trim_zeros(W))/2.,top=np.max(Y)*2.)
	1708	else:
	1709	Plot.set_ylim(bottom=np.min(np.trim_zeros(YB))/2.,top=np.max(Y)*2.)
[762]	1710	if G2frame.logPlot:
[1201]	1711	if 'PWDR' in plottype:
[1205]	1712	Plot.set_yscale("log",nonposy='mask')
	1713	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
	1714	Plot.plot(X,Z,colors[(N+1)%6],picker=False)
[1341]	1715	Plot.plot(X,W,colors[(N+2)%6],picker=False) #background
[1201]	1716	elif 'SASD' in plottype:
[1205]	1717	Plot.set_xscale("log",nonposx='mask')
[1343]	1718	Ibeg = np.searchsorted(X,limits[1][0])
	1719	Ifin = np.searchsorted(X,limits[1][1])
	1720	if G2frame.Weight:
	1721	Plot.set_yscale("linear")
	1722	DS = (YB-ZB)*np.sqrt(xye[2])
	1723	Plot.plot(X[Ibeg:Ifin],DS[Ibeg:Ifin],colors[(N+3)%6],picker=False)
	1724	Plot.axhline(0.,color=wx.BLACK)
	1725	Plot.set_ylim(bottom=np.min(DS[Ibeg:Ifin])1.2,top=np.max(DS[Ibeg:Ifin])1.2)
	1726	else:
	1727	Plot.set_yscale("log",nonposy='mask')
	1728	if G2frame.ErrorBars:
	1729	if G2frame.sqPlot:
	1730	Plot.errorbar(X,YB,yerr=X*4Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
	1731	ecolor=colors[N%6],picker=3.,clip_on=False)
	1732	else:
	1733	Plot.errorbar(X,YB,yerr=Sample['Scale'][0]np.sqrt(1./(Pattern[0]['wtFactor']xye[2])),
	1734	ecolor=colors[N%6],picker=3.,clip_on=False)
[1264]	1735	else:
[1343]	1736	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
	1737	Plot.plot(X,W,colors[(N+2)%6],picker=False) #const. background
	1738	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
[1205]	1739	elif G2frame.Weight and 'PWDR' in plottype:
[762]	1740	DY = xye[1]*np.sqrt(xye[2])
[1343]	1741	Ymax = max(DY)
[762]	1742	DZ = xye[3]*np.sqrt(xye[2])
[1672]	1743	DS = xye[5]np.sqrt(xye[2])-YmaxPattern[0]['delOffset']
[1343]	1744	ObsLine = Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False) #Io/sig(Io)
	1745	Plot.plot(X,DZ,colors[(N+1)%6],picker=False) #Ic/sig(Io)
	1746	DifLine = Plot.plot(X,DS,colors[(N+3)%6],picker=1.) #(Io-Ic)/sig(Io)
[762]	1747	Plot.axhline(0.,color=wx.BLACK)
	1748	else:
[1300]	1749	if G2frame.SubBack:
[1344]	1750	if 'PWDR' in plottype:
	1751	Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=False,clip_on=False) #Io-Ib
	1752	Plot.plot(X,Z-W,colors[(N+1)%6],picker=False) #Ic-Ib
	1753	else:
	1754	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
	1755	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
[792]	1756	else:
[1344]	1757	if 'PWDR' in plottype:
	1758	ObsLine = Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False) #Io
	1759	Plot.plot(X,Z,colors[(N+1)%6],picker=False) #Ic
	1760	else:
	1761	Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False)
	1762	Plot.plot(X,ZB,colors[(N+1)%6],picker=False)
[1201]	1763	if 'PWDR' in plottype:
[1343]	1764	Plot.plot(X,W,colors[(N+2)%6],picker=False) #Ib
	1765	DifLine = Plot.plot(X,D,colors[(N+3)%6],picker=1.) #Io-Ic
[762]	1766	Plot.axhline(0.,color=wx.BLACK)
	1767	Page.canvas.SetToolTipString('')
[1774]	1768	if PickId:
	1769	if G2frame.PatternTree.GetItemText(PickId) == 'Peak List':
	1770	tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete'
	1771	Page.canvas.SetToolTipString(tip)
	1772	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))
	1773	for item in data['peaks']:
	1774	if G2frame.plotStyle['qPlot']:
	1775	Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
	1776	elif G2frame.plotStyle['dPlot']:
	1777	Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
	1778	else:
	1779	Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
	1780	if G2frame.PatternTree.GetItemText(PickId) == 'Limits':
	1781	tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move'
	1782	Page.canvas.SetToolTipString(tip)
	1783	data = G2frame.LimitsTable.GetData()
	1784
[1339]	1785	else: #not picked
[762]	1786	if G2frame.logPlot:
[1201]	1787	if 'PWDR' in plottype:
[1199]	1788	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
[1201]	1789	elif 'SASD' in plottype:
[1244]	1790	Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask')
[762]	1791	else:
[1217]	1792	if 'PWDR' in plottype:
	1793	Plot.plot(X,Y,colors[N%6],picker=False)
	1794	elif 'SASD' in plottype:
[1244]	1795	Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask')
[1232]	1796	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
[1343]	1797
	1798	if G2frame.logPlot and 'PWDR' in plottype:
	1799	Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.)
[762]	1800	if PickId and not G2frame.Contour:
[796]	1801	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
[762]	1802	if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
[1882]	1803	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))
[1618]	1804	if not len(peaks): return # are there any peaks?
[1607]	1805	for peak in peaks[0]:
[1586]	1806	if peak[2]:
[1715]	1807	if G2frame.plotStyle['qPlot']:
[1586]	1808	Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b')
[1715]	1809	if G2frame.plotStyle['dPlot']:
[1586]	1810	Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b')
	1811	else:
	1812	Plot.axvline(peak[0],color='b')
[762]	1813	for hkl in G2frame.HKL:
[1571]	1814	clr = 'r'
	1815	if len(hkl) > 6 and hkl[3]:
	1816	clr = 'g'
[1715]	1817	if G2frame.plotStyle['qPlot']:
[1578]	1818	Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5))
[1715]	1819	if G2frame.plotStyle['dPlot']:
[1578]	1820	Plot.axvline(G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5))
[762]	1821	else:
[1578]	1822	Plot.axvline(hkl[-2],color=clr,dashes=(5,5))
[762]	1823	elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \
	1824	'PWDR' in G2frame.PatternTree.GetItemText(PickId):
[808]	1825	refColors=['b','r','c','g','m','k']
[762]	1826	Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
	1827	for pId,phase in enumerate(Phases):
[1944]	1828	peaks = Phases[phase].get('RefList',[])
[1107]	1829	if not len(peaks):
[762]	1830	continue
[1660]	1831	if Phases[phase].get('Super',False):
[1596]	1832	peak = np.array([[peak[5],peak[6]] for peak in peaks])
	1833	else:
	1834	peak = np.array([[peak[4],peak[5]] for peak in peaks])
[1672]	1835	pos = Pattern[0]['refOffset']-pIdYmaxPattern[0]['refDelt']*np.ones_like(peak)
[1715]	1836	if G2frame.plotStyle['qPlot']:
[808]	1837	Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
[1715]	1838	elif G2frame.plotStyle['dPlot']:
[1462]	1839	Plot.plot(peak.T[0],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
[762]	1840	else:
[808]	1841	Plot.plot(peak.T[1],pos,refColors[pId%6]+'\|',mew=1,ms=8,picker=3.,label=phase)
[762]	1842	if len(Phases):
	1843	handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason
	1844	if handles:
	1845	Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one
	1846
	1847	if G2frame.Contour:
	1848	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
	1849	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
	1850	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
	1851	Page.figure.colorbar(Img)
	1852	else:
	1853	G2frame.Lines = Lines
[1889]	1854	if G2frame.PatternTree.GetItemText(PickId) == 'Background':
	1855	# plot fixed background points
	1856	backDict = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Background'))[1]
	1857	try:
	1858	Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
	1859	except TypeError:
	1860	Parms = None
	1861	for x,y in backDict.get('FixedPoints',[]):
	1862	# "normal" intensity modes only!
	1863	if G2frame.SubBack or G2frame.Weight or G2frame.Contour or not G2frame.SinglePlot:
	1864	break
	1865	if y < 0 and (G2frame.plotStyle['sqrtPlot'] or G2frame.logPlot):
	1866	y = Page.figure.gca().get_ylim()[0] # put out of range point at bottom of plot
	1867	elif G2frame.plotStyle['sqrtPlot']:
	1868	y = math.sqrt(y)
	1869	if G2frame.plotStyle['qPlot']: #Q - convert from 2-theta
	1870	if Parms:
	1871	x = 2*np.pi/G2lat.Pos2dsp(Parms,x)
	1872	else:
	1873	break
	1874	elif G2frame.plotStyle['dPlot']: #d - convert from 2-theta
	1875	if Parms:
	1876	x = G2lat.Dsp2pos(Parms,x)
	1877	else:
	1878	break
	1879	Plot.plot(x,y,'rD',clip_on=False,picker=3.)
[762]	1880	if not newPlot:
	1881	Page.toolbar.push_current()
[1907]	1882	Plot.set_xlim(G2frame.xylim[0])
	1883	Plot.set_ylim(G2frame.xylim[1])
[1281]	1884	# xylim = []
[762]	1885	Page.toolbar.push_current()
	1886	Page.toolbar.draw()
	1887	else:
[1907]	1888	G2frame.xylim = Plot.get_xlim(),Plot.get_ylim()
[762]	1889	Page.canvas.draw()
[1369]	1890	olderr = np.seterr(invalid='ignore') #ugh - this removes a matplotlib error for mouse clicks in log plots
	1891	# and sqrt(-ve) in np.where usage
[762]	1892	# G2frame.Pwdr = True
	1893
	1894	################################################################################
	1895	##### PlotDeltSig
	1896	################################################################################
	1897
	1898	def PlotDeltSig(G2frame,kind):
[939]	1899	'needs a doc string'
[762]	1900	try:
	1901	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
	1902	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	1903	Page.figure.clf()
	1904	Plot = Page.figure.gca() #get a fresh plot after clf()
	1905	except ValueError:
	1906	newPlot = True
	1907	G2frame.Cmax = 1.0
	1908	Plot = G2frame.G2plotNB.addMpl('Error analysis').gca()
	1909	plotNum = G2frame.G2plotNB.plotList.index('Error analysis')
	1910	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[796]	1911	Page.Choice = None
[762]	1912	PatternId = G2frame.PatternId
	1913	Pattern = G2frame.PatternTree.GetItemPyData(PatternId)
	1914	Pattern.append(G2frame.PatternTree.GetItemText(PatternId))
	1915	wtFactor = Pattern[0]['wtFactor']
	1916	if kind == 'PWDR':
	1917	limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1]
	1918	xye = np.array(Pattern[1])
	1919	xmin = np.searchsorted(xye[0],limits[0])
	1920	xmax = np.searchsorted(xye[0],limits[1])
	1921	DS = xye[5][xmin:xmax]np.sqrt(wtFactorxye[2][xmin:xmax])
	1922	elif kind == 'HKLF':
[1788]	1923	refl = Pattern[1]['RefList']
	1924	im = 0
	1925	if Pattern[1]['Super']:
	1926	im = 1
[762]	1927	DS = []
	1928	for ref in refl:
[1788]	1929	if ref[6+im] > 0.:
	1930	DS.append((ref[5+im]-ref[7+im])/ref[6+im])
[762]	1931	Page.SetFocus()
	1932	G2frame.G2plotNB.status.DestroyChildren()
	1933	DS.sort()
	1934	EDS = np.zeros_like(DS)
	1935	DX = np.linspace(0.,1.,num=len(DS),endpoint=True)
	1936	oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0
	1937	T = np.sqrt(np.log(1.0/DX**2))
	1938	top = 2.515517+0.802853T+0.010328T**2
	1939	bot = 1.0+1.432788T+0.189269T*2+0.001308T**3
	1940	EDS = np.where(DX>0,-(T-top/bot),(T-top/bot))
	1941	low1 = np.searchsorted(EDS,-1.)
	1942	hi1 = np.searchsorted(EDS,1.)
	1943	slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1)
	1944	frac = 100.*(hi1-low1)/len(DS)
	1945	G2frame.G2plotNB.status.SetStatusText( \
	1946	'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1)
	1947	Plot.set_title('Normal probability for '+Pattern[-1])
	1948	Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14)
	1949	Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14)
	1950	Plot.plot(EDS,DS,'r+',label='result')
	1951	Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal')
	1952	Plot.legend(loc='upper left')
	1953	np.seterr(invalid='warn')
	1954	Page.canvas.draw()
	1955
	1956	################################################################################
	1957	##### PlotISFG
	1958	################################################################################
	1959
	1960	def PlotISFG(G2frame,newPlot=False,type=''):
[1201]	1961	''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single
[762]	1962	or multiple plots with waterfall and contour plots as options
	1963	'''
	1964	if not type:
	1965	type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()]
	1966	if type not in ['I(Q)','S(Q)','F(Q)','G(R)']:
	1967	return
	1968	superMinusOne = unichr(0xaf)+unichr(0xb9)
	1969
	1970	def OnPlotKeyPress(event):
	1971	newPlot = False
	1972	if event.key == 'u':
	1973	if G2frame.Contour:
	1974	G2frame.Cmax = min(1.0,G2frame.Cmax*1.2)
[1672]	1975	elif Pattern[0]['Offset'][0] < 100.:
	1976	Pattern[0]['Offset'][0] += 1.
[762]	1977	elif event.key == 'd':
	1978	if G2frame.Contour:
	1979	G2frame.Cmax = max(0.0,G2frame.Cmax*0.8)
[1672]	1980	elif Pattern[0]['Offset'][0] > 0.:
	1981	Pattern[0]['Offset'][0] -= 1.
[762]	1982	elif event.key == 'l':
[1672]	1983	Pattern[0]['Offset'][1] -= 1.
[762]	1984	elif event.key == 'r':
[1672]	1985	Pattern[0]['Offset'][1] += 1.
[762]	1986	elif event.key == 'o':
[1672]	1987	Pattern[0]['Offset'] = [0,0]
[762]	1988	elif event.key == 'c':
	1989	newPlot = True
[1205]	1990	G2frame.Contour = not G2frame.Contour
	1991	if not G2frame.Contour:
[762]	1992	G2frame.SinglePlot = False
[1672]	1993	Pattern[0]['Offset'] = [0.,0.]
[762]	1994	elif event.key == 's':
	1995	if G2frame.Contour:
	1996	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
	1997	choice.sort()
	1998	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
	1999	if dlg.ShowModal() == wx.ID_OK:
	2000	sel = dlg.GetSelection()
	2001	G2frame.ContourColor = choice[sel]
	2002	else:
	2003	G2frame.ContourColor = 'Paired'
	2004	dlg.Destroy()
[1205]	2005	else:
	2006	G2frame.SinglePlot = not G2frame.SinglePlot
[762]	2007	elif event.key == 'i': #for smoothing contour plot
	2008	choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning',
	2009	'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel',
	2010	'mitchell','sinc','lanczos']
	2011	dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice)
	2012	if dlg.ShowModal() == wx.ID_OK:
	2013	sel = dlg.GetSelection()
	2014	G2frame.Interpolate = choice[sel]
	2015	else:
	2016	G2frame.Interpolate = 'nearest'
	2017	dlg.Destroy()
	2018	elif event.key == 't' and not G2frame.Contour:
[1205]	2019	G2frame.Legend = not G2frame.Legend
[762]	2020	PlotISFG(G2frame,newPlot=newPlot,type=type)
	2021
	2022	def OnKeyBox(event):
	2023	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type):
	2024	event.key = cb.GetValue()[0]
	2025	cb.SetValue(' key press')
	2026	wx.CallAfter(OnPlotKeyPress,event)
[1005]	2027	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
[762]	2028
	2029	def OnMotion(event):
	2030	xpos = event.xdata
	2031	if xpos: #avoid out of frame mouse position
	2032	ypos = event.ydata
	2033	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	2034	try:
	2035	if G2frame.Contour:
	2036	G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1)
	2037	else:
	2038	G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1)
	2039	except TypeError:
	2040	G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1)
	2041
	2042	xylim = []
	2043	try:
	2044	plotNum = G2frame.G2plotNB.plotList.index(type)
	2045	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2046	if not newPlot:
	2047	Plot = Page.figure.gca() #get previous plot & get limits
	2048	xylim = Plot.get_xlim(),Plot.get_ylim()
	2049	Page.figure.clf()
	2050	Plot = Page.figure.gca()
	2051	except ValueError:
	2052	newPlot = True
	2053	G2frame.Cmax = 1.0
	2054	Plot = G2frame.G2plotNB.addMpl(type).gca()
	2055	plotNum = G2frame.G2plotNB.plotList.index(type)
	2056	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2057	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
	2058	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2059
	2060	Page.SetFocus()
	2061	G2frame.G2plotNB.status.DestroyChildren()
	2062	if G2frame.Contour:
[796]	2063	Page.Choice = (' key press','d: lower contour max','u: raise contour max',
[762]	2064	'i: interpolation method','s: color scheme','c: contour off')
	2065	else:
[796]	2066	Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up',
[762]	2067	'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot')
[796]	2068	Page.keyPress = OnPlotKeyPress
[762]	2069	PatternId = G2frame.PatternId
	2070	PickId = G2frame.PickId
	2071	Plot.set_title(type)
	2072	if type == 'G(R)':
	2073	Plot.set_xlabel(r'$R,\AA$',fontsize=14)
	2074	else:
	2075	Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14)
	2076	Plot.set_ylabel(r''+type,fontsize=14)
	2077	colors=['b','g','r','c','m','k']
	2078	name = G2frame.PatternTree.GetItemText(PatternId)[4:]
	2079	Pattern = []
	2080	if G2frame.SinglePlot:
	2081	name = G2frame.PatternTree.GetItemText(PatternId)
	2082	name = type+name[4:]
	2083	Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name)
	2084	Pattern = G2frame.PatternTree.GetItemPyData(Id)
	2085	if Pattern:
	2086	Pattern.append(name)
	2087	PlotList = [Pattern,]
	2088	else:
	2089	PlotList = []
	2090	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
	2091	while item:
	2092	if 'PDF' in G2frame.PatternTree.GetItemText(item):
	2093	name = type+G2frame.PatternTree.GetItemText(item)[4:]
	2094	Id = G2gd.GetPatternTreeItemId(G2frame,item,name)
	2095	Pattern = G2frame.PatternTree.GetItemPyData(Id)
	2096	if Pattern:
	2097	Pattern.append(name)
	2098	PlotList.append(Pattern)
	2099	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
	2100	PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls'))
	2101	numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol'])
	2102	Xb = [0.,10.]
	2103	Yb = [0.,-40.np.pinumbDen]
[1835]	2104	Ymax = 0.01
[762]	2105	lenX = 0
	2106	for Pattern in PlotList:
[1613]	2107	try:
	2108	xye = Pattern[1]
	2109	except IndexError:
	2110	return
[762]	2111	Ymax = max(Ymax,max(xye[1]))
[1672]	2112	offset = Pattern[0]['Offset'][0]*Ymax/100.0
[762]	2113	if G2frame.Contour:
	2114	ContourZ = []
	2115	ContourY = []
	2116	Nseq = 0
	2117	for N,Pattern in enumerate(PlotList):
	2118	xye = Pattern[1]
	2119	if PickId:
	2120	ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId)
	2121	X = xye[0]
	2122	if not lenX:
	2123	lenX = len(X)
	2124	Y = xye[1]+offset*N
	2125	if G2frame.Contour:
	2126	if lenX == len(X):
	2127	ContourY.append(N)
	2128	ContourZ.append(Y)
	2129	ContourX = X
	2130	Nseq += 1
	2131	Plot.set_ylabel('Data sequence',fontsize=12)
	2132	else:
[1672]	2133	X = xye[0]+Pattern[0]['Offset'][1].005N
[762]	2134	if ifpicked:
	2135	Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False)
	2136	Page.canvas.SetToolTipString('')
	2137	else:
	2138	if G2frame.Legend:
	2139	Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1])
	2140	else:
	2141	Plot.plot(X,Y,colors[N%6],picker=False)
	2142	if type == 'G(R)':
	2143	Plot.plot(Xb,Yb,color='k',dashes=(5,5))
	2144	elif type == 'F(Q)':
	2145	Plot.axhline(0.,color=wx.BLACK)
	2146	elif type == 'S(Q)':
	2147	Plot.axhline(1.,color=wx.BLACK)
	2148	if G2frame.Contour:
	2149	acolor = mpl.cm.get_cmap(G2frame.ContourColor)
	2150	Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate,
	2151	extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
	2152	Page.figure.colorbar(Img)
	2153	elif G2frame.Legend:
	2154	Plot.legend(loc='best')
	2155	if not newPlot:
	2156	Page.toolbar.push_current()
	2157	Plot.set_xlim(xylim[0])
	2158	Plot.set_ylim(xylim[1])
	2159	xylim = []
	2160	Page.toolbar.push_current()
	2161	Page.toolbar.draw()
	2162	else:
	2163	Page.canvas.draw()
	2164
	2165	################################################################################
[1443]	2166	##### PlotCalib
	2167	################################################################################
	2168
[1445]	2169	def PlotCalib(G2frame,Inst,XY,Sigs,newPlot=False):
[1443]	2170	'''plot of CW or TOF peak calibration
	2171	'''
	2172	def OnMotion(event):
	2173	xpos = event.xdata
	2174	if xpos: #avoid out of frame mouse position
	2175	ypos = event.ydata
	2176	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	2177	try:
[1493]	2178	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3g'%(xpos,Title,ypos),1)
[1443]	2179	except TypeError:
	2180	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
[1445]	2181	found = []
	2182	wid = 1
	2183	view = Page.toolbar._views.forward()
	2184	if view:
	2185	view = view[0][:2]
	2186	wid = view[1]-view[0]
	2187	found = XY[np.where(np.fabs(XY.T[0]-xpos) < 0.005*wid)]
	2188	if len(found):
	2189	pos = found[0][1]
	2190	if 'C' in Inst['Type'][0]:
	2191	Page.canvas.SetToolTipString('position=%.4f'%(pos))
	2192	else:
	2193	Page.canvas.SetToolTipString('position=%.2f'%(pos))
	2194	else:
	2195	Page.canvas.SetToolTipString('')
[1443]	2196
	2197	Title = 'Position calibration'
	2198	try:
	2199	plotNum = G2frame.G2plotNB.plotList.index(Title)
	2200	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2201	if not newPlot:
	2202	Plot = Page.figure.gca()
	2203	xylim = Plot.get_xlim(),Plot.get_ylim()
	2204	Page.figure.clf()
	2205	Plot = Page.figure.gca()
	2206	except ValueError:
	2207	newPlot = True
	2208	Plot = G2frame.G2plotNB.addMpl(Title).gca()
	2209	plotNum = G2frame.G2plotNB.plotList.index(Title)
	2210	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2211	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2212
	2213	Page.Choice = None
	2214	Page.SetFocus()
	2215	G2frame.G2plotNB.status.DestroyChildren()
	2216	Plot.set_title(Title)
	2217	Plot.set_xlabel(r'd-spacing',fontsize=14)
	2218	if 'C' in Inst['Type'][0]:
	2219	Plot.set_ylabel(r'$\mathsf{\Delta(2\theta)}$',fontsize=14)
	2220	else:
	2221	Plot.set_ylabel(r'$\mathsf{\Delta}T/T$',fontsize=14)
[1493]	2222	for ixy,xyw in enumerate(XY):
	2223	if len(xyw) > 2:
	2224	X,Y,W = xyw
	2225	else:
	2226	X,Y = xyw
	2227	W = 0.
[1443]	2228	Yc = G2lat.Dsp2pos(Inst,X)
	2229	if 'C' in Inst['Type'][0]:
	2230	Y = Y-Yc
[1445]	2231	E = Sigs[ixy]
[1493]	2232	bin = W/2.
[1443]	2233	else:
	2234	Y = (Y-Yc)/Yc
[1445]	2235	E = Sigs[ixy]/Yc
[1493]	2236	bin = W/(2.*Yc)
[1445]	2237	if E:
	2238	Plot.errorbar(X,Y,ecolor='k',yerr=E)
[1493]	2239	if ixy:
	2240	Plot.plot(X,Y,'kx',picker=3)
	2241	else:
	2242	Plot.plot(X,Y,'kx',label='peak')
	2243	if W:
	2244	if ixy:
	2245	Plot.plot(X,bin,'b+')
	2246	else:
	2247	Plot.plot(X,bin,'b+',label='bin width')
	2248	Plot.plot(X,-bin,'b+')
[1459]	2249	Plot.axhline(0.,color='r',linestyle='--')
[1493]	2250	Plot.legend(loc='best')
[1443]	2251	if not newPlot:
	2252	Page.toolbar.push_current()
	2253	Plot.set_xlim(xylim[0])
	2254	Plot.set_ylim(xylim[1])
[1445]	2255	# xylim = []
[1443]	2256	Page.toolbar.push_current()
	2257	Page.toolbar.draw()
	2258	else:
	2259	Page.canvas.draw()
	2260
	2261	################################################################################
[762]	2262	##### PlotXY
	2263	################################################################################
	2264
[1402]	2265	def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,Title=''):
[762]	2266	'''simple plot of xy data, used for diagnostic purposes
	2267	'''
	2268	def OnMotion(event):
	2269	xpos = event.xdata
	2270	if xpos: #avoid out of frame mouse position
	2271	ypos = event.ydata
	2272	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	2273	try:
[1402]	2274	G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,Title,ypos),1)
[762]	2275	except TypeError:
[1402]	2276	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
[762]	2277
	2278	try:
[1402]	2279	plotNum = G2frame.G2plotNB.plotList.index(Title)
[762]	2280	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2281	if not newPlot:
	2282	Plot = Page.figure.gca()
	2283	xylim = Plot.get_xlim(),Plot.get_ylim()
	2284	Page.figure.clf()
	2285	Plot = Page.figure.gca()
	2286	except ValueError:
	2287	newPlot = True
[1402]	2288	Plot = G2frame.G2plotNB.addMpl(Title).gca()
	2289	plotNum = G2frame.G2plotNB.plotList.index(Title)
[762]	2290	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2291	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2292
[796]	2293	Page.Choice = None
[762]	2294	Page.SetFocus()
	2295	G2frame.G2plotNB.status.DestroyChildren()
[1402]	2296	Plot.set_title(Title)
	2297	if labelX:
	2298	Plot.set_xlabel(r''+labelX,fontsize=14)
[1180]	2299	else:
	2300	Plot.set_xlabel(r'X',fontsize=14)
[1402]	2301	if labelY:
	2302	Plot.set_ylabel(r''+labelY,fontsize=14)
[1180]	2303	else:
	2304	Plot.set_ylabel(r'Y',fontsize=14)
[762]	2305	colors=['b','g','r','c','m','k']
[1180]	2306	for ixy,xy in enumerate(XY):
	2307	X,Y = xy
[1402]	2308	Plot.plot(X,Y,colors[ixy%6]+'+',picker=False)
[1180]	2309	if len(XY2):
	2310	for ixy,xy in enumerate(XY2):
	2311	X,Y = xy
[1402]	2312	Plot.plot(X,Y,colors[ixy%6],picker=False)
[762]	2313	if not newPlot:
	2314	Page.toolbar.push_current()
	2315	Plot.set_xlim(xylim[0])
	2316	Plot.set_ylim(xylim[1])
	2317	xylim = []
	2318	Page.toolbar.push_current()
	2319	Page.toolbar.draw()
	2320	else:
	2321	Page.canvas.draw()
	2322
	2323	################################################################################
[1180]	2324	##### PlotStrain
	2325	################################################################################
	2326
[1184]	2327	def PlotStrain(G2frame,data,newPlot=False):
[1180]	2328	'''plot of strain data, used for diagnostic purposes
	2329	'''
	2330	def OnMotion(event):
	2331	xpos = event.xdata
	2332	if xpos: #avoid out of frame mouse position
	2333	ypos = event.ydata
	2334	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	2335	try:
[1185]	2336	G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1)
[1180]	2337	except TypeError:
[1184]	2338	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
[1180]	2339
	2340	try:
[1184]	2341	plotNum = G2frame.G2plotNB.plotList.index('Strain')
[1180]	2342	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2343	if not newPlot:
	2344	Plot = Page.figure.gca()
	2345	xylim = Plot.get_xlim(),Plot.get_ylim()
	2346	Page.figure.clf()
	2347	Plot = Page.figure.gca()
	2348	except ValueError:
	2349	newPlot = True
[1184]	2350	Plot = G2frame.G2plotNB.addMpl('Strain').gca()
	2351	plotNum = G2frame.G2plotNB.plotList.index('Strain')
[1180]	2352	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2353	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2354
	2355	Page.Choice = None
	2356	Page.SetFocus()
	2357	G2frame.G2plotNB.status.DestroyChildren()
[1184]	2358	Plot.set_title('Strain')
[1185]	2359	Plot.set_ylabel(r'd-spacing',fontsize=14)
	2360	Plot.set_xlabel(r'Azimuth',fontsize=14)
[1180]	2361	colors=['b','g','r','c','m','k']
	2362	for N,item in enumerate(data['d-zero']):
[1185]	2363	Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y
[1180]	2364	Plot.plot(X,Y,colors[N%6]+'+',picker=False)
[1185]	2365	Y,X = np.array(item['ImtaCalc'])
[1180]	2366	Plot.plot(X,Y,colors[N%6],picker=False)
	2367	if not newPlot:
	2368	Page.toolbar.push_current()
	2369	Plot.set_xlim(xylim[0])
	2370	Plot.set_ylim(xylim[1])
	2371	xylim = []
	2372	Page.toolbar.push_current()
	2373	Page.toolbar.draw()
	2374	else:
	2375	Page.canvas.draw()
[1244]	2376
	2377	################################################################################
	2378	##### PlotSASDSizeDist
	2379	################################################################################
	2380
[1273]	2381	def PlotSASDSizeDist(G2frame):
[1244]	2382
[1269]	2383	def OnPageChanged(event):
	2384	PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
	2385	if 'Powder' in PlotText:
	2386	PlotPatterns(G2frame,plotType='SASD',newPlot=True)
	2387	elif 'Size' in PlotText:
[1273]	2388	PlotSASDSizeDist(G2frame)
[1269]	2389
[1244]	2390	def OnMotion(event):
	2391	xpos = event.xdata
	2392	if xpos: #avoid out of frame mouse position
	2393	ypos = event.ydata
	2394	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	2395	try:
[1250]	2396	G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1)
[1244]	2397	except TypeError:
	2398	G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1)
[1180]	2399
[1244]	2400	try:
	2401	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
	2402	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2403	Page.figure.clf()
	2404	Plot = Page.figure.gca() #get a fresh plot after clf()
	2405	except ValueError:
	2406	newPlot = True
	2407	Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca()
[1269]	2408	G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged)
[1244]	2409	plotNum = G2frame.G2plotNB.plotList.index('Size Distribution')
	2410	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2411	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2412	Page.Choice = None
	2413	Page.SetFocus()
	2414	PatternId = G2frame.PatternId
	2415	data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models'))
	2416	Bins,Dbins,BinMag = data['Size']['Distribution']
	2417	Plot.set_title('Size Distribution')
	2418	Plot.set_xlabel(r'$D, \AA$',fontsize=14)
[1246]	2419	Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14)
[1244]	2420	if data['Size']['logBins']:
	2421	Plot.set_xscale("log",nonposy='mask')
	2422	Plot.set_xlim([np.min(2.Bins)/2.,np.max(2.Bins)*2.])
[1269]	2423	Plot.bar(2.Bins-Dbins,BinMag,2.Dbins,facecolor='white') #plot diameters
[1272]	2424	if 'Size Calc' in data:
	2425	Rbins,Dist = data['Size Calc']
[1269]	2426	for i in range(len(Rbins)):
[1274]	2427	if len(Rbins[i]):
	2428	Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters
[1244]	2429	Page.canvas.draw()
	2430
[1180]	2431	################################################################################
[762]	2432	##### PlotPowderLines
	2433	################################################################################
	2434
	2435	def PlotPowderLines(G2frame):
	2436	''' plotting of powder lines (i.e. no powder pattern) as sticks
	2437	'''
	2438
	2439	def OnMotion(event):
	2440	xpos = event.xdata
	2441	if xpos: #avoid out of frame mouse position
	2442	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	2443	G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)])
	2444	if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']:
	2445	found = []
[1933]	2446	if len(G2frame.HKL):
[762]	2447	view = Page.toolbar._views.forward()[0][:2]
	2448	wid = view[1]-view[0]
[1933]	2449	found = G2frame.HKL[np.where(np.fabs(G2frame.HKL.T[-1]-xpos) < 0.002*wid)]
[762]	2450	if len(found):
	2451	h,k,l = found[0][:3]
	2452	Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l)))
	2453	else:
	2454	Page.canvas.SetToolTipString('')
	2455
	2456	try:
	2457	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
	2458	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2459	Page.figure.clf()
	2460	Plot = Page.figure.gca()
	2461	except ValueError:
	2462	Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca()
	2463	plotNum = G2frame.G2plotNB.plotList.index('Powder Lines')
	2464	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2465	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2466
[796]	2467	Page.Choice = None
[762]	2468	Page.SetFocus()
	2469	Plot.set_title('Powder Pattern Lines')
	2470	Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14)
	2471	PickId = G2frame.PickId
	2472	PatternId = G2frame.PatternId
[1445]	2473	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))[0]
[762]	2474	for peak in peaks:
	2475	Plot.axvline(peak[0],color='b')
	2476	for hkl in G2frame.HKL:
[1571]	2477	Plot.axvline(hkl[-1],color='r',dashes=(5,5))
[762]	2478	xmin = peaks[0][0]
	2479	xmax = peaks[-1][0]
	2480	delt = xmax-xmin
	2481	xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)]
	2482	Plot.set_xlim(xlim)
	2483	Page.canvas.draw()
	2484	Page.toolbar.push_current()
	2485
	2486	################################################################################
	2487	##### PlotPeakWidths
	2488	################################################################################
	2489
	2490	def PlotPeakWidths(G2frame):
[798]	2491	''' Plotting of instrument broadening terms as function of 2-theta
[762]	2492	Seen when "Instrument Parameters" chosen from powder pattern data tree
	2493	'''
[803]	2494	# sig = lambda Th,U,V,W: 1.17741math.sqrt(Utand(Th)*2+Vtand(Th)+W)*math.pi/18000.
	2495	# gam = lambda Th,X,Y: (X/cosd(Th)+Ytand(Th))math.pi/18000.
[1898]	2496	# 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.)
[797]	2497	# gamFW2 = lambda s,g: math.sqrt(s*2+(0.4654996g)*2)+.5345004g #Ubaldo Bafile - private communication
[762]	2498	PatternId = G2frame.PatternId
	2499	limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
	2500	if limitID:
[1017]	2501	limits = G2frame.PatternTree.GetItemPyData(limitID)[:2]
[762]	2502	else:
	2503	return
[796]	2504	Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \
[762]	2505	G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
[792]	2506	if 'C' in Parms['Type'][0]:
[798]	2507	lam = G2mth.getWave(Parms)
[792]	2508	else:
	2509	difC = Parms['difC'][0]
[1451]	2510	try: # PATCH: deal with older peak lists, before changed to dict to implement TOF
	2511	peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))['peaks']
	2512	except TypeError:
	2513	print "Your peak list needs reformatting...",
	2514	item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')
	2515	G2frame.PatternTree.SelectItem(item)
	2516	item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters')
	2517	G2frame.PatternTree.SelectItem(item)
	2518	print "done"
	2519	return
[762]	2520	try:
	2521	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
	2522	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2523	Page.figure.clf()
	2524	Plot = Page.figure.gca()
	2525	except ValueError:
	2526	Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca()
	2527	plotNum = G2frame.G2plotNB.plotList.index('Peak Widths')
	2528	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[796]	2529	Page.Choice = None
[762]	2530	Page.SetFocus()
	2531
	2532	Page.canvas.SetToolTipString('')
	2533	colors=['b','g','r','c','m','k']
	2534	X = []
	2535	Y = []
	2536	Z = []
	2537	W = []
[792]	2538	if 'C' in Parms['Type'][0]:
[797]	2539	Plot.set_title('Instrument and sample peak widths')
[1032]	2540	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
	2541	Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14)
[792]	2542	try:
[797]	2543	Xmin,Xmax = limits[1]
[798]	2544	X = np.linspace(Xmin,Xmax,num=101,endpoint=True)
	2545	Q = 4.np.pinpsind(X/2.)/lam
	2546	Z = np.ones_like(X)
	2547	data = G2mth.setPeakparms(Parms,Parms2,X,Z)
	2548	s = 1.17741np.sqrt(data[4])np.pi/18000.
	2549	g = data[6]*np.pi/18000.
[998]	2550	G = G2pwd.getgamFW(g,s)
[798]	2551	Y = s/nptand(X/2.)
	2552	Z = g/nptand(X/2.)
	2553	W = G/nptand(X/2.)
	2554	Plot.plot(Q,Y,color='r',label='Gaussian')
	2555	Plot.plot(Q,Z,color='g',label='Lorentzian')
	2556	Plot.plot(Q,W,color='b',label='G+L')
	2557
[803]	2558	fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True)
	2559	sf = 1.17741np.sqrt(fit[4])np.pi/18000.
	2560	gf = fit[6]*np.pi/18000.
[998]	2561	Gf = G2pwd.getgamFW(gf,sf)
[803]	2562	Yf = sf/nptand(X/2.)
	2563	Zf = gf/nptand(X/2.)
	2564	Wf = Gf/nptand(X/2.)
	2565	Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit')
	2566	Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit')
	2567	Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
	2568
[792]	2569	X = []
	2570	Y = []
	2571	Z = []
	2572	W = []
	2573	V = []
	2574	for peak in peaks:
	2575	X.append(4.0math.pisind(peak[0]/2.0)/lam)
	2576	try:
	2577	s = 1.17741math.sqrt(peak[4])math.pi/18000.
	2578	except ValueError:
	2579	s = 0.01
	2580	g = peak[6]*math.pi/18000.
[998]	2581	G = G2pwd.getgamFW(g,s)
[792]	2582	Y.append(s/tand(peak[0]/2.))
	2583	Z.append(g/tand(peak[0]/2.))
	2584	W.append(G/tand(peak[0]/2.))
[803]	2585	if len(peaks):
	2586	Plot.plot(X,Y,'+',color='r',label='G peak')
	2587	Plot.plot(X,Z,'+',color='g',label='L peak')
	2588	Plot.plot(X,W,'+',color='b',label='G+L peak')
[792]	2589	Plot.legend(loc='best')
	2590	Page.canvas.draw()
	2591	except ValueError:
	2592	print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \
	2593	'%.3f'%(2*theta)
	2594	G2frame.G2plotNB.Delete('Peak Widths')
[1462]	2595	else: #'T'OF
[797]	2596	Plot.set_title('Instrument and sample peak coefficients')
[1032]	2597	Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14)
	2598	Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14)
[797]	2599	Xmin,Xmax = limits[1]
[798]	2600	T = np.linspace(Xmin,Xmax,num=101,endpoint=True)
	2601	Z = np.ones_like(T)
	2602	data = G2mth.setPeakparms(Parms,Parms2,T,Z)
	2603	ds = T/difC
	2604	Q = 2.*np.pi/ds
	2605	A = data[4]
	2606	B = data[6]
	2607	S = 1.17741*np.sqrt(data[8])/T
	2608	G = data[10]/T
	2609	Plot.plot(Q,A,color='r',label='Alpha')
	2610	Plot.plot(Q,B,color='g',label='Beta')
	2611	Plot.plot(Q,S,color='b',label='Gaussian')
	2612	Plot.plot(Q,G,color='m',label='Lorentzian')
[803]	2613
	2614	fit = G2mth.setPeakparms(Parms,Parms2,T,Z)
	2615	ds = T/difC
	2616	Q = 2.*np.pi/ds
	2617	Af = fit[4]
	2618	Bf = fit[6]
	2619	Sf = 1.17741*np.sqrt(fit[8])/T
	2620	Gf = fit[10]/T
	2621	Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit')
	2622	Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit')
	2623	Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit')
	2624	Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit')
	2625
[797]	2626	T = []
	2627	A = []
	2628	B = []
[798]	2629	S = []
	2630	G = []
[797]	2631	W = []
[798]	2632	Q = []
[797]	2633	V = []
	2634	for peak in peaks:
	2635	T.append(peak[0])
	2636	A.append(peak[4])
	2637	B.append(peak[6])
[798]	2638	Q.append(2.np.pidifC/peak[0])
	2639	S.append(1.17741*np.sqrt(peak[8])/peak[0])
	2640	G.append(peak[10]/peak[0])
[797]	2641
	2642
[798]	2643	Plot.plot(Q,A,'+',color='r',label='Alpha peak')
	2644	Plot.plot(Q,B,'+',color='g',label='Beta peak')
	2645	Plot.plot(Q,S,'+',color='b',label='Gaussian peak')
	2646	Plot.plot(Q,G,'+',color='m',label='Lorentzian peak')
[797]	2647	Plot.legend(loc='best')
	2648	Page.canvas.draw()
[762]	2649
	2650
	2651	################################################################################
	2652	##### PlotSizeStrainPO
	2653	################################################################################
	2654
[1731]	2655	def PlotSizeStrainPO(G2frame,data,hist='',Start=False):
[762]	2656	'''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
	2657	'''
	2658
	2659	PatternId = G2frame.PatternId
	2660	generalData = data['General']
	2661	SGData = generalData['SGData']
	2662	SGLaue = SGData['SGLaue']
	2663	if Start: #initialize the spherical harmonics qlmn arrays
	2664	ptx.pyqlmninit()
	2665	Start = False
	2666	# MuStrKeys = G2spc.MustrainNames(SGData)
	2667	cell = generalData['Cell'][1:]
	2668	A,B = G2lat.cell2AB(cell[:6])
	2669	Vol = cell[6]
	2670	useList = data['Histograms']
	2671	phase = generalData['Name']
	2672	plotType = generalData['Data plot type']
	2673	plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
	2674	for ptype in plotDict:
	2675	G2frame.G2plotNB.Delete(ptype)
[1800]	2676	if plotType in ['None'] or not useList:
[762]	2677	return
[1731]	2678	if hist == '':
	2679	hist = useList.keys()[0]
[762]	2680	numPlots = len(useList)
	2681
[1835]	2682	try:
	2683	plotNum = G2frame.G2plotNB.plotList.index(plotType)
	2684	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2685	Page.figure.clf()
	2686	Plot = Page.figure.gca()
	2687	if not Page.IsShown():
	2688	Page.Show()
	2689	except ValueError:
	2690	if plotType in ['Mustrain','Size']:
	2691	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType))
	2692	else:
	2693	Plot = G2frame.G2plotNB.addMpl(plotType).gca()
	2694	plotNum = G2frame.G2plotNB.plotList.index(plotType)
	2695	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[796]	2696	Page.Choice = None
[762]	2697	G2frame.G2plotNB.status.SetStatusText('',1)
	2698
[1731]	2699	PHI = np.linspace(0.,360.,30,True)
	2700	PSI = np.linspace(0.,180.,30,True)
	2701	X = np.outer(npsind(PHI),npsind(PSI))
	2702	Y = np.outer(npcosd(PHI),npsind(PSI))
	2703	Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
	2704	try: #temp patch instead of 'mustrain' for old files with 'microstrain'
	2705	coeff = useList[hist][plotDict[plotType]]
	2706	except KeyError:
	2707	return
	2708	if plotType in ['Mustrain','Size']:
	2709	if coeff[0] == 'isotropic':
	2710	X *= coeff[1][0]
	2711	Y *= coeff[1][0]
	2712	Z *= coeff[1][0]
	2713	elif coeff[0] == 'uniaxial':
	2714
	2715	def uniaxCalc(xyz,iso,aniso,axes):
	2716	Z = np.array(axes)
	2717	cp = abs(np.dot(xyz,Z))
	2718	sp = np.sqrt(1.-cp**2)
	2719	R = isoaniso/np.sqrt((isocp)*2+(anisosp)**2)
	2720	return R*xyz
[762]	2721
[1731]	2722	iso,aniso = coeff[1][:2]
	2723	axes = np.inner(A,np.array(coeff[3]))
	2724	axes /= nl.norm(axes)
	2725	Shkl = np.array(coeff[1])
	2726	XYZ = np.dstack((X,Y,Z))
	2727	XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
	2728	X,Y,Z = np.dsplit(XYZ,3)
	2729	X = X[:,:,0]
	2730	Y = Y[:,:,0]
	2731	Z = Z[:,:,0]
	2732
	2733	elif coeff[0] == 'ellipsoidal':
	2734
	2735	def ellipseCalc(xyz,E,R):
	2736	XYZ = xyz*E.T
	2737	return np.inner(XYZ.T,R)
	2738
	2739	S6 = coeff[4]
	2740	Sij = G2lat.U6toUij(S6)
	2741	E,R = nl.eigh(Sij)
	2742	XYZ = np.dstack((X,Y,Z))
	2743	XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R))
	2744	X,Y,Z = np.dsplit(XYZ,3)
	2745	X = X[:,:,0]
	2746	Y = Y[:,:,0]
	2747	Z = Z[:,:,0]
	2748
	2749	elif coeff[0] == 'generalized':
	2750
	2751	def genMustrain(xyz,SGData,A,Shkl):
	2752	uvw = np.inner(A.T,xyz)
	2753	Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
	2754	Sum = np.sum(np.multiply(Shkl,Strm))
	2755	Sum = np.where(Sum > 0.01,Sum,0.01)
	2756	Sum = np.sqrt(Sum)
	2757	return Sum*xyz
	2758
	2759	Shkl = np.array(coeff[4])
	2760	if np.any(Shkl):
	2761	XYZ = np.dstack((X,Y,Z))
	2762	XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
	2763	X,Y,Z = np.dsplit(XYZ,3)
	2764	X = X[:,:,0]
	2765	Y = Y[:,:,0]
	2766	Z = Z[:,:,0]
[762]	2767
[1731]	2768	if np.any(X) and np.any(Y) and np.any(Z):
	2769	errFlags = np.seterr(all='ignore')
	2770	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
	2771	np.seterr(all='ignore')
	2772	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
	2773	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
	2774	Plot.set_xlim3d(XYZlim)
	2775	Plot.set_ylim3d(XYZlim)
	2776	Plot.set_zlim3d(XYZlim)
	2777	Plot.set_aspect('equal')
	2778	if plotType == 'Size':
	2779	Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model')
	2780	Plot.set_xlabel(r'X, $\mu$m')
	2781	Plot.set_ylabel(r'Y, $\mu$m')
	2782	Plot.set_zlabel(r'Z, $\mu$m')
	2783	else:
	2784	Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model')
	2785	Plot.set_xlabel(r'X, $\mu$strain')
	2786	Plot.set_ylabel(r'Y, $\mu$strain')
	2787	Plot.set_zlabel(r'Z, $\mu$strain')
	2788	else:
	2789	h,k,l = generalData['POhkl']
	2790	if coeff[0] == 'MD':
	2791	print 'March-Dollase preferred orientation plot'
	2792
	2793	else:
	2794	PH = np.array(generalData['POhkl'])
	2795	phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
	2796	SHCoef = {}
	2797	for item in coeff[5]:
	2798	L,N = eval(item.strip('C'))
	2799	SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]
	2800	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
	2801	X = np.linspace(0,90.0,26)
	2802	Y = G2lat.polfcal(ODFln,'0',X,0.0)
	2803	Plot.plot(X,Y,color='k',label=str(PH))
	2804	Plot.legend(loc='best')
[1779]	2805	Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase+'\n'+hist)
[1731]	2806	Plot.set_xlabel(r'$\psi$',fontsize=16)
	2807	Plot.set_ylabel('MRD',fontsize=14)
[762]	2808	Page.canvas.draw()
	2809
	2810	################################################################################
	2811	##### PlotTexture
	2812	################################################################################
[1804]	2813
[762]	2814	def PlotTexture(G2frame,data,Start=False):
[1804]	2815	'''Pole figure, inverse pole figure plotting.
[762]	2816	dict generalData contains all phase info needed which is in data
	2817	'''
	2818
	2819	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
	2820	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
	2821	PatternId = G2frame.PatternId
	2822	generalData = data['General']
	2823	SGData = generalData['SGData']
[1799]	2824	pName = generalData['Name']
[762]	2825	textureData = generalData['SH Texture']
	2826	G2frame.G2plotNB.Delete('Texture')
	2827	if not textureData['Order']:
	2828	return #no plot!!
	2829	SHData = generalData['SH Texture']
	2830	SHCoef = SHData['SH Coeff'][1]
	2831	cell = generalData['Cell'][1:7]
	2832	Amat,Bmat = G2lat.cell2AB(cell)
	2833	sq2 = 1.0/math.sqrt(2.0)
	2834
	2835	def rp2xyz(r,p):
	2836	z = npcosd(r)
	2837	xy = np.sqrt(1.-z**2)
	2838	return xynpsind(p),xynpcosd(p),z
	2839
	2840	def OnMotion(event):
	2841	SHData = data['General']['SH Texture']
	2842	if event.xdata and event.ydata: #avoid out of frame errors
	2843	xpos = event.xdata
	2844	ypos = event.ydata
	2845	if 'Inverse' in SHData['PlotType']:
	2846	r = xpos2+ypos2
	2847	if r <= 1.0:
	2848	if 'equal' in G2frame.Projection:
	2849	r,p = 2.npasind(np.sqrt(r)sq2),npatan2d(ypos,xpos)
	2850	else:
	2851	r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos)
	2852	ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,]))
[1844]	2853	xyz = np.inner(Bmat,np.array([rp2xyz(r,p)]))
[762]	2854	y,x,z = list(xyz/np.max(np.abs(xyz)))
	2855
	2856	G2frame.G2plotNB.status.SetFields(['',
	2857	'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
	2858
	2859	elif 'Axial' in SHData['PlotType']:
	2860	pass
	2861
	2862	else: #ordinary pole figure
	2863	z = xpos2+ypos2
	2864	if z <= 1.0:
	2865	z = np.sqrt(z)
	2866	if 'equal' in G2frame.Projection:
	2867	r,p = 2.npasind(zsq2),npatan2d(ypos,xpos)
	2868	else:
	2869	r,p = 2.*npatand(z),npatan2d(ypos,xpos)
	2870	pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,]))
	2871	G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
	2872
	2873	try:
	2874	plotNum = G2frame.G2plotNB.plotList.index('Texture')
	2875	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2876	Page.figure.clf()
	2877	Plot = Page.figure.gca()
	2878	if not Page.IsShown():
	2879	Page.Show()
	2880	except ValueError:
[1804]	2881	if '3D' in SHData['PlotType']:
	2882	Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D('Texture'))
	2883	else:
	2884	Plot = G2frame.G2plotNB.addMpl('Texture').gca()
[762]	2885	plotNum = G2frame.G2plotNB.plotList.index('Texture')
	2886	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	2887	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	2888
[796]	2889	Page.Choice = None
[762]	2890	Page.SetFocus()
	2891	G2frame.G2plotNB.status.SetFields(['',''])
	2892	PH = np.array(SHData['PFhkl'])
	2893	phi,beta = G2lat.CrsAng(PH,cell,SGData)
	2894	ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
[1780]	2895	if not np.any(ODFln):
	2896	return
[762]	2897	PX = np.array(SHData['PFxyz'])
	2898	gam = atan2d(PX[0],PX[1])
	2899	xy = math.sqrt(PX[0]2+PX[1]2)
	2900	xyz = math.sqrt(PX[0]2+PX[1]2+PX[2]**2)
	2901	psi = asind(xy/xyz)
	2902	IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']])
	2903	if 'Axial' in SHData['PlotType']:
	2904	X = np.linspace(0,90.0,26)
	2905	Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0)
	2906	Plot.plot(X,Y,color='k',label=str(SHData['PFhkl']))
	2907	Plot.legend(loc='best')
[1799]	2908	h,k,l = SHData['PFhkl']
	2909	Plot.set_title('%d %d %d Axial distribution for %s'%(h,k,l,pName))
[762]	2910	Plot.set_xlabel(r'$\psi$',fontsize=16)
	2911	Plot.set_ylabel('MRD',fontsize=14)
	2912
	2913	else:
	2914	npts = 201
	2915	if 'Inverse' in SHData['PlotType']:
	2916	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
	2917	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
	2918	if 'equal' in G2frame.Projection:
	2919	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
	2920	else:
	2921	R = np.where(R <= 1.,2.*npatand(R),0.0)
	2922	Z = np.zeros_like(R)
	2923	Z = G2lat.invpolfcal(IODFln,SGData,R,P)
	2924	Z = np.reshape(Z,(npts,npts))
	2925	try:
[1780]	2926	CS = Plot.contour(Y,X,Z,aspect='equal')
	2927	Plot.clabel(CS,fontsize=9,inline=1)
[762]	2928	except ValueError:
	2929	pass
[1780]	2930	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
[762]	2931	Page.figure.colorbar(Img)
[1799]	2932	x,y,z = SHData['PFxyz']
[1804]	2933	Plot.axis('off')
[1799]	2934	Plot.set_title('%d %d %d Inverse pole figure for %s'%(int(x),int(y),int(z),pName))
[762]	2935	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
[1804]	2936
	2937	elif '3D' in SHData['PlotType']:
	2938	PSI,GAM = np.mgrid[0:31,0:31]
	2939	PSI = PSI.flatten()*6.
	2940	GAM = GAM.flatten()*12.
	2941	P = G2lat.polfcal(ODFln,SamSym[textureData['Model']],PSI,GAM).reshape((31,31))
	2942	GAM = np.linspace(0.,360.,31,True)
	2943	PSI = np.linspace(0.,180.,31,True)
	2944	X = np.outer(npsind(GAM),npsind(PSI))*P.T
	2945	Y = np.outer(npcosd(GAM),npsind(PSI))*P.T
	2946	Z = np.outer(np.ones(np.size(GAM)),npcosd(PSI))*P.T
	2947	h,k,l = SHData['PFhkl']
	2948
	2949	if np.any(X) and np.any(Y) and np.any(Z):
	2950	errFlags = np.seterr(all='ignore')
	2951	Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
	2952	np.seterr(all='ignore')
	2953	xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
	2954	XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
	2955	Plot.set_xlim3d(XYZlim)
	2956	Plot.set_ylim3d(XYZlim)
	2957	Plot.set_zlim3d(XYZlim)
	2958	Plot.set_aspect('equal')
	2959	Plot.set_title('%d %d %d Pole distribution for %s'%(h,k,l,pName))
	2960	Plot.set_xlabel(r'X, MRD')
	2961	Plot.set_ylabel(r'Y, MRD')
	2962	Plot.set_zlabel(r'Z, MRD')
[762]	2963	else:
[1806]	2964	PFproj = textureData.get('PFproj','XY')
	2965	PRrev = textureData.get('PFrev',False)
[762]	2966	X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts))
	2967	R,P = np.sqrt(X2+Y2).flatten(),npatan2d(X,Y).flatten()
	2968	if 'equal' in G2frame.Projection:
	2969	R = np.where(R <= 1.,2.npasind(Rsq2),0.0)
	2970	else:
	2971	R = np.where(R <= 1.,2.*npatand(R),0.0)
	2972	Z = np.zeros_like(R)
	2973	Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P)
	2974	Z = np.reshape(Z,(npts,npts))
	2975	try:
	2976	CS = Plot.contour(Y,X,Z,aspect='equal')
	2977	Plot.clabel(CS,fontsize=9,inline=1)
	2978	except ValueError:
	2979	pass
	2980	Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1])
	2981	Page.figure.colorbar(Img)
[1799]	2982	h,k,l = SHData['PFhkl']
[1804]	2983	Plot.axis('off')
[1799]	2984	Plot.set_title('%d %d %d Pole figure for %s'%(h,k,l,pName))
[762]	2985	Plot.set_xlabel(G2frame.Projection.capitalize()+' projection')
	2986	Page.canvas.draw()
	2987
	2988	################################################################################
[1625]	2989	##### Plot Modulation
[1601]	2990	################################################################################
	2991
[1625]	2992	def ModulationPlot(G2frame,data,atom,ax,off=0):
	2993	global Off,Atom,Ax
	2994	Off = off
	2995	Atom = atom
	2996	Ax = ax
	2997	def OnMotion(event):
	2998	xpos = event.xdata
	2999	if xpos: #avoid out of frame mouse position
	3000	ypos = event.ydata
	3001	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	3002	try:
	3003	G2frame.G2plotNB.status.SetStatusText('t =%9.3f %s =%9.3f'%(xpos,GkDelta+Ax,ypos),1)
	3004	except TypeError:
	3005	G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1)
[1601]	3006
[1625]	3007	def OnPlotKeyPress(event):
	3008	global Off,Atom,Ax
[1694]	3009	newPlot = False
[1625]	3010	if event.key == '0':
	3011	Off = 0
[1694]	3012	elif event.key in ['+','=']:
[1625]	3013	Off += 1
	3014	elif event.key == '-':
[1626]	3015	Off -= 1
[1630]	3016	elif event.key in ['l','r',] and mapData['Flip']:
[1626]	3017	roll = 1
	3018	if event.key == 'l':
	3019	roll = -1
	3020	rho = Map['rho']
	3021	Map['rho'] = np.roll(rho,roll,axis=3)
[1625]	3022	wx.CallAfter(ModulationPlot,G2frame,data,Atom,Ax,Off)
	3023
[1601]	3024	try:
	3025	plotNum = G2frame.G2plotNB.plotList.index('Modulation')
	3026	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3027	Page.figure.clf()
	3028	Plot = Page.figure.gca()
	3029	if not Page.IsShown():
	3030	Page.Show()
	3031	except ValueError:
	3032	Plot = G2frame.G2plotNB.addMpl('Modulation').gca()
	3033	plotNum = G2frame.G2plotNB.plotList.index('Modulation')
	3034	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[1625]	3035	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	3036	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
[1630]	3037
[1625]	3038	Page.SetFocus()
[1604]	3039	General = data['General']
	3040	cx,ct,cs,cia = General['AtomPtrs']
[1630]	3041	mapData = General['Map']
	3042	if mapData['Flip']:
	3043	Page.Choice = ['+: shift up','-: shift down','0: reset shift','l: move left','r: move right']
	3044	else:
	3045	Page.Choice = ['+: shift up','-: shift down','0: reset shift']
	3046	Page.keyPress = OnPlotKeyPress
[1604]	3047	Map = General['4DmapData']
	3048	MapType = Map['MapType']
	3049	rhoSize = np.array(Map['rho'].shape)
	3050	atxyz = np.array(atom[cx:cx+3])
[1625]	3051	waveType = atom[-1]['SS1']['waveType']
	3052	Spos = atom[-1]['SS1']['Spos']
	3053	tau = np.linspace(0.,2.,101)
	3054	wave = np.zeros((3,101))
	3055	if len(Spos):
	3056	scof = []
	3057	ccof = []
	3058	for i,spos in enumerate(Spos):
	3059	if waveType in ['Sawtooth','ZigZag'] and not i:
	3060	Toff = spos[0][0]
	3061	slopes = np.array(spos[0][1:])
	3062	if waveType == 'Sawtooth':
	3063	wave = G2mth.posSawtooth(tau,Toff,slopes)
	3064	elif waveType == 'ZigZag':
	3065	wave = G2mth.posZigZag(tau,Toff,slopes)
	3066	else:
	3067	scof.append(spos[0][:3])
	3068	ccof.append(spos[0][3:])
[1958]	3069	wave += G2mth.posFourier(tau,np.array(scof),np.array(ccof),1) #hmm, why -1 work for Na2CO3?
[1633]	3070	if mapData['Flip']:
	3071	Title = 'Charge flip'
	3072	else:
	3073	Title = MapType
	3074	Title += ' map for atom '+atom[0]+ \
[1604]	3075	' at %.4f %.4f %.4f'%(atxyz[0],atxyz[1],atxyz[2])
	3076	ix = -np.array(np.rint(rhoSize[:3]*atxyz),dtype='i')
	3077	ix += (rhoSize[:3]/2)
	3078	ix = ix%rhoSize[:3]
	3079	rho = np.roll(np.roll(np.roll(Map['rho'],ix[0],axis=0),ix[1],axis=1),ix[2],axis=2)
	3080	ix = rhoSize[:3]/2
	3081	ib = 4
	3082	if Ax == 'x':
	3083	slab = np.sum(np.sum(rho[:,ix[1]-ib:ix[1]+ib,ix[2]-ib:ix[2]+ib,:],axis=2),axis=1)
[1626]	3084	Plot.plot(tau,wave[0])
[1604]	3085	elif Ax == 'y':
	3086	slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,:,ix[2]-ib:ix[2]+ib,:],axis=2),axis=0)
[1626]	3087	Plot.plot(tau,wave[1])
[1604]	3088	elif Ax == 'z':
	3089	slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,ix[1]-ib:ix[1]+ib,:,:],axis=1),axis=0)
[1626]	3090	Plot.plot(tau,wave[2])
[1604]	3091	Plot.set_title(Title)
	3092	Plot.set_xlabel('t')
	3093	Plot.set_ylabel(r'$\mathsf{\Delta}$%s'%(Ax))
[1633]	3094	Slab = np.hstack((slab,slab,slab))
	3095	Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Off.005,.5+Off.005))
[1604]	3096	Page.canvas.draw()
[1625]	3097
[1601]	3098	################################################################################
[762]	3099	##### PlotCovariance
	3100	################################################################################
	3101
[859]	3102	def PlotCovariance(G2frame,Data):
[939]	3103	'needs a doc string'
[762]	3104	if not Data:
	3105	print 'No covariance matrix available'
	3106	return
	3107	varyList = Data['varyList']
	3108	values = Data['variables']
	3109	Xmax = len(varyList)
	3110	covMatrix = Data['covMatrix']
	3111	sig = np.sqrt(np.diag(covMatrix))
	3112	xvar = np.outer(sig,np.ones_like(sig))
	3113	covArray = np.divide(np.divide(covMatrix,xvar),xvar.T)
	3114	title = ' for\n'+Data['title']
[1297]	3115	newAtomDict = Data.get('newAtomDict',{})
[1772]	3116	G2frame.G2plotNB.Delete('Covariance')
[859]	3117
[762]	3118
	3119	def OnPlotKeyPress(event):
	3120	newPlot = False
	3121	if event.key == 's':
	3122	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
	3123	choice.sort()
	3124	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
	3125	if dlg.ShowModal() == wx.ID_OK:
	3126	sel = dlg.GetSelection()
	3127	G2frame.VcovColor = choice[sel]
	3128	else:
	3129	G2frame.VcovColor = 'RdYlGn'
	3130	dlg.Destroy()
[859]	3131	PlotCovariance(G2frame,Data)
[762]	3132
	3133	def OnMotion(event):
	3134	if event.button:
	3135	ytics = imgAx.get_yticks()
	3136	ytics = np.where(ytics<len(varyList),ytics,-1)
	3137	ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics]
[817]	3138	imgAx.set_yticklabels(ylabs)
[762]	3139	if event.xdata and event.ydata: #avoid out of frame errors
	3140	xpos = int(event.xdata+.5)
	3141	ypos = int(event.ydata+.5)
	3142	if -1 < xpos < len(varyList) and -1 < ypos < len(varyList):
	3143	if xpos == ypos:
	3144	value = values[xpos]
	3145	name = varyList[xpos]
	3146	if varyList[xpos] in newAtomDict:
	3147	name,value = newAtomDict[name]
	3148	msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos])
	3149	else:
	3150	msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos])
	3151	Page.canvas.SetToolTipString(msg)
[796]	3152	G2frame.G2plotNB.status.SetFields(['',msg])
[817]	3153
[762]	3154	try:
	3155	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
	3156	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3157	Page.figure.clf()
	3158	Plot = Page.figure.gca()
	3159	if not Page.IsShown():
	3160	Page.Show()
	3161	except ValueError:
	3162	Plot = G2frame.G2plotNB.addMpl('Covariance').gca()
	3163	plotNum = G2frame.G2plotNB.plotList.index('Covariance')
	3164	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3165	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	3166	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
[796]	3167	Page.Choice = ['s: to change colors']
	3168	Page.keyPress = OnPlotKeyPress
[762]	3169	Page.SetFocus()
	3170	G2frame.G2plotNB.status.SetFields(['',''])
	3171	acolor = mpl.cm.get_cmap(G2frame.VcovColor)
[837]	3172	Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower',
	3173	vmin=-1.,vmax=1.)
[762]	3174	imgAx = Img.get_axes()
	3175	ytics = imgAx.get_yticks()
	3176	ylabs = [varyList[int(i)] for i in ytics[:-1]]
	3177	imgAx.set_yticklabels(ylabs)
	3178	colorBar = Page.figure.colorbar(Img)
	3179	Plot.set_title('V-Cov matrix'+title)
	3180	Plot.set_xlabel('Variable number')
	3181	Plot.set_ylabel('Variable name')
	3182	Page.canvas.draw()
	3183
	3184	################################################################################
[818]	3185	##### PlotTorsion
	3186	################################################################################
	3187
	3188	def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]):
[939]	3189	'needs a doc string'
[818]	3190
	3191	global names
	3192	names = Names
	3193	sum = np.sum(Torsion)
	3194	torsion = np.log(2*Torsion+1.)/sum
	3195	tMin = np.min(torsion)
	3196	tMax = np.max(torsion)
	3197	torsion = 3.*(torsion-tMin)/(tMax-tMin)
	3198	X = np.linspace(0.,360.,num=45)
	3199
[1098]	3200	def OnPick(event):
	3201	ind = event.ind[0]
	3202	msg = 'atoms:'+names[ind]
	3203	Page.canvas.SetToolTipString(msg)
[1099]	3204	try:
	3205	page = G2frame.dataDisplay.GetSelection()
	3206	except:
	3207	return
	3208	if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints':
	3209	torGrid = G2frame.dataDisplay.GetPage(page).Torsions
	3210	torGrid.ClearSelection()
	3211	for row in range(torGrid.GetNumberRows()):
	3212	if names[ind] in torGrid.GetCellValue(row,0):
	3213	torGrid.SelectRow(row)
	3214	torGrid.ForceRefresh()
	3215
[818]	3216	def OnMotion(event):
	3217	if event.xdata and event.ydata: #avoid out of frame errors
	3218	xpos = event.xdata
	3219	ypos = event.ydata
	3220	msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos)
	3221	Page.canvas.SetToolTipString(msg)
	3222
	3223	try:
	3224	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
	3225	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3226	Page.figure.clf()
	3227	Plot = Page.figure.gca()
	3228	if not Page.IsShown():
	3229	Page.Show()
	3230	except ValueError:
	3231	Plot = G2frame.G2plotNB.addMpl('Torsion').gca()
	3232	plotNum = G2frame.G2plotNB.plotList.index('Torsion')
	3233	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[1098]	3234	Page.canvas.mpl_connect('pick_event', OnPick)
[818]	3235	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	3236
	3237	Page.SetFocus()
[1098]	3238	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms'])
[818]	3239	Plot.plot(X,torsion,'b+')
	3240	if len(Coeff):
	3241	X2 = np.linspace(0.,360.,45)
	3242	Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2])
	3243	Plot.plot(X2,Y2,'r')
	3244	if len(Angles):
	3245	Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles])
[1098]	3246	Plot.plot(Angles,Eval,'ro',picker=5)
[818]	3247	Plot.set_xlim((0.,360.))
	3248	Plot.set_title('Torsion angles for '+TorName+' in '+phaseName)
	3249	Plot.set_xlabel('angle',fontsize=16)
	3250	Plot.set_ylabel('Energy',fontsize=16)
	3251	Page.canvas.draw()
	3252
	3253	################################################################################
[817]	3254	##### PlotRama
	3255	################################################################################
	3256
[818]	3257	def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]):
[939]	3258	'needs a doc string'
[817]	3259
[818]	3260	global names
	3261	names = Names
	3262	rama = np.log(2*Rama+1.)
[817]	3263	ramaMax = np.max(rama)
	3264	rama = np.reshape(rama,(45,45))
[818]	3265	global Phi,Psi
	3266	Phi = []
	3267	Psi = []
[817]	3268
	3269	def OnPlotKeyPress(event):
	3270	newPlot = False
	3271	if event.key == 's':
	3272	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
	3273	choice.sort()
	3274	dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice)
	3275	if dlg.ShowModal() == wx.ID_OK:
	3276	sel = dlg.GetSelection()
	3277	G2frame.RamaColor = choice[sel]
	3278	else:
	3279	G2frame.RamaColor = 'RdYlGn'
	3280	dlg.Destroy()
[818]	3281	PlotRama(G2frame,phaseName,Rama)
[817]	3282
[1098]	3283	def OnPick(event):
	3284	ind = event.ind[0]
	3285	msg = 'atoms:'+names[ind]
	3286	Page.canvas.SetToolTipString(msg)
[1099]	3287	try:
	3288	page = G2frame.dataDisplay.GetSelection()
	3289	except:
	3290	return
	3291	if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints':
	3292	ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas
	3293	ramaGrid.ClearSelection()
	3294	for row in range(ramaGrid.GetNumberRows()):
	3295	if names[ind] in ramaGrid.GetCellValue(row,0):
	3296	ramaGrid.SelectRow(row)
	3297	ramaGrid.ForceRefresh()
[1098]	3298
[817]	3299	def OnMotion(event):
	3300	if event.xdata and event.ydata: #avoid out of frame errors
	3301	xpos = event.xdata
	3302	ypos = event.ydata
	3303	msg = 'phi/psi: %5.3f %5.3f'%(xpos,ypos)
	3304	Page.canvas.SetToolTipString(msg)
[818]	3305
[817]	3306	try:
	3307	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
	3308	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3309	Page.figure.clf()
	3310	Plot = Page.figure.gca()
	3311	if not Page.IsShown():
	3312	Page.Show()
	3313	except ValueError:
	3314	Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca()
	3315	plotNum = G2frame.G2plotNB.plotList.index('Ramachandran')
	3316	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[1098]	3317	Page.canvas.mpl_connect('pick_event', OnPick)
[817]	3318	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	3319	Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)
	3320
	3321	Page.Choice = ['s: to change colors']
	3322	Page.keyPress = OnPlotKeyPress
	3323	Page.SetFocus()
[1098]	3324	G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms'])
[817]	3325	acolor = mpl.cm.get_cmap(G2frame.RamaColor)
[818]	3326	if RamaName == 'All' or '-1' in RamaName:
	3327	if len(Coeff):
	3328	X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45))
	3329	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
	3330	Plot.contour(X,Y,np.reshape(Z,(45,45)))
	3331	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
	3332	extent=[-180,180,-180,180],origin='lower')
	3333	if len(PhiPsi):
	3334	Phi,Psi = PhiPsi.T
	3335	Phi = np.where(Phi>180.,Phi-360.,Phi)
	3336	Psi = np.where(Psi>180.,Psi-360.,Psi)
[1098]	3337	Plot.plot(Phi,Psi,'ro',picker=5)
[818]	3338	Plot.set_xlim((-180.,180.))
	3339	Plot.set_ylim((-180.,180.))
	3340	else:
	3341	if len(Coeff):
	3342	X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45))
	3343	Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())])
	3344	Plot.contour(X,Y,np.reshape(Z,(45,45)))
	3345	Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest',
	3346	extent=[0,360,0,360],origin='lower')
	3347	if len(PhiPsi):
	3348	Phi,Psi = PhiPsi.T
[1098]	3349	Plot.plot(Phi,Psi,'ro',picker=5)
[818]	3350	Plot.set_xlim((0.,360.))
	3351	Plot.set_ylim((0.,360.))
	3352	Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName)
[817]	3353	Plot.set_xlabel(r'$\phi$',fontsize=16)
	3354	Plot.set_ylabel(r'$\psi$',fontsize=16)
[818]	3355	colorBar = Page.figure.colorbar(Img)
[817]	3356	Page.canvas.draw()
	3357
	3358
	3359	################################################################################
[762]	3360	##### PlotSeq
	3361	################################################################################
[1312]	3362	def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX,fitnum=None,fitvals=None):
[1282]	3363	'''Plot a result from a sequential refinement
[1284]	3364
	3365	:param wx.Frame G2frame: The main GSAS-II tree "window"
	3366	:param list ColumnList: list of int values corresponding to columns
	3367	selected as y values
	3368	:param function TableGet: a function that takes a column number
	3369	as argument and returns the column label, the values and there ESDs (or None)
	3370	:param function SelectX: a function that returns a selected column
	3371	number (or None) as the X-axis selection
	3372	'''
[1403]	3373	global Title,xLabel,yLabel
	3374	xLabel = yLabel = Title = ''
[1295]	3375	def OnMotion(event):
	3376	if event.xdata and event.ydata: #avoid out of frame errors
	3377	xpos = event.xdata
	3378	ypos = event.ydata
	3379	msg = '%5.3f %.6g'%(xpos,ypos)
	3380	Page.canvas.SetToolTipString(msg)
	3381
[1284]	3382	def OnKeyPress(event):
[1403]	3383	global Title,xLabel,yLabel
[1284]	3384	if event.key == 's':
	3385	G2frame.seqXaxis = G2frame.seqXselect()
	3386	Draw()
[1403]	3387	elif event.key == 't':
[1831]	3388	dlg = G2G.MultiStringDialog(G2frame,'Set titles & labels',[' Title ',' x-Label ',' y-Label '],
[1403]	3389	[Title,xLabel,yLabel])
	3390	if dlg.Show():
	3391	Title,xLabel,yLabel = dlg.GetValues()
	3392	dlg.Destroy()
	3393	Draw()
[1806]	3394	elif event.key == 'l':
	3395	G2frame.seqLines = not G2frame.seqLines
	3396	wx.CallAfter(Draw)
[1334]	3397
[1284]	3398	def Draw():
[1403]	3399	global Title,xLabel,yLabel
[762]	3400	Page.SetFocus()
[1806]	3401	G2frame.G2plotNB.status.SetStatusText( \
	3402	'press L to toggle lines, S to select X axis, T to change titles (reselect column to show?)',1)
[1284]	3403	Plot.clear()
	3404	if G2frame.seqXaxis is not None:
[1312]	3405	xName,X,Xsig = Page.seqTableGet(G2frame.seqXaxis)
[1284]	3406	else:
	3407	X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1)
[1282]	3408	xName = 'Data sequence number'
[1312]	3409	for col in Page.seqYaxisList:
	3410	name,Y,sig = Page.seqTableGet(col)
[1579]	3411	# deal with missing (None) values
	3412	Xnew = []
	3413	Ynew = []
	3414	Ysnew = []
	3415	for i in range(len(X)):
	3416	if X[i] is None or Y[i] is None: continue
	3417	Xnew.append(X[i])
	3418	Ynew.append(Y[i])
[1619]	3419	if sig: Ysnew.append(sig[i])
[1579]	3420	if Ysnew:
[1334]	3421	if G2frame.seqReverse and not G2frame.seqXaxis:
[1579]	3422	Ynew = Ynew[::-1]
	3423	Ysnew = Ysnew[::-1]
[1806]	3424	if G2frame.seqLines:
	3425	Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name)
	3426	else:
	3427	Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name,linestyle='None',marker='x')
[1284]	3428	else:
[1334]	3429	if G2frame.seqReverse and not G2frame.seqXaxis:
[1579]	3430	Ynew = Ynew[::-1]
	3431	Plot.plot(Xnew,Ynew)
	3432	Plot.plot(Xnew,Ynew,'o',label=name)
	3433	if Page.fitvals: # TODO: deal with fitting of None values
[1334]	3434	if G2frame.seqReverse and not G2frame.seqXaxis:
	3435	Page.fitvals = Page.fitvals[::-1]
	3436	Plot.plot(X,Page.fitvals,label='Fit')
[1312]	3437
[1284]	3438	Plot.legend(loc='best')
[1403]	3439	if Title:
	3440	Plot.set_title(Title)
	3441	else:
	3442	Plot.set_title('')
	3443	if xLabel:
	3444	Plot.set_xlabel(xLabel)
	3445	else:
	3446	Plot.set_xlabel(xName)
	3447	if yLabel:
	3448	Plot.set_ylabel(yLabel)
	3449	else:
	3450	Plot.set_ylabel('Parameter values')
[1806]	3451	Page.canvas.draw()
[1396]	3452
	3453	G2frame.seqXselect = SelectX
	3454	try:
	3455	G2frame.seqXaxis
	3456	except:
	3457	G2frame.seqXaxis = None
	3458
	3459	if fitnum is None:
	3460	label = 'Sequential refinement'
	3461	else:
	3462	label = 'Parametric fit #'+str(fitnum+1)
	3463	try:
	3464	plotNum = G2frame.G2plotNB.plotList.index(label)
	3465	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3466	Page.figure.clf()
	3467	Plot = Page.figure.gca()
	3468	if not Page.IsShown():
	3469	Page.Show()
	3470	except ValueError:
	3471	Plot = G2frame.G2plotNB.addMpl(label).gca()
	3472	plotNum = G2frame.G2plotNB.plotList.index(label)
	3473	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3474	Page.canvas.mpl_connect('key_press_event', OnKeyPress)
	3475	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
[1806]	3476	Page.Choice = ['l - toggle lines','s - select x-axis','t - change titles',]
[1396]	3477	Page.keyPress = OnKeyPress
	3478	Page.seqYaxisList = ColumnList
	3479	Page.seqTableGet = TableGet
	3480	Page.fitvals = fitvals
	3481
[1284]	3482	Draw()
[1396]	3483	G2frame.G2plotNB.nb.SetSelection(plotNum) # raises plot tab
[1284]	3484
[762]	3485	################################################################################
	3486	##### PlotExposedImage & PlotImage
	3487	################################################################################
	3488
	3489	def PlotExposedImage(G2frame,newPlot=False,event=None):
	3490	'''General access module for 2D image plotting
	3491	'''
	3492	plotNo = G2frame.G2plotNB.nb.GetSelection()
	3493	if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image':
	3494	PlotImage(G2frame,newPlot,event,newImage=True)
	3495	elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration':
	3496	PlotIntegration(G2frame,newPlot,event)
	3497
[1128]	3498	def OnStartMask(G2frame):
[1124]	3499	'''Initiate the start of a Frame or Polygon map
	3500
	3501	:param wx.Frame G2frame: The main GSAS-II tree "window"
	3502	:param str eventkey: a single letter ('f' or 'p') that
	3503	determines what type of mask is created.
	3504	'''
	3505	Masks = G2frame.PatternTree.GetItemPyData(
	3506	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
[1128]	3507	if G2frame.MaskKey == 'f':
[1124]	3508	Masks['Frames'] = []
[1128]	3509	elif G2frame.MaskKey == 'p':
[1124]	3510	Masks['Polygons'].append([])
[1128]	3511	elif G2frame.MaskKey == 's':
	3512	Masks['Points'].append([])
	3513	elif G2frame.MaskKey == 'a':
	3514	Masks['Arcs'].append([])
	3515	elif G2frame.MaskKey == 'r':
	3516	Masks['Rings'].append([])
[1124]	3517	G2imG.UpdateMasks(G2frame,Masks)
	3518	PlotImage(G2frame,newImage=True)
[1188]	3519
	3520	def OnStartNewDzero(G2frame):
	3521	'''Initiate the start of adding a new d-zero to a strain data set
[1124]	3522
[1188]	3523	:param wx.Frame G2frame: The main GSAS-II tree "window"
	3524	:param str eventkey: a single letter ('a') that
	3525	triggers the addition of a d-zero.
	3526	'''
[1350]	3527	G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',0)
[1386]	3528	G2frame.PickId = G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain')
	3529	data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
	3530	return data
[1188]	3531
[762]	3532	def PlotImage(G2frame,newPlot=False,event=None,newImage=True):
	3533	'''Plot of 2D detector images as contoured plot. Also plot calibration ellipses,
	3534	masks, etc.
	3535	'''
	3536	from matplotlib.patches import Ellipse,Arc,Circle,Polygon
	3537	import numpy.ma as ma
[1151]	3538	Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.))
[1386]	3539	global Data,Masks,StrSta
[762]	3540	colors=['b','g','r','c','m','k']
	3541	Data = G2frame.PatternTree.GetItemPyData(
	3542	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
[1134]	3543	# patch
	3544	if 'invert_x' not in Data:
	3545	Data['invert_x'] = False
	3546	Data['invert_y'] = True
	3547	# end patch
[762]	3548	Masks = G2frame.PatternTree.GetItemPyData(
	3549	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks'))
	3550	try: #may be absent
	3551	StrSta = G2frame.PatternTree.GetItemPyData(
	3552	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain'))
	3553	except TypeError: #is missing
	3554	StrSta = {}
	3555
	3556	def OnImMotion(event):
	3557	Page.canvas.SetToolTipString('')
	3558	sizexy = Data['size']
[1763]	3559	FlatBkg = Data.get('Flat Bkg',0.)
[762]	3560	if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors
[1231]	3561	Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata))
[762]	3562	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	3563	item = G2frame.itemPicked
	3564	pixelSize = Data['pixelSize']
	3565	scalex = 1000./pixelSize[0]
	3566	scaley = 1000./pixelSize[1]
	3567	if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls':
	3568	if 'Text' in str(item):
	3569	Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata))
	3570	else:
	3571	xcent,ycent = Data['center']
	3572	xpos = event.xdata-xcent
	3573	ypos = event.ydata-ycent
	3574	tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data)
	3575	if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']:
	3576	Page.canvas.SetToolTipString('%6d deg'%(azm))
	3577	elif 'line1' in str(item) or 'line2' in str(item):
[1231]	3578	Page.canvas.SetToolTipString('%8.3f deg'%(tth))
[762]	3579	else:
	3580	xpos = event.xdata
	3581	ypos = event.ydata
	3582	xpix = xpos*scalex
	3583	ypix = ypos*scaley
	3584	Int = 0
	3585	if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]):
[1763]	3586	Int = G2frame.ImageZ[ypix][xpix]-int(FlatBkg)
[1153]	3587	tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data)
[762]	3588	Q = 2.*math.pi/dsp
[1188]	3589	fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)]
[1128]	3590	if G2frame.MaskKey in ['p','f']:
[1188]	3591	fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon'
	3592	elif G2frame.StrainKey:
	3593	fields[0] = 'd-zero pick active'
	3594	G2frame.G2plotNB.status.SetFields(fields)
[762]	3595
	3596	def OnImPlotKeyPress(event):
	3597	try:
	3598	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
	3599	except TypeError:
	3600	return
	3601	if PickName == 'Masks':
[1212]	3602	if event.key in ['l','p','f','s','a','r']:
[1128]	3603	G2frame.MaskKey = event.key
	3604	OnStartMask(G2frame)
[1232]	3605	PlotImage(G2frame,newPlot=False)
[1128]	3606
[1188]	3607	elif PickName == 'Stress/Strain':
	3608	if event.key in ['a',]:
	3609	G2frame.StrainKey = event.key
[1386]	3610	StrSta = OnStartNewDzero(G2frame)
[1232]	3611	PlotImage(G2frame,newPlot=False)
[1188]	3612
[762]	3613	elif PickName == 'Image Controls':
[1134]	3614	if event.key in ['c',]:
[762]	3615	Xpos = event.xdata
	3616	if not Xpos: #got point out of frame
	3617	return
	3618	Ypos = event.ydata
	3619	dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?',
	3620	'Center change',style=wx.OK\|wx.CANCEL)
	3621	try:
	3622	if dlg.ShowModal() == wx.ID_OK:
	3623	print 'move center to: ',Xpos,Ypos
	3624	Data['center'] = [Xpos,Ypos]
	3625	G2imG.UpdateImageControls(G2frame,Data,Masks)
[1232]	3626	PlotImage(G2frame,newPlot=False)
[762]	3627	finally:
	3628	dlg.Destroy()
[1232]	3629	return
[762]	3630	elif event.key == 'l':
[1205]	3631	G2frame.logPlot = not G2frame.logPlot
[1134]	3632	elif event.key in ['x',]:
[1205]	3633	Data['invert_x'] = not Data['invert_x']
[1134]	3634	elif event.key in ['y',]:
[1205]	3635	Data['invert_y'] = not Data['invert_y']
[1232]	3636	PlotImage(G2frame,newPlot=True)
[762]	3637
	3638	def OnKeyBox(event):
	3639	if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'):
	3640	event.key = cb.GetValue()[0]
	3641	cb.SetValue(' key press')
[1134]	3642	if event.key in ['l','s','a','r','p','x','y']:
[762]	3643	wx.CallAfter(OnImPlotKeyPress,event)
[1005]	3644	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
[762]	3645
	3646	def OnImPick(event):
	3647	if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']:
	3648	return
[1128]	3649	if G2frame.itemPicked is not None: return
	3650	G2frame.itemPicked = event.artist
	3651	G2frame.mousePicked = event.mouseevent
[762]	3652
	3653	def OnImRelease(event):
	3654	try:
	3655	PickName = G2frame.PatternTree.GetItemText(G2frame.PickId)
	3656	except TypeError:
	3657	return
[1185]	3658	if PickName not in ['Image Controls','Masks','Stress/Strain']:
[762]	3659	return
	3660	pixelSize = Data['pixelSize']
[1763]	3661	FlatBkg = Data.get('Flat Bkg',0.)
[762]	3662	scalex = 1000./pixelSize[0]
	3663	scaley = 1000./pixelSize[1]
[1377]	3664	# pixLimit = Data['pixLimit'] #can be too tight
	3665	pixLimit = 20 #this makes the search box 40x40 pixels
[762]	3666	if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ):
	3667	Xpos = event.xdata
	3668	if not (Xpos and G2frame.ifGetRing): #got point out of frame
	3669	return
	3670	Ypos = event.ydata
	3671	if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected
	3672	if event.button == 1:
	3673	Xpix = Xpos*scalex
	3674	Ypix = Ypos*scaley
[1763]	3675	xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ-FlatBkg,pixLimit,Xpix,Ypix)
[762]	3676	if I and J:
	3677	xpos += .5 #shift to pixel center
	3678	ypos += .5
	3679	xpos /= scalex #convert to mm
	3680	ypos /= scaley
	3681	Data['ring'].append([xpos,ypos])
	3682	elif event.button == 3:
[1319]	3683	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...',0)
[762]	3684	if G2img.ImageCalibrate(G2frame,Data):
[1319]	3685	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check',0)
[762]	3686	print 'Calibration successful'
	3687	else:
[1319]	3688	G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose',0)
[762]	3689	print 'Calibration failed'
	3690	G2frame.ifGetRing = False
	3691	G2imG.UpdateImageControls(G2frame,Data,Masks)
	3692	return
	3693	PlotImage(G2frame,newImage=False)
	3694	return
[1128]	3695	elif G2frame.MaskKey and PickName == 'Masks':
	3696	Xpos,Ypos = [event.xdata,event.ydata]
	3697	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
	3698	return
	3699	if G2frame.MaskKey == 's' and event.button == 1:
	3700	Masks['Points'][-1] = [Xpos,Ypos,1.]
	3701	G2frame.MaskKey = ''
	3702	elif G2frame.MaskKey == 'r' and event.button == 1:
	3703	tth = G2img.GetTth(Xpos,Ypos,Data)
	3704	Masks['Rings'][-1] = [tth,0.1]
	3705	G2frame.MaskKey = ''
	3706	elif G2frame.MaskKey == 'a' and event.button == 1:
	3707	tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data)
	3708	azm = int(azm)
	3709	Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1]
	3710	G2frame.MaskKey = ''
	3711	elif G2frame.MaskKey =='p':
	3712	polygon = Masks['Polygons'][-1]
[1131]	3713	if len(polygon) > 2 and event.button == 3:
[1128]	3714	x0,y0 = polygon[0]
	3715	polygon.append([x0,y0])
	3716	G2frame.MaskKey = ''
[1268]	3717	G2frame.G2plotNB.status.SetFields(['','Polygon closed'])
[1128]	3718	else:
	3719	G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)])
	3720	polygon.append([Xpos,Ypos])
	3721	elif G2frame.MaskKey =='f':
	3722	frame = Masks['Frames']
[1131]	3723	if len(frame) > 2 and event.button == 3:
[1128]	3724	x0,y0 = frame[0]
	3725	frame.append([x0,y0])
	3726	G2frame.MaskKey = ''
[1268]	3727	G2frame.G2plotNB.status.SetFields(['','Frame closed'])
[1128]	3728	else:
	3729	G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)])
	3730	frame.append([Xpos,Ypos])
	3731	G2imG.UpdateMasks(G2frame,Masks)
	3732	PlotImage(G2frame,newImage=False)
[1188]	3733	elif PickName == 'Stress/Strain' and G2frame.StrainKey:
[1185]	3734	Xpos,Ypos = [event.xdata,event.ydata]
	3735	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
	3736	return
	3737	dsp = G2img.GetDsp(Xpos,Ypos,Data)
[1761]	3738	StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':0.5,
[1185]	3739	'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]})
[1763]	3740	R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ-FlatBkg,Data)
[1185]	3741	if not len(R):
	3742	del StrSta['d-zero'][-1]
	3743	G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection')
[1188]	3744	StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True)
	3745	G2frame.StrainKey = ''
[1185]	3746	G2imG.UpdateStressStrain(G2frame,StrSta)
	3747	PlotStrain(G2frame,StrSta)
	3748	PlotImage(G2frame,newPlot=False)
[762]	3749	else:
[1128]	3750	Xpos,Ypos = [event.xdata,event.ydata]
	3751	if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected
	3752	return
	3753	if G2frame.ifGetRing: #delete a calibration ring pick
	3754	xypos = [Xpos,Ypos]
	3755	rings = Data['ring']
	3756	for ring in rings:
	3757	if np.allclose(ring,xypos,.01,0):
	3758	rings.remove(ring)
	3759	else:
[1153]	3760	tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3]
[1128]	3761	itemPicked = str(G2frame.itemPicked)
	3762	if 'Line2D' in itemPicked and PickName == 'Image Controls':
	3763	if 'line1' in itemPicked:
	3764	Data['IOtth'][0] = max(tth,0.001)
	3765	elif 'line2' in itemPicked:
	3766	Data['IOtth'][1] = tth
	3767	elif 'line3' in itemPicked:
	3768	Data['LRazimuth'][0] = int(azm)
	3769	elif 'line4' in itemPicked and not Data['fullIntegrate']:
	3770	Data['LRazimuth'][1] = int(azm)
[1163]	3771
	3772	Data['LRazimuth'][0] %= 360
	3773	Data['LRazimuth'][1] %= 360
[1128]	3774	if Data['LRazimuth'][0] > Data['LRazimuth'][1]:
[1163]	3775	Data['LRazimuth'][1] += 360
	3776	if Data['fullIntegrate']:
	3777	Data['LRazimuth'][1] = Data['LRazimuth'][0]+360
[1128]	3778
	3779	if Data['IOtth'][0] > Data['IOtth'][1]:
	3780	Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0]
	3781
	3782	G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0]))
	3783	G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1]))
	3784	G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0]))
	3785	G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1]))
	3786	elif 'Circle' in itemPicked and PickName == 'Masks':
	3787	spots = Masks['Points']
	3788	newPos = itemPicked.split(')')[0].split('(')[2].split(',')
	3789	newPos = np.array([float(newPos[0]),float(newPos[1])])
	3790	for spot in spots:
[1579]	3791	if spot and np.allclose(np.array([spot[:2]]),newPos):
[1128]	3792	spot[:2] = Xpos,Ypos
	3793	G2imG.UpdateMasks(G2frame,Masks)
	3794	elif 'Line2D' in itemPicked and PickName == 'Masks':
	3795	Obj = G2frame.itemPicked.findobj()
	3796	rings = Masks['Rings']
	3797	arcs = Masks['Arcs']
	3798	polygons = Masks['Polygons']
	3799	frame = Masks['Frames']
	3800	for ring in G2frame.ringList:
	3801	if Obj == ring[0]:
	3802	rN = ring[1]
	3803	if ring[2] == 'o':
	3804	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2.
	3805	else:
	3806	rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2.
	3807	for arc in G2frame.arcList:
	3808	if Obj == arc[0]:
	3809	aN = arc[1]
	3810	if arc[2] == 'o':
	3811	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2
	3812	elif arc[2] == 'i':
	3813	arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2
	3814	elif arc[2] == 'l':
	3815	arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data))
	3816	else:
	3817	arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data))
[1266]	3818	for poly in G2frame.polyList: #merging points problem here?
[1128]	3819	if Obj == poly[0]:
	3820	ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0]
[1121]	3821	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
[1128]	3822	pN = poly[1]
	3823	for i,xy in enumerate(polygons[pN]):
[1121]	3824	if np.allclose(np.array([xy]),oldPos,atol=1.0):
[1266]	3825	if event.button == 1:
	3826	polygons[pN][i] = Xpos,Ypos
	3827	elif event.button == 3:
	3828	polygons[pN].insert(i,[Xpos,Ypos])
	3829	break
[1128]	3830	if frame:
	3831	oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata])
	3832	for i,xy in enumerate(frame):
	3833	if np.allclose(np.array([xy]),oldPos,atol=1.0):
[1266]	3834	if event.button == 1:
	3835	frame[i] = Xpos,Ypos
	3836	elif event.button == 3:
	3837	frame.insert(i,[Xpos,Ypos])
	3838	break
[1128]	3839	G2imG.UpdateMasks(G2frame,Masks)
	3840	# else: #keep for future debugging
	3841	# print str(G2frame.itemPicked),event.xdata,event.ydata,event.button
	3842	PlotImage(G2frame,newImage=True)
[762]	3843	G2frame.itemPicked = None
	3844
	3845	try:
	3846	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
	3847	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3848	if not newPlot:
	3849	Plot = Page.figure.gca() #get previous powder plot & get limits
	3850	xylim = Plot.get_xlim(),Plot.get_ylim()
	3851	if newImage:
	3852	Page.figure.clf()
	3853	Plot = Page.figure.gca() #get a fresh plot after clf()
	3854	except ValueError:
	3855	Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca()
	3856	plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image')
	3857	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	3858	Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress)
	3859	Page.canvas.mpl_connect('motion_notify_event', OnImMotion)
	3860	Page.canvas.mpl_connect('pick_event', OnImPick)
	3861	Page.canvas.mpl_connect('button_release_event', OnImRelease)
	3862	xylim = []
[796]	3863	Page.Choice = None
[762]	3864	if not event: #event from GUI TextCtrl - don't want focus to change to plot!!!
	3865	Page.SetFocus()
	3866	Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:]
	3867	G2frame.G2plotNB.status.DestroyChildren()
	3868	if G2frame.logPlot:
	3869	Title = 'log('+Title+')'
	3870	Plot.set_title(Title)
	3871	try:
	3872	if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]:
[1134]	3873	Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',)
[762]	3874	if G2frame.logPlot:
[796]	3875	Page.Choice[1] = 'l: log(I) off'
	3876	Page.keyPress = OnImPlotKeyPress
[1128]	3877	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]:
[1212]	3878	Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask',
[1128]	3879	'p: polygon mask','f: frame mask',)
[1212]	3880	if G2frame.logPlot:
	3881	Page.Choice[1] = 'l: log(I) off'
[1128]	3882	Page.keyPress = OnImPlotKeyPress
[1188]	3883	elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]:
	3884	Page.Choice = (' key press','a: add new ring',)
	3885	Page.keyPress = OnImPlotKeyPress
[762]	3886	except TypeError:
	3887	pass
	3888	size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image)
[1418]	3889	dark = Data.get('dark image',[0,''])
[1399]	3890	if dark[0]:
	3891	darkfile = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,
	3892	G2frame.root,dark[0]))[1]
[762]	3893	if imagefile != G2frame.oldImagefile:
	3894	imagefile = G2IO.CheckImageFile(G2frame,imagefile)
	3895	if not imagefile:
	3896	G2frame.G2plotNB.Delete('2D Powder Image')
	3897	return
	3898	G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile])
	3899	G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True)
[1399]	3900	if dark[0]:
	3901	darkImg = G2IO.GetImageData(G2frame,darkfile,imageOnly=True)
	3902	G2frame.ImageZ += dark[1]*darkImg
[762]	3903	G2frame.oldImagefile = imagefile
	3904
	3905	imScale = 1
	3906	if len(G2frame.ImageZ) > 1024:
	3907	imScale = len(G2frame.ImageZ)/1024
	3908	sizexy = Data['size']
	3909	pixelSize = Data['pixelSize']
	3910	scalex = 1000./pixelSize[0]
	3911	scaley = 1000./pixelSize[1]
	3912	Xmax = sizexy[0]*pixelSize[0]/1000.
	3913	Ymax = sizexy[1]*pixelSize[1]/1000.
	3914	xlim = (0,Xmax)
	3915	ylim = (Ymax,0)
	3916	Imin,Imax = Data['range'][1]
	3917	acolor = mpl.cm.get_cmap(Data['color'])
	3918	xcent,ycent = Data['center']
	3919	Plot.set_xlabel('Image x-axis, mm',fontsize=12)
	3920	Plot.set_ylabel('Image y-axis, mm',fontsize=12)
	3921	#do threshold mask - "real" mask - others are just bondaries
	3922	Zlim = Masks['Thresholds'][1]
[1763]	3923	FlatBkg = Data.get('Flat Bkg',0.0)
[762]	3924	wx.BeginBusyCursor()
	3925	try:
	3926
	3927	if newImage:
[1212]	3928	Imin,Imax = Data['range'][1]
[1764]	3929	MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]+FlatBkg),Zlim[1]+FlatBkg)
[762]	3930	MaskA = ma.getmaskarray(MA)
[1763]	3931	A = G2img.ImageCompress(MA,imScale)-FlatBkg
[762]	3932	AM = G2img.ImageCompress(MaskA,imScale)
	3933	if G2frame.logPlot:
[1212]	3934	A = np.where(A>Imin,np.where(A<Imax,A,0),0)
[762]	3935	A = np.where(A>0,np.log(A),0)
	3936	AM = np.where(AM>0,np.log(AM),0)
	3937	Imin,Imax = [np.amin(A),np.amax(A)]
	3938	ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds',
	3939	interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0])
	3940	Img = Plot.imshow(A,aspect='equal',cmap=acolor,
	3941	interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0])
	3942
	3943	Plot.plot(xcent,ycent,'x')
	3944	#G2frame.PatternTree.GetItemText(item)
	3945	if Data['showLines']:
	3946	LRAzim = Data['LRazimuth'] #NB: integers
	3947	Nazm = Data['outAzimuths']
	3948	delAzm = float(LRAzim[1]-LRAzim[0])/Nazm
	3949	AzmthOff = Data['azmthOff']
	3950	IOtth = Data['IOtth']
	3951	wave = Data['wavelength']
	3952	dspI = wave/(2.0*sind(IOtth[0]/2.0))
	3953	ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola)
	3954	dspO = wave/(2.0*sind(IOtth[1]/2.0))
	3955	ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse
	3956	Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff
	3957	if ellI:
	3958	xyI = []
	3959	for azm in Azm:
[1163]	3960	xy = G2img.GetDetectorXY(dspI,azm,Data)
	3961	if np.any(xy):
	3962	xyI.append(xy)
	3963	if len(xyI):
	3964	xyI = np.array(xyI)
	3965	arcxI,arcyI = xyI.T
	3966	Plot.plot(arcxI,arcyI,picker=3)
[762]	3967	if ellO:
	3968	xyO = []
	3969	for azm in Azm:
[1163]	3970	xy = G2img.GetDetectorXY(dspO,azm,Data)
	3971	if np.any(xy):
	3972	xyO.append(xy)
	3973	if len(xyO):
	3974	xyO = np.array(xyO)
	3975	arcxO,arcyO = xyO.T
	3976	Plot.plot(arcxO,arcyO,picker=3)
[762]	3977	if ellO and ellI:
	3978	Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3)
	3979	Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3)
	3980	for i in range(Nazm):
	3981	cake = LRAzim[0]+i*delAzm-AzmthOff
	3982	if Data['centerAzm']:
	3983	cake += delAzm/2.
	3984	ind = np.searchsorted(Azm,cake)
	3985	Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5))
	3986
	3987	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls':
	3988	for xring,yring in Data['ring']:
	3989	Plot.plot(xring,yring,'r+',picker=3)
	3990	if Data['setRings']:
	3991	N = 0
	3992	for ring in Data['rings']:
	3993	xring,yring = np.array(ring).T[:2]
[1185]	3994	Plot.plot(xring,yring,'.',color=colors[N%6])
[762]	3995	N += 1
[1151]	3996	for ellipse in Data['ellipses']: #what about hyperbola?
[762]	3997	cent,phi,[width,height],col = ellipse
[1151]	3998	if width > 0: #ellipses
	3999	Plot.add_artist(Ellipse([cent[0],cent[1]],2width,2height,phi,ec=col,fc='none'))
	4000	Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center')
[762]	4001	if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain':
[1180]	4002	for N,ring in enumerate(StrSta['d-zero']):
[762]	4003	xring,yring = ring['ImxyObs']
[1185]	4004	Plot.plot(xring,yring,colors[N%6]+'.')
[762]	4005	#masks - mask lines numbered after integration limit lines
	4006	spots = Masks['Points']
	4007	rings = Masks['Rings']
	4008	arcs = Masks['Arcs']
	4009	polygons = Masks['Polygons']
[1121]	4010	if 'Frames' not in Masks:
	4011	Masks['Frames'] = []
	4012	frame = Masks['Frames']
[1128]	4013	for spot in spots:
	4014	if spot:
	4015	x,y,d = spot
	4016	Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3))
[762]	4017	G2frame.ringList = []
[1128]	4018	for iring,ring in enumerate(rings):
	4019	if ring:
	4020	tth,thick = ring
	4021	wave = Data['wavelength']
[1151]	4022	xy1 = []
	4023	xy2 = []
	4024	Azm = np.linspace(0,362,181)
	4025	for azm in Azm:
	4026	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
	4027	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
	4028	x1,y1 = np.array(xy1).T
	4029	x2,y2 = np.array(xy2).T
[1128]	4030	G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o'])
	4031	G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i'])
[762]	4032	G2frame.arcList = []
[1128]	4033	for iarc,arc in enumerate(arcs):
	4034	if arc:
	4035	tth,azm,thick = arc
	4036	wave = Data['wavelength']
[1151]	4037	xy1 = []
	4038	xy2 = []
	4039	aR = azm[0],azm[1],azm[1]-azm[0]
	4040	if azm[1]-azm[0] > 180:
	4041	aR[2] /= 2
	4042	Azm = np.linspace(aR[0],aR[1],aR[2])
	4043	for azm in Azm:
	4044	xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola
	4045	xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola
	4046	x1,y1 = np.array(xy1).T
	4047	x2,y2 = np.array(xy2).T
[1128]	4048	G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o'])
	4049	G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i'])
	4050	G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l'])
	4051	G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u'])
[762]	4052	G2frame.polyList = []
	4053	for ipoly,polygon in enumerate(polygons):
[1128]	4054	if polygon:
	4055	x,y = np.hsplit(np.array(polygon),2)
	4056	G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly])
	4057	Plot.plot(x,y,'r')
[1121]	4058	G2frame.frameList = []
	4059	if frame:
	4060	x,y = np.hsplit(np.array(frame),2)
	4061	G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0])
	4062	Plot.plot(x,y,'g')
[762]	4063	if newImage:
	4064	colorBar = Page.figure.colorbar(Img)
	4065	Plot.set_xlim(xlim)
	4066	Plot.set_ylim(ylim)
[1134]	4067	if Data['invert_x']:
	4068	Plot.invert_xaxis()
	4069	if Data['invert_y']:
	4070	Plot.invert_yaxis()
[762]	4071	if not newPlot and xylim:
	4072	Page.toolbar.push_current()
	4073	Plot.set_xlim(xylim[0])
	4074	Plot.set_ylim(xylim[1])
	4075	xylim = []
	4076	Page.toolbar.push_current()
	4077	Page.toolbar.draw()
[1473]	4078	# patch for wx 2.9 on Mac, to force a redraw
	4079	i,j= wx.__version__.split('.')[0:2]
	4080	if int(i)+int(j)/10. > 2.8 and 'wxOSX' in wx.PlatformInfo:
	4081	Page.canvas.draw()
[762]	4082	else:
	4083	Page.canvas.draw()
	4084	finally:
	4085	wx.EndBusyCursor()
	4086
	4087	################################################################################
	4088	##### PlotIntegration
	4089	################################################################################
	4090
	4091	def PlotIntegration(G2frame,newPlot=False,event=None):
	4092	'''Plot of 2D image after image integration with 2-theta and azimuth as coordinates
	4093	'''
	4094
	4095	def OnMotion(event):
	4096	Page.canvas.SetToolTipString('')
	4097	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	4098	azm = event.ydata
	4099	tth = event.xdata
	4100	if azm and tth:
	4101	G2frame.G2plotNB.status.SetFields(\
	4102	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
	4103
	4104	try:
	4105	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
	4106	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	4107	if not newPlot:
	4108	Plot = Page.figure.gca() #get previous plot & get limits
	4109	xylim = Plot.get_xlim(),Plot.get_ylim()
	4110	Page.figure.clf()
	4111	Plot = Page.figure.gca() #get a fresh plot after clf()
	4112
	4113	except ValueError:
	4114	Plot = G2frame.G2plotNB.addMpl('2D Integration').gca()
	4115	plotNum = G2frame.G2plotNB.plotList.index('2D Integration')
	4116	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	4117	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	4118	Page.views = False
	4119	view = False
[796]	4120	Page.Choice = None
[762]	4121	if not event:
	4122	Page.SetFocus()
	4123
	4124	Data = G2frame.PatternTree.GetItemPyData(
	4125	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
	4126	image = G2frame.Integrate[0]
	4127	xsc = G2frame.Integrate[1]
	4128	ysc = G2frame.Integrate[2]
	4129	Imin,Imax = Data['range'][1]
	4130	acolor = mpl.cm.get_cmap(Data['color'])
	4131	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
	4132	Plot.set_ylabel('azimuth',fontsize=12)
	4133	Plot.set_xlabel('2-theta',fontsize=12)
	4134	Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \
	4135	extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto')
	4136	colorBar = Page.figure.colorbar(Img)
[1148]	4137	# if Data['ellipses']:
	4138	# for ellipse in Data['ellipses']:
	4139	# x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
	4140	# tth,azm = G2img.GetTthAzm(x,y,Data)
	4141	## azm = np.where(azm < 0.,azm+360,azm)
	4142	# Plot.plot(tth,azm,'b,')
[762]	4143	if not newPlot:
	4144	Page.toolbar.push_current()
	4145	Plot.set_xlim(xylim[0])
	4146	Plot.set_ylim(xylim[1])
	4147	xylim = []
	4148	Page.toolbar.push_current()
	4149	Page.toolbar.draw()
	4150	else:
	4151	Page.canvas.draw()
	4152
	4153	################################################################################
	4154	##### PlotTRImage
	4155	################################################################################
	4156
	4157	def PlotTRImage(G2frame,tax,tay,taz,newPlot=False):
	4158	'''a test plot routine - not normally used
	4159	'''
	4160
	4161	def OnMotion(event):
	4162	Page.canvas.SetToolTipString('')
	4163	Page.canvas.SetCursor(wx.CROSS_CURSOR)
	4164	azm = event.xdata
	4165	tth = event.ydata
	4166	if azm and tth:
	4167	G2frame.G2plotNB.status.SetFields(\
	4168	['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)])
	4169
	4170	try:
	4171	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
	4172	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	4173	if not newPlot:
	4174	Plot = Page.figure.gca() #get previous plot & get limits
	4175	xylim = Plot.get_xlim(),Plot.get_ylim()
	4176	Page.figure.clf()
	4177	Plot = Page.figure.gca() #get a fresh plot after clf()
	4178
	4179	except ValueError:
	4180	Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca()
	4181	plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image')
	4182	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	4183	Page.canvas.mpl_connect('motion_notify_event', OnMotion)
	4184	Page.views = False
	4185	view = False
[796]	4186	Page.Choice = None
[762]	4187	Page.SetFocus()
	4188
	4189	Data = G2frame.PatternTree.GetItemPyData(
	4190	G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls'))
	4191	Imin,Imax = Data['range'][1]
	4192	step = (Imax-Imin)/5.
	4193	V = np.arange(Imin,Imax,step)
	4194	acolor = mpl.cm.get_cmap(Data['color'])
	4195	Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:])
	4196	Plot.set_xlabel('azimuth',fontsize=12)
	4197	Plot.set_ylabel('2-theta',fontsize=12)
	4198	Plot.contour(tax,tay,taz,V,cmap=acolor)
	4199	if Data['showLines']:
	4200	IOtth = Data['IOtth']
	4201	if Data['fullIntegrate']:
	4202	LRAzim = [-180,180]
	4203	else:
	4204	LRAzim = Data['LRazimuth'] #NB: integers
	4205	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True)
	4206	Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True)
	4207	if not Data['fullIntegrate']:
	4208	Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True)
	4209	Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True)
	4210	if Data['setRings']:
	4211	rings = np.concatenate((Data['rings']),axis=0)
	4212	for xring,yring,dsp in rings:
	4213	x,y = G2img.GetTthAzm(xring,yring,Data)
	4214	Plot.plot(y,x,'r+')
	4215	if Data['ellipses']:
	4216	for ellipse in Data['ellipses']:
	4217	ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color
	4218	x,y = np.hsplit(ring,2)
	4219	tth,azm = G2img.GetTthAzm(x,y,Data)
	4220	Plot.plot(azm,tth,'b,')
	4221	if not newPlot:
	4222	Page.toolbar.push_current()
	4223	Plot.set_xlim(xylim[0])
	4224	Plot.set_ylim(xylim[1])
	4225	xylim = []
	4226	Page.toolbar.push_current()
	4227	Page.toolbar.draw()
	4228	else:
	4229	Page.canvas.draw()
	4230
	4231	################################################################################
	4232	##### PlotStructure
	4233	################################################################################
	4234
[1381]	4235	def PlotStructure(G2frame,data,firstCall=False):
[762]	4236	'''Crystal structure plotting package. Can show structures as balls, sticks, lines,
	4237	thermal motion ellipsoids and polyhedra
	4238	'''
[839]	4239
[951]	4240	def FindPeaksBonds(XYZ):
[1460]	4241	rFact = data['Drawing'].get('radiusFactor',0.85) #data['Drawing'] could be empty!
[951]	4242	Bonds = [[] for x in XYZ]
	4243	for i,xyz in enumerate(XYZ):
	4244	Dx = XYZ-xyz
	4245	dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1))
	4246	IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2))
	4247	for j in IndB[0]:
	4248	Bonds[i].append(Dx[j]/2.)
	4249	Bonds[j].append(-Dx[j]/2.)
	4250	return Bonds
	4251
[1383]	4252	# PlotStructure initialization here
[762]	4253	ForthirdPI = 4.0*math.pi/3.0
	4254	generalData = data['General']
	4255	cell = generalData['Cell'][1:7]
	4256	Vol = generalData['Cell'][7:8][0]
	4257	Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse
	4258	Gmat,gmat = G2lat.cell2Gmat(cell)
	4259	A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	4260	B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
[951]	4261	SGData = generalData['SGData']
[1633]	4262	if generalData['Type'] in ['modulated','magnetic']:
	4263	SSGData = generalData['SSGData']
[762]	4264	Mydir = generalData['Mydir']
[1951]	4265	Super = generalData.get('Super',0)
[762]	4266	atomData = data['Atoms']
	4267	mapPeaks = []
[1470]	4268	drawingData = data['Drawing']
	4269	if not drawingData:
	4270	return #nothing setup, nothing to draw
[762]	4271	if 'Map Peaks' in data:
[766]	4272	mapPeaks = np.array(data['Map Peaks'])
[777]	4273	peakMax = 100.
	4274	if len(mapPeaks):
	4275	peakMax = np.max(mapPeaks.T[0])
[855]	4276	resRBData = data['RBModels'].get('Residue',[])
	4277	vecRBData = data['RBModels'].get('Vector',[])
	4278	rbAtmDict = {}
	4279	for rbObj in resRBData+vecRBData:
	4280	exclList = ['X' for i in range(len(rbObj['Ids']))]
	4281	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
[851]	4282	testRBObj = data.get('testRBObj',{})
	4283	rbObj = testRBObj.get('rbObj',{})
[934]	4284	MCSA = data.get('MCSA',{})
[936]	4285	mcsaModels = MCSA.get('Models',[])
[1474]	4286	if len(mcsaModels) > 1:
[953]	4287	XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA)
	4288	mcsaXYZ = []
	4289	mcsaTypes = []
[1471]	4290	neqv = 0
[953]	4291	for xyz,atyp in zip(XYZs,Types):
[1471]	4292	equiv = G2spc.GenAtom(xyz,SGData,All=True,Move=False)
	4293	neqv = max(neqv,len(equiv))
	4294	for item in equiv:
[953]	4295	mcsaXYZ.append(item[0])
	4296	mcsaTypes.append(atyp)
[1471]	4297	mcsaXYZ = np.array(mcsaXYZ)
	4298	mcsaTypes = np.array(mcsaTypes)
	4299	nuniq = mcsaXYZ.shape[0]/neqv
	4300	mcsaXYZ = np.reshape(mcsaXYZ,(nuniq,neqv,3))
	4301	mcsaTypes = np.reshape(mcsaTypes,(nuniq,neqv))
	4302	cent = np.fix(np.sum(mcsaXYZ+2.,axis=0)/nuniq)-2
	4303	cent[0] = [0,0,0] #make sure 1st one isn't moved
	4304	mcsaXYZ = np.swapaxes(mcsaXYZ,0,1)-cent[:,np.newaxis,:]
	4305	mcsaTypes = np.swapaxes(mcsaTypes,0,1)
	4306	mcsaXYZ = np.reshape(mcsaXYZ,(nuniq*neqv,3))
	4307	mcsaTypes = np.reshape(mcsaTypes,(nuniq*neqv))
[953]	4308	mcsaBonds = FindPeaksBonds(mcsaXYZ)
[851]	4309	drawAtoms = drawingData.get('Atoms',[])
[762]	4310	mapData = {}
	4311	flipData = {}
	4312	rhoXYZ = []
[840]	4313	showBonds = False
[762]	4314	if 'Map' in generalData:
	4315	mapData = generalData['Map']
[863]	4316	showBonds = mapData.get('Show bonds',False)
[762]	4317	if 'Flip' in generalData:
	4318	flipData = generalData['Flip']
	4319	Wt = np.array([255,255,255])
	4320	Rd = np.array([255,0,0])
	4321	Gr = np.array([0,255,0])
[1378]	4322	wxGreen = wx.Colour(0,255,0)
[762]	4323	Bl = np.array([0,0,255])
[853]	4324	Or = np.array([255,128,0])
[1378]	4325	wxOrange = wx.Colour(255,128,0)
[762]	4326	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]])
	4327	uEdges = np.array([
	4328	[uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]],
	4329	[uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]],
	4330	[uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
	4331	mD = 0.1
	4332	mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
	4333	mapPeakVecs = np.inner(mV,Bmat)
	4334
[1559]	4335	backColor = np.array(list(drawingData['backColor'])+[0,])
	4336	Bc = np.array(list(drawingData['backColor']))
	4337	uColors = [Rd,Gr,Bl,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc]
[762]	4338	altDown = False
	4339	shiftDown = False
	4340	ctrlDown = False
[1633]	4341	G2frame.tau = 0.
[762]	4342
	4343	def OnKeyBox(event):
	4344	mode = cb.GetValue()
	4345	if mode in ['jpeg','bmp','tiff',]:
[1397]	4346	try:
	4347	import Image as Im
	4348	except ImportError:
	4349	try:
	4350	from PIL import Image as Im
	4351	except ImportError:
	4352	print "PIL/pillow Image module not present. Cannot save images without this"
	4353	raise Exception("PIL/pillow Image module not found")
[837]	4354	Fname = os.path.join(Mydir,generalData['Name']+'.'+mode)
[762]	4355	size = Page.canvas.GetSize()
	4356	glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
	4357	if mode in ['jpeg',]:
	4358	Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE)
[1608]	4359	im = Im.new("RGBA", (size[0],size[1]))
[762]	4360	else:
	4361	Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE)
[1608]	4362	im = Im.new("RGB", (size[0],size[1]))
[762]	4363	im.fromstring(Pix)
	4364	im.save(Fname,mode)
	4365	cb.SetValue(' save as/key:')
	4366	G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1)
	4367	else:
	4368	event.key = cb.GetValue()[0]
	4369	cb.SetValue(' save as/key:')
	4370	wx.CallAfter(OnKey,event)
[1005]	4371	Page.canvas.SetFocus() # redirect the Focus from the button back to the plot
[762]	4372
	4373	def OnKey(event): #on key UP!!
[1951]	4374	keyBox = False
[762]	4375	try:
	4376	keyCode = event.GetKeyCode()
	4377	if keyCode > 255:
	4378	keyCode = 0
	4379	key = chr(keyCode)
	4380	except AttributeError: #if from OnKeyBox above
[1951]	4381	keyBox = True
[762]	4382	key = str(event.key).upper()
	4383	indx = drawingData['selectedAtoms']
[910]	4384	cx,ct = drawingData['atomPtrs'][:2]
[762]	4385	if key in ['C']:
	4386	drawingData['viewPoint'] = [[.5,.5,.5],[0,0]]
	4387	drawingData['viewDir'] = [0,0,1]
	4388	drawingData['oldxy'] = []
	4389	V0 = np.array([0,0,1])
	4390	V = np.inner(Amat,V0)
	4391	V /= np.sqrt(np.sum(V**2))
	4392	A = np.arccos(np.sum(V*V0))
	4393	Q = G2mth.AV2Q(A,[0,1,0])
	4394	drawingData['Quaternion'] = Q
	4395	SetViewPointText(drawingData['viewPoint'][0])
	4396	SetViewDirText(drawingData['viewDir'])
	4397	Q = drawingData['Quaternion']
	4398	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
	4399	elif key in ['N']:
	4400	drawAtoms = drawingData['Atoms']
[1005]	4401	if not len(drawAtoms): #no atoms
	4402	return
[762]	4403	pI = drawingData['viewPoint'][1]
[1005]	4404	if not len(pI):
	4405	pI = [0,0]
[762]	4406	if indx:
	4407	pI[0] = indx[pI[1]]
	4408	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
	4409	pI[1] += 1
	4410	if pI[1] >= len(indx):
	4411	pI[1] = 0
	4412	else:
	4413	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
	4414	pI[0] += 1
	4415	if pI[0] >= len(drawAtoms):
	4416	pI[0] = 0
	4417	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
	4418	SetViewPointText(drawingData['viewPoint'][0])
	4419	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
	4420
	4421	elif key in ['P']:
	4422	drawAtoms = drawingData['Atoms']
[1005]	4423	if not len(drawAtoms): #no atoms
	4424	return
[762]	4425	pI = drawingData['viewPoint'][1]
[1005]	4426	if not len(pI):
	4427	pI = [0,0]
[762]	4428	if indx:
	4429	pI[0] = indx[pI[1]]
	4430	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
	4431	pI[1] -= 1
	4432	if pI[1] < 0:
	4433	pI[1] = len(indx)-1
	4434	else:
	4435	Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3]
	4436	pI[0] -= 1
	4437	if pI[0] < 0:
	4438	pI[0] = len(drawAtoms)-1
	4439	drawingData['viewPoint'] = [[Tx,Ty,Tz],pI]
	4440	SetViewPointText(drawingData['viewPoint'][0])
	4441	G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+str(pI),1)
	4442	elif key in ['U','D','L','R'] and mapData['Flip'] == True:
	4443	dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]}
	4444	SetMapRoll(dirDict[key])
[1623]	4445	if 'rho' in generalData.get('4DmapData',{}):
	4446	Set4DMapRoll(dirDict[key])
[762]	4447	SetPeakRoll(dirDict[key])
	4448	SetMapPeaksText(mapPeaks)
[1694]	4449	elif key in ['+','-','=','0'] and generalData['Type'] in ['modulated','magnetic']:
[1951]	4450	if keyBox:
	4451	OnKeyPressed(event)
[1958]	4452	return
	4453	Draw('key up')
[1951]	4454
	4455	def OnKeyPressed(event): #On key down for repeating operation - used to change tau...
	4456	try:
	4457	keyCode = event.GetKeyCode()
	4458	if keyCode > 255:
	4459	keyCode = 0
	4460	key = chr(keyCode)
	4461	except AttributeError: #if from OnKeyBox above
	4462	key = str(event.key).upper()
	4463	if key in ['+','-','=','0'] and generalData['Type'] in ['modulated','magnetic']:
[1633]	4464	if key == '0':
	4465	G2frame.tau = 0.
[1694]	4466	elif key in ['+','=']:
[1633]	4467	G2frame.tau += 0.05
[1694]	4468	elif key == '-':
[1633]	4469	G2frame.tau -= 0.05
	4470	G2frame.tau %= 1. #force 0-1 range
[1951]	4471	G2frame.G2plotNB.status.SetStatusText('Modulation tau = %.2f'%(G2frame.tau),1)
[1958]	4472	data['Drawing']['Atoms'],Fade = G2mth.ApplyModulation(data,G2frame.tau) #modifies drawing atom array!
[1951]	4473	SetDrawAtomsText(data['Drawing']['Atoms'])
	4474	G2phG.FindBondsDraw(data) #rebuild bonds & polygons
[1958]	4475	if not np.any(Fade):
	4476	Fade += 1
	4477	Draw('key down',Fade)
[762]	4478
	4479	def GetTruePosition(xy,Add=False):
	4480	View = glGetIntegerv(GL_VIEWPORT)
	4481	Proj = glGetDoublev(GL_PROJECTION_MATRIX)
	4482	Model = glGetDoublev(GL_MODELVIEW_MATRIX)
	4483	Zmax = 1.
	4484	if Add:
	4485	Indx = GetSelectedAtoms()
	4486	if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
	4487	for i,peak in enumerate(mapPeaks):
	4488	x,y,z = peak[1:4]
	4489	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
	4490	XY = [int(X),int(View[3]-Y)]
	4491	if np.allclose(xy,XY,atol=10) and Z < Zmax:
	4492	Zmax = Z
	4493	try:
	4494	Indx.remove(i)
	4495	ClearSelectedAtoms()
	4496	for id in Indx:
	4497	SetSelectedAtoms(id,Add)
	4498	except:
	4499	SetSelectedAtoms(i,Add)
	4500	else:
[910]	4501	cx = drawingData['atomPtrs'][0]
[762]	4502	for i,atom in enumerate(drawAtoms):
	4503	x,y,z = atom[cx:cx+3]
	4504	X,Y,Z = gluProject(x,y,z,Model,Proj,View)
	4505	XY = [int(X),int(View[3]-Y)]
	4506	if np.allclose(xy,XY,atol=10) and Z < Zmax:
	4507	Zmax = Z
	4508	try:
	4509	Indx.remove(i)
	4510	ClearSelectedAtoms()
	4511	for id in Indx:
	4512	SetSelectedAtoms(id,Add)
	4513	except:
	4514	SetSelectedAtoms(i,Add)
	4515
	4516	def OnMouseDown(event):
	4517	xy = event.GetPosition()
	4518	if event.ShiftDown():
	4519	if event.LeftIsDown():
	4520	GetTruePosition(xy)
	4521	elif event.RightIsDown():
	4522	GetTruePosition(xy,True)
	4523	else:
	4524	drawingData['oldxy'] = list(xy)
	4525
	4526	def OnMouseMove(event):
	4527	if event.ShiftDown(): #don't want any inadvertant moves when picking
	4528	return
	4529	newxy = event.GetPosition()
	4530
[851]	4531	if event.Dragging():
[860]	4532	if event.AltDown() and rbObj:
[851]	4533	if event.LeftIsDown():
	4534	SetRBRotation(newxy)
	4535	Q = rbObj['Orient'][0]
	4536	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
	4537	elif event.RightIsDown():
	4538	SetRBTranslation(newxy)
	4539	Tx,Ty,Tz = rbObj['Orig'][0]
	4540	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1)
	4541	elif event.MiddleIsDown():
	4542	SetRBRotationZ(newxy)
	4543	Q = rbObj['Orient'][0]
	4544	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
	4545	Draw('move')
	4546	elif not event.ControlDown():
	4547	if event.LeftIsDown():
	4548	SetRotation(newxy)
	4549	Q = drawingData['Quaternion']
	4550	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
	4551	elif event.RightIsDown():
	4552	SetTranslation(newxy)
	4553	Tx,Ty,Tz = drawingData['viewPoint'][0]
[1928]	4554	rho = G2mth.getRho([Tx,Ty,Tz],mapData)
	4555	G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f; density: %.4f'%(Tx,Ty,Tz,rho),1)
[851]	4556	elif event.MiddleIsDown():
	4557	SetRotationZ(newxy)
	4558	Q = drawingData['Quaternion']
	4559	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
	4560	Draw('move')
	4561
[762]	4562
	4563	def OnMouseWheel(event):
	4564	if event.ShiftDown():
	4565	return
[924]	4566	drawingData['cameraPos'] += event.GetWheelRotation()/24.
[762]	4567	drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos']))
	4568	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1)
	4569	page = getSelection()
	4570	if page:
	4571	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
[924]	4572	G2frame.dataDisplay.cameraPosTxt.SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos']))
	4573	G2frame.dataDisplay.cameraSlider.SetValue(drawingData['cameraPos'])
[762]	4574	Draw('wheel')
	4575
	4576	def getSelection():
	4577	try:
	4578	return G2frame.dataDisplay.GetSelection()
	4579	except AttributeError:
[1306]	4580	G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!',1)
[762]	4581	return 0
	4582
	4583	def SetViewPointText(VP):
	4584	page = getSelection()
	4585	if page:
	4586	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
[924]	4587	G2frame.dataDisplay.viewPoint.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
[762]	4588
[851]	4589	def SetRBOrigText():
	4590	page = getSelection()
	4591	if page:
	4592	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
	4593	for i,sizer in enumerate(testRBObj['Sizers']['Xsizers']):
	4594	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orig'][0][i]))
	4595
	4596	def SetRBOrienText():
	4597	page = getSelection()
	4598	if page:
	4599	if G2frame.dataDisplay.GetPageText(page) == 'RB Models':
	4600	for i,sizer in enumerate(testRBObj['Sizers']['Osizers']):
	4601	sizer.SetValue('%8.5f'%(testRBObj['rbObj']['Orient'][0][i]))
	4602
[762]	4603	def SetViewDirText(VD):
	4604	page = getSelection()
	4605	if page:
	4606	if G2frame.dataDisplay.GetPageText(page) == 'Draw Options':
[922]	4607	G2frame.dataDisplay.viewDir.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
[762]	4608
	4609	def SetMapPeaksText(mapPeaks):
	4610	page = getSelection()
	4611	if page:
	4612	if G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
	4613	G2frame.MapPeaksTable.SetData(mapPeaks)
	4614	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
	4615	names = [child.GetName() for child in panel]
[1880]	4616	try:
	4617	panel[names.index('GridWindow')].Refresh()
	4618	except ValueError: #different wx versions!
	4619	panel[names.index('grid window')].Refresh()
[762]	4620
[1951]	4621	def SetDrawAtomsText(drawAtoms):
	4622	page = getSelection()
	4623	if page:
	4624	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
	4625	table = G2frame.atomTable.GetData()
	4626	for i,atom in enumerate(drawAtoms):
	4627	table[i][2:5] = atom[2:5]
	4628	G2frame.atomTable.SetData(table)
	4629	panel = G2frame.dataDisplay.GetPage(page).GetChildren()
	4630	names = [child.GetName() for child in panel]
	4631	try:
	4632	panel[names.index('GridWindow')].Refresh()
	4633	except ValueError: #different wx versions!
	4634	panel[names.index('grid window')].Refresh()
	4635
[762]	4636	def ClearSelectedAtoms():
	4637	page = getSelection()
	4638	if page:
	4639	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
	4640	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms
	4641	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
	4642	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
	4643	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
	4644	G2frame.dataDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms
	4645
	4646
	4647	def SetSelectedAtoms(ind,Add=False):
	4648	page = getSelection()
	4649	if page:
	4650	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
	4651	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms
	4652	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
	4653	G2frame.dataDisplay.GetPage(page).SelectRow(ind,Add)
	4654	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
[807]	4655	Id = drawAtoms[ind][-3]
[762]	4656	for i,atom in enumerate(atomData):
	4657	if atom[-1] == Id:
	4658	G2frame.dataDisplay.GetPage(page).SelectRow(i) #this is the Atoms grid in Atoms
	4659
	4660	def GetSelectedAtoms():
	4661	page = getSelection()
	4662	Ind = []
	4663	if page:
	4664	if G2frame.dataDisplay.GetPageText(page) == 'Draw Atoms':
	4665	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms
	4666	elif G2frame.dataDisplay.GetPageText(page) == 'Map peaks':
	4667	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows()
	4668	elif G2frame.dataDisplay.GetPageText(page) == 'Atoms':
	4669	Ind = G2frame.dataDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms
	4670	return Ind
	4671
	4672	def SetBackground():
	4673	R,G,B,A = Page.camera['backColor']
	4674	glClearColor(R,G,B,A)
	4675	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
	4676
	4677	def SetLights():
	4678	glEnable(GL_DEPTH_TEST)
	4679	glShadeModel(GL_SMOOTH)
	4680	glEnable(GL_LIGHTING)
	4681	glEnable(GL_LIGHT0)
	4682	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
	4683	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
	4684	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
	4685
[1623]	4686	def GetRoll(newxy,rhoshape):
[762]	4687	Q = drawingData['Quaternion']
	4688	dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,]))
[1623]	4689	dxy = np.array(dxy*rhoshape)
[762]	4690	roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0))
	4691	return roll
	4692
	4693	def SetMapRoll(newxy):
	4694	rho = mapData['rho']
[1623]	4695	roll = GetRoll(newxy,rho.shape)
[762]	4696	mapData['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
	4697	drawingData['oldxy'] = list(newxy)
	4698
[1623]	4699	def Set4DMapRoll(newxy):
	4700	rho = generalData['4DmapData']['rho']
	4701	roll = GetRoll(newxy,rho.shape[:3])
	4702	generalData['4DmapData']['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2)
	4703
[762]	4704	def SetPeakRoll(newxy):
	4705	rho = mapData['rho']
[1623]	4706	roll = GetRoll(newxy,rho.shape)
[762]	4707	steps = 1./np.array(rho.shape)
	4708	dxy = roll*steps
	4709	for peak in mapPeaks:
	4710	peak[1:4] += dxy
	4711	peak[1:4] %= 1.
	4712	peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2))
	4713
	4714	def SetTranslation(newxy):
	4715	#first get translation vector in screen coords.
	4716	oldxy = drawingData['oldxy']
	4717	if not len(oldxy): oldxy = list(newxy)
	4718	dxy = newxy-oldxy
	4719	drawingData['oldxy'] = list(newxy)
	4720	V = np.array([-dxy[0],dxy[1],0.])
	4721	#then transform to rotated crystal coordinates & apply to view point
	4722	Q = drawingData['Quaternion']
	4723	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
	4724	Tx,Ty,Tz = drawingData['viewPoint'][0]
	4725	Tx += V[0]*0.01
	4726	Ty += V[1]*0.01
	4727	Tz += V[2]*0.01
	4728	drawingData['viewPoint'][0] = Tx,Ty,Tz
	4729	SetViewPointText([Tx,Ty,Tz])
	4730
[851]	4731	def SetRBTranslation(newxy):
	4732	#first get translation vector in screen coords.
	4733	oldxy = drawingData['oldxy']
	4734	if not len(oldxy): oldxy = list(newxy)
	4735	dxy = newxy-oldxy
	4736	drawingData['oldxy'] = list(newxy)
	4737	V = np.array([-dxy[0],dxy[1],0.])
	4738	#then transform to rotated crystal coordinates & apply to RB origin
	4739	Q = drawingData['Quaternion']
	4740	V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V))
	4741	Tx,Ty,Tz = rbObj['Orig'][0]
	4742	Tx -= V[0]*0.01
	4743	Ty -= V[1]*0.01
	4744	Tz -= V[2]*0.01
	4745	rbObj['Orig'][0] = Tx,Ty,Tz
	4746	SetRBOrigText()
	4747
[762]	4748	def SetRotation(newxy):
[1383]	4749	'Perform a rotation in x-y space due to a left-mouse drag'
	4750	#first get rotation vector in screen coords. & angle increment
[762]	4751	oldxy = drawingData['oldxy']
	4752	if not len(oldxy): oldxy = list(newxy)
	4753	dxy = newxy-oldxy
	4754	drawingData['oldxy'] = list(newxy)
	4755	V = np.array([dxy[1],dxy[0],0.])
	4756	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
[1383]	4757	if not A: return # nothing changed, nothing to do
	4758	# next transform vector back to xtal coordinates via inverse quaternion
	4759	# & make new quaternion
[762]	4760	Q = drawingData['Quaternion']
	4761	V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V))
	4762	DQ = G2mth.AVdeg2Q(A,V)
	4763	Q = G2mth.prodQQ(Q,DQ)
	4764	drawingData['Quaternion'] = Q
[1383]	4765	# finally get new view vector - last row of rotation matrix
[762]	4766	VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2])
	4767	VD /= np.sqrt(np.sum(VD**2))
	4768	drawingData['viewDir'] = VD
	4769	SetViewDirText(VD)
	4770
	4771	def SetRotationZ(newxy):
	4772	#first get rotation vector (= view vector) in screen coords. & angle increment
	4773	View = glGetIntegerv(GL_VIEWPORT)
	4774	cent = [View[2]/2,View[3]/2]
	4775	oldxy = drawingData['oldxy']
	4776	if not len(oldxy): oldxy = list(newxy)
	4777	dxy = newxy-oldxy
	4778	drawingData['oldxy'] = list(newxy)
	4779	V = drawingData['viewDir']
	4780	A = [0,0]
	4781	A[0] = dxy[1]*.25
	4782	A[1] = dxy[0]*.25
	4783	if newxy[0] > cent[0]:
	4784	A[0] *= -1
	4785	if newxy[1] < cent[1]:
	4786	A[1] *= -1
	4787	# next transform vector back to xtal coordinates & make new quaternion
	4788	Q = drawingData['Quaternion']
	4789	V = np.inner(Amat,V)
	4790	Qx = G2mth.AVdeg2Q(A[0],V)
	4791	Qy = G2mth.AVdeg2Q(A[1],V)
	4792	Q = G2mth.prodQQ(Q,Qx)
	4793	Q = G2mth.prodQQ(Q,Qy)
	4794	drawingData['Quaternion'] = Q
	4795
[851]	4796	def SetRBRotation(newxy):
	4797	#first get rotation vector in screen coords. & angle increment
	4798	oldxy = drawingData['oldxy']
	4799	if not len(oldxy): oldxy = list(newxy)
	4800	dxy = newxy-oldxy
	4801	drawingData['oldxy'] = list(newxy)
	4802	V = np.array([dxy[1],dxy[0],0.])
	4803	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
	4804	# next transform vector back to xtal coordinates via inverse quaternion
	4805	# & make new quaternion
	4806	Q = rbObj['Orient'][0] #rotate RB to Cart
	4807	QC = drawingData['Quaternion'] #rotate Cart to drawing
	4808	V = G2mth.prodQVQ(G2mth.invQ(QC),V)
	4809	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
	4810	DQ = G2mth.AVdeg2Q(A,V)
	4811	Q = G2mth.prodQQ(Q,DQ)
	4812	rbObj['Orient'][0] = Q
	4813	SetRBOrienText()
	4814
	4815	def SetRBRotationZ(newxy):
	4816	#first get rotation vector (= view vector) in screen coords. & angle increment
	4817	View = glGetIntegerv(GL_VIEWPORT)
	4818	cent = [View[2]/2,View[3]/2]
	4819	oldxy = drawingData['oldxy']
	4820	if not len(oldxy): oldxy = list(newxy)
	4821	dxy = newxy-oldxy
	4822	drawingData['oldxy'] = list(newxy)
	4823	V = drawingData['viewDir']
	4824	A = [0,0]
	4825	A[0] = dxy[1]*.25
	4826	A[1] = dxy[0]*.25
	4827	if newxy[0] < cent[0]:
	4828	A[0] *= -1
	4829	if newxy[1] > cent[1]:
	4830	A[1] *= -1
	4831	# next transform vector back to RB coordinates & make new quaternion
	4832	Q = rbObj['Orient'][0] #rotate RB to cart
	4833	V = np.inner(Amat,V)
	4834	V = -G2mth.prodQVQ(G2mth.invQ(Q),V)
	4835	Qx = G2mth.AVdeg2Q(A[0],V)
	4836	Qy = G2mth.AVdeg2Q(A[1],V)
	4837	Q = G2mth.prodQQ(Q,Qx)
	4838	Q = G2mth.prodQQ(Q,Qy)
	4839	rbObj['Orient'][0] = Q
	4840	SetRBOrienText()
	4841
[762]	4842	def RenderBox():
	4843	glEnable(GL_COLOR_MATERIAL)
	4844	glLineWidth(2)
	4845	glEnable(GL_BLEND)
	4846	glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
	4847	glEnable(GL_LINE_SMOOTH)
	4848	glBegin(GL_LINES)
	4849	for line,color in zip(uEdges,uColors):
	4850	glColor3ubv(color)
	4851	glVertex3fv(line[0])
	4852	glVertex3fv(line[1])
	4853	glEnd()
	4854	glColor4ubv([0,0,0,0])
	4855	glDisable(GL_LINE_SMOOTH)
	4856	glDisable(GL_BLEND)
	4857	glDisable(GL_COLOR_MATERIAL)
	4858
	4859	def RenderUnitVectors(x,y,z):
	4860	xyz = np.array([x,y,z])
	4861	glEnable(GL_COLOR_MATERIAL)
	4862	glLineWidth(1)
	4863	glPushMatrix()
	4864	glTranslate(x,y,z)
	4865	glScalef(1/cell[0],1/cell[1],1/cell[2])
	4866	glBegin(GL_LINES)
	4867	for line,color in zip(uEdges,uColors)[:3]:
	4868	glColor3ubv(color)
	4869	glVertex3fv(-line[1]/2.)
	4870	glVertex3fv(line[1]/2.)
	4871	glEnd()
	4872	glPopMatrix()
	4873	glColor4ubv([0,0,0,0])
	4874	glDisable(GL_COLOR_MATERIAL)
	4875
	4876	def RenderSphere(x,y,z,radius,color):
	4877	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	4878	glPushMatrix()
	4879	glTranslate(x,y,z)
	4880	glMultMatrixf(B4mat.T)
	4881	q = gluNewQuadric()
	4882	gluSphere(q,radius,20,10)
	4883	glPopMatrix()
	4884
	4885	def RenderDots(XYZ,RC):
	4886	glEnable(GL_COLOR_MATERIAL)
	4887	XYZ = np.array(XYZ)
	4888	glPushMatrix()
	4889	for xyz,rc in zip(XYZ,RC):
	4890	x,y,z = xyz
	4891	r,c = rc
	4892	glColor3ubv(c)
	4893	glPointSize(r*50)
	4894	glBegin(GL_POINTS)
	4895	glVertex3fv(xyz)
	4896	glEnd()
	4897	glPopMatrix()
	4898	glColor4ubv([0,0,0,0])
	4899	glDisable(GL_COLOR_MATERIAL)
	4900
	4901	def RenderSmallSphere(x,y,z,radius,color):
	4902	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	4903	glPushMatrix()
	4904	glTranslate(x,y,z)
	4905	glMultMatrixf(B4mat.T)
	4906	q = gluNewQuadric()
	4907	gluSphere(q,radius,4,2)
	4908	glPopMatrix()
	4909
	4910	def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color):
	4911	s1,s2,s3 = E
	4912	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	4913	glPushMatrix()
	4914	glTranslate(x,y,z)
	4915	glMultMatrixf(B4mat.T)
	4916	glMultMatrixf(R4.T)
	4917	glEnable(GL_NORMALIZE)
	4918	glScale(s1,s2,s3)
	4919	q = gluNewQuadric()
	4920	gluSphere(q,ellipseProb,20,10)
	4921	glDisable(GL_NORMALIZE)
	4922	glPopMatrix()
	4923
	4924	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
	4925	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	4926	glPushMatrix()
	4927	glTranslate(x,y,z)
	4928	glMultMatrixf(B4mat.T)
	4929	for bond in Bonds:
	4930	glPushMatrix()
	4931	Dx = np.inner(Amat,bond)
	4932	Z = np.sqrt(np.sum(Dx**2))
	4933	if Z:
	4934	azm = atan2d(-Dx[1],-Dx[0])
	4935	phi = acosd(Dx[2]/Z)
	4936	glRotate(-azm,0,0,1)
	4937	glRotate(phi,1,0,0)
	4938	q = gluNewQuadric()
	4939	gluCylinder(q,radius,radius,Z,slice,2)
	4940	glPopMatrix()
	4941	glPopMatrix()
	4942
	4943	def RenderLines(x,y,z,Bonds,color):
[935]	4944	glShadeModel(GL_FLAT)
[762]	4945	xyz = np.array([x,y,z])
	4946	glEnable(GL_COLOR_MATERIAL)
	4947	glLineWidth(1)
	4948	glColor3fv(color)
	4949	glPushMatrix()
	4950	glBegin(GL_LINES)
	4951	for bond in Bonds:
	4952	glVertex3fv(xyz)
	4953	glVertex3fv(xyz+bond)
	4954	glEnd()
	4955	glColor4ubv([0,0,0,0])
	4956	glPopMatrix()
	4957	glDisable(GL_COLOR_MATERIAL)
[935]	4958	glShadeModel(GL_SMOOTH)
[762]	4959
	4960	def RenderPolyhedra(x,y,z,Faces,color):
[961]	4961	glShadeModel(GL_FLAT)
[762]	4962	glPushMatrix()
	4963	glTranslate(x,y,z)
	4964	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	4965	glShadeModel(GL_SMOOTH)
	4966	glMultMatrixf(B4mat.T)
	4967	for face,norm in Faces:
	4968	glPolygonMode(GL_FRONT_AND_BACK,GL_FILL)
	4969	glFrontFace(GL_CW)
	4970	glNormal3fv(norm)
	4971	glBegin(GL_TRIANGLES)
	4972	for vert in face:
	4973	glVertex3fv(vert)
	4974	glEnd()
	4975	glPopMatrix()
[961]	4976	glShadeModel(GL_SMOOTH)
[762]	4977
[766]	4978	def RenderMapPeak(x,y,z,color,den):
[935]	4979	glShadeModel(GL_FLAT)
[762]	4980	xyz = np.array([x,y,z])
	4981	glEnable(GL_COLOR_MATERIAL)
	4982	glLineWidth(3)
[766]	4983	glColor3fv(color*den/255)
[762]	4984	glPushMatrix()
	4985	glBegin(GL_LINES)
	4986	for vec in mapPeakVecs:
	4987	glVertex3fv(vec[0]+xyz)
	4988	glVertex3fv(vec[1]+xyz)
	4989	glEnd()
	4990	glColor4ubv([0,0,0,0])
	4991	glPopMatrix()
	4992	glDisable(GL_COLOR_MATERIAL)
[935]	4993	glShadeModel(GL_SMOOTH)
[762]	4994
	4995	def RenderBackbone(Backbone,BackboneColor,radius):
	4996	glPushMatrix()
	4997	glMultMatrixf(B4mat.T)
	4998	glEnable(GL_COLOR_MATERIAL)
	4999	glShadeModel(GL_SMOOTH)
	5000	gleSetJoinStyle(TUBE_NORM_EDGE \| TUBE_JN_ANGLE \| TUBE_JN_CAP)
	5001	glePolyCylinder(Backbone,BackboneColor,radius)
	5002	glPopMatrix()
	5003	glDisable(GL_COLOR_MATERIAL)
	5004
[987]	5005	def RenderLabel(x,y,z,label,r,color,matRot):
	5006	'''
[1378]	5007	color wx.Colour object
[987]	5008	'''
[762]	5009	glPushMatrix()
	5010	glTranslate(x,y,z)
	5011	glMultMatrixf(B4mat.T)
	5012	glDisable(GL_LIGHTING)
[935]	5013	glRasterPos3f(0,0,0)
[987]	5014	glMultMatrixf(matRot)
	5015	glRotate(180,1,0,0) #fix to flip about x-axis
	5016	text = gltext.Text(text=label,font=Font,foreground=color)
	5017	text.draw_text(scale=0.025)
[762]	5018	glEnable(GL_LIGHTING)
	5019	glPopMatrix()
	5020
	5021	def RenderMap(rho,rhoXYZ,indx,Rok):
[935]	5022	glShadeModel(GL_FLAT)
[762]	5023	cLevel = drawingData['contourLevel']
	5024	XYZ = []
	5025	RC = []
	5026	for i,xyz in enumerate(rhoXYZ):
	5027	if not Rok[i]:
	5028	x,y,z = xyz
	5029	I,J,K = indx[i]
	5030	alpha = 1.0
	5031	if cLevel < 1.:
	5032	alpha = (abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)
	5033	if rho[I,J,K] < 0.:
	5034	XYZ.append(xyz)
	5035	RC.append([0.1*alpha,Rd])
	5036	else:
	5037	XYZ.append(xyz)
	5038	RC.append([0.1*alpha,Gr])
	5039	RenderDots(XYZ,RC)
[935]	5040	glShadeModel(GL_SMOOTH)
[762]	5041
[1958]	5042	def Draw(caller='',Fade=None):
[762]	5043	#useful debug?
	5044	# if caller:
	5045	# print caller
	5046	# end of useful debug
	5047	mapData = generalData['Map']
	5048	pageName = ''
	5049	page = getSelection()
	5050	if page:
	5051	pageName = G2frame.dataDisplay.GetPageText(page)
	5052	rhoXYZ = []
	5053	if len(mapData['rho']):
	5054	VP = np.array(drawingData['viewPoint'][0])-np.array([.5,.5,.5])
	5055	contLevel = drawingData['contourLevel']*mapData['rhoMax']
[1951]	5056	if 'delt-F' in mapData['MapType'] or 'N' in mapData.get('Type',''):
[762]	5057	rho = ma.array(mapData['rho'],mask=(np.abs(mapData['rho'])<contLevel))
	5058	else:
	5059	rho = ma.array(mapData['rho'],mask=(mapData['rho']<contLevel))
	5060	steps = 1./np.array(rho.shape)
	5061	incre = np.where(VP>=0,VP%steps,VP%steps-steps)
	5062	Vsteps = -np.array(VP/steps,dtype='i')
	5063	rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2)
	5064	indx = np.array(ma.nonzero(rho)).T
	5065	rhoXYZ = indx*steps+VP-incre
	5066	Nc = len(rhoXYZ)
	5067	rcube = 2000.Vol/(ForthirdPINc)
	5068	rmax = math.exp(math.log(rcube)/3.)**2
	5069	radius = min(drawingData['mapSize']**2,rmax)
	5070	view = np.array(drawingData['viewPoint'][0])
	5071	Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius
	5072	Ind = GetSelectedAtoms()
	5073	VS = np.array(Page.canvas.GetSize())
	5074	aspect = float(VS[0])/float(VS[1])
	5075	cPos = drawingData['cameraPos']
	5076	Zclip = drawingData['Zclip']*cPos/200.
	5077	Q = drawingData['Quaternion']
	5078	Tx,Ty,Tz = drawingData['viewPoint'][0]
	5079	cx,ct,cs,ci = drawingData['atomPtrs']
	5080	bondR = drawingData['bondRadius']
	5081	G,g = G2lat.cell2Gmat(cell)
	5082	GS = G
	5083	GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1])
	5084	GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2])
	5085	GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2])
	5086	ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.)
	5087
	5088	SetBackground()
	5089	glInitNames()
	5090	glPushName(0)
	5091
	5092	glMatrixMode(GL_PROJECTION)
	5093	glLoadIdentity()
	5094	glViewport(0,0,VS[0],VS[1])
	5095	gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip)
	5096	gluLookAt(0,0,cPos,0,0,0,0,1,0)
	5097	SetLights()
	5098
	5099	glMatrixMode(GL_MODELVIEW)
	5100	glLoadIdentity()
	5101	matRot = G2mth.Q2Mat(Q)
	5102	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	5103	glMultMatrixf(matRot.T)
	5104	glMultMatrixf(A4mat.T)
	5105	glTranslate(-Tx,-Ty,-Tz)
	5106	if drawingData['unitCellBox']:
	5107	RenderBox()
	5108	if drawingData['showABC']:
	5109	x,y,z = drawingData['viewPoint'][0]
	5110	RenderUnitVectors(x,y,z)
	5111	Backbones = {}
	5112	BackboneColor = []
	5113	time0 = time.time()
	5114	# glEnable(GL_BLEND)
	5115	# glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA)
[1958]	5116	if Fade == None:
	5117	atmFade = np.ones(len(drawingData['Atoms']))
	5118	else:
	5119	atmFade = Fade
[762]	5120	for iat,atom in enumerate(drawingData['Atoms']):
	5121	x,y,z = atom[cx:cx+3]
	5122	Bonds = atom[-2]
	5123	Faces = atom[-1]
	5124	try:
	5125	atNum = generalData['AtomTypes'].index(atom[ct])
	5126	except ValueError:
	5127	atNum = -1
	5128	CL = atom[cs+2]
[1958]	5129	if not atmFade[iat]:
	5130	continue
	5131	atColor = atmFade[iat]*np.array(CL)/255.
[855]	5132	if drawingData['showRigidBodies'] and atom[ci] in rbAtmDict:
	5133	bndColor = Or
	5134	else:
	5135	bndColor = atColor
[762]	5136	if iat in Ind and G2frame.dataDisplay.GetPageText(getSelection()) != 'Map peaks':
[855]	5137	atColor = np.array(Gr)/255.
[762]	5138	# color += [.25,]
	5139	radius = 0.5
	5140	if atom[cs] != '':
	5141	try:
	5142	glLoadName(atom[-3])
	5143	except: #problem with old files - missing code
	5144	pass
	5145	if 'balls' in atom[cs]:
	5146	vdwScale = drawingData['vdwScale']
	5147	ballScale = drawingData['ballScale']
	5148	if atNum < 0:
	5149	radius = 0.2
	5150	elif 'H' == atom[ct]:
	5151	if drawingData['showHydrogen']:
	5152	if 'vdW' in atom[cs] and atNum >= 0:
	5153	radius = vdwScale*generalData['vdWRadii'][atNum]
	5154	else:
	5155	radius = ballScale*drawingData['sizeH']
	5156	else:
	5157	radius = 0.0
	5158	else:
	5159	if 'vdW' in atom[cs]:
	5160	radius = vdwScale*generalData['vdWRadii'][atNum]
	5161	else:
	5162	radius = ballScale*generalData['BondRadii'][atNum]
[855]	5163	RenderSphere(x,y,z,radius,atColor)
[762]	5164	if 'sticks' in atom[cs]:
[855]	5165	RenderBonds(x,y,z,Bonds,bondR,bndColor)
[762]	5166	elif 'ellipsoids' in atom[cs]:
[855]	5167	RenderBonds(x,y,z,Bonds,bondR,bndColor)
[762]	5168	if atom[cs+3] == 'A':
	5169	Uij = atom[cs+5:cs+11]
	5170	U = np.multiply(G2spc.Uij2U(Uij),GS)
	5171	U = np.inner(Amat,np.inner(U,Amat).T)
	5172	E,R = nl.eigh(U)
	5173	R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	5174	E = np.sqrt(E)
	5175	if atom[ct] == 'H' and not drawingData['showHydrogen']:
	5176	pass
	5177	else:
[855]	5178	RenderEllipsoid(x,y,z,ellipseProb,E,R4,atColor)
[762]	5179	else:
	5180	if atom[ct] == 'H' and not drawingData['showHydrogen']:
	5181	pass
	5182	else:
	5183	radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
[855]	5184	RenderSphere(x,y,z,radius,atColor)
[762]	5185	elif 'lines' in atom[cs]:
	5186	radius = 0.1
[855]	5187	RenderLines(x,y,z,Bonds,bndColor)
[762]	5188	# RenderBonds(x,y,z,Bonds,0.05,color,6)
	5189	elif atom[cs] == 'sticks':
	5190	radius = 0.1
[855]	5191	RenderBonds(x,y,z,Bonds,bondR,bndColor)
[762]	5192	elif atom[cs] == 'polyhedra':
[855]	5193	RenderPolyhedra(x,y,z,Faces,atColor)
[762]	5194	elif atom[cs] == 'backbone':
	5195	if atom[ct-1].split()[0] in ['C','N']:
	5196	if atom[2] not in Backbones:
	5197	Backbones[atom[2]] = []
	5198	Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
[855]	5199	BackboneColor.append(list(atColor))
[762]	5200
	5201	if atom[cs+1] == 'type':
[987]	5202	RenderLabel(x,y,z,' '+atom[ct],radius,wxGreen,matRot)
[762]	5203	elif atom[cs+1] == 'name':
[987]	5204	RenderLabel(x,y,z,' '+atom[ct-1],radius,wxGreen,matRot)
[762]	5205	elif atom[cs+1] == 'number':
[987]	5206	RenderLabel(x,y,z,' '+str(iat),radius,wxGreen,matRot)
[762]	5207	elif atom[cs+1] == 'residue' and atom[ct-1] == 'CA':
[987]	5208	RenderLabel(x,y,z,' '+atom[ct-4],radius,wxGreen,matRot)
[762]	5209	elif atom[cs+1] == '1-letter' and atom[ct-1] == 'CA':
[987]	5210	RenderLabel(x,y,z,' '+atom[ct-3],radius,wxGreen,matRot)
[762]	5211	elif atom[cs+1] == 'chain' and atom[ct-1] == 'CA':
[987]	5212	RenderLabel(x,y,z,' '+atom[ct-2],radius,wxGreen,matRot)
[762]	5213	# glDisable(GL_BLEND)
	5214	if len(rhoXYZ):
	5215	RenderMap(rho,rhoXYZ,indx,Rok)
	5216	if len(mapPeaks):
[839]	5217	XYZ = mapPeaks.T[1:4].T
	5218	mapBonds = FindPeaksBonds(XYZ)
[1669]	5219	for ind,[mag,x,y,z] in enumerate(mapPeaks[:,:4]):
[762]	5220	if ind in Ind and pageName == 'Map peaks':
[766]	5221	RenderMapPeak(x,y,z,Gr,1.0)
[762]	5222	else:
[1646]	5223	if mag > 0.:
	5224	RenderMapPeak(x,y,z,Wt,mag/peakMax)
	5225	else:
	5226	RenderMapPeak(x,y,z,Rd,-mag/peakMax)
[840]	5227	if showBonds:
	5228	RenderLines(x,y,z,mapBonds[ind],Wt)
[851]	5229	if len(testRBObj) and pageName == 'RB Models':
[885]	5230	XYZ = G2mth.UpdateRBXYZ(Bmat,testRBObj['rbObj'],testRBObj['rbData'],testRBObj['rbType'])[0]
[851]	5231	rbBonds = FindPeaksBonds(XYZ)
	5232	for ind,[x,y,z] in enumerate(XYZ):
	5233	aType = testRBObj['rbAtTypes'][ind]
[935]	5234	name = ' '+aType+str(ind)
[851]	5235	color = np.array(testRBObj['AtInfo'][aType][1])
	5236	RenderSphere(x,y,z,0.2,color/255.)
	5237	RenderBonds(x,y,z,rbBonds[ind],0.03,Gr)
[987]	5238	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
[934]	5239	if len(mcsaModels) > 1 and pageName == 'MC/SA': #skip the default MD entry
[951]	5240	for ind,[x,y,z] in enumerate(mcsaXYZ):
[953]	5241	aType = mcsaTypes[ind]
[935]	5242	name = ' '+aType+str(ind)
[934]	5243	color = np.array(MCSA['AtInfo'][aType][1])
	5244	RenderSphere(x,y,z,0.2,color/255.)
[951]	5245	RenderBonds(x,y,z,mcsaBonds[ind],0.03,Gr)
[987]	5246	RenderLabel(x,y,z,name,0.2,wxOrange,matRot)
[762]	5247	if Backbones:
	5248	for chain in Backbones:
	5249	Backbone = Backbones[chain]
	5250	RenderBackbone(Backbone,BackboneColor,bondR)
	5251	# print time.time()-time0
[1379]	5252	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
[762]	5253	Page.canvas.SwapBuffers()
[1379]	5254
[762]	5255	def OnSize(event):
	5256	Draw('size')
	5257
	5258	def OnFocus(event): #not needed?? Bind commented out below
	5259	Draw('focus')
	5260
[1383]	5261	# PlotStructure execution starts here (N.B. initialization above)
[762]	5262	try:
	5263	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
[1448]	5264	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
[762]	5265	except ValueError:
	5266	Plot = G2frame.G2plotNB.addOgl(generalData['Name'])
	5267	plotNum = G2frame.G2plotNB.plotList.index(generalData['Name'])
	5268	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	5269	Page.views = False
	5270	view = False
	5271	altDown = False
[1448]	5272	G2frame.G2plotNB.nb.SetSelection(plotNum) # make sure plot tab is raised for wx >2.8
[985]	5273	Font = Page.GetFont()
[762]	5274	Page.SetFocus()
[796]	5275	Page.Choice = None
[1439]	5276	if mapData.get('Flip',False):
[993]	5277	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2',
	5278	'u: roll up','d: roll down','l: roll left','r: roll right']
[762]	5279	else:
	5280	choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2','n: next','p: previous']
[1633]	5281	if generalData['Type'] in ['modulated','magnetic',] and len(drawAtoms):
	5282	choice += ['+: increase tau','-: decrease tau','0: set tau = 0']
	5283
[1928]	5284	Tx,Ty,Tz = drawingData['viewPoint'][0]
	5285	rho = G2mth.getRho([Tx,Ty,Tz],mapData)
	5286	G2frame.G2plotNB.status.SetStatusText('View point: %.4f, %.4f, %.4f; density: %.4f'%(Tx,Ty,Tz,rho),1)
	5287
[762]	5288	cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN\|wx.CB_READONLY,choices=choice)
	5289	cb.Bind(wx.EVT_COMBOBOX, OnKeyBox)
	5290	cb.SetValue(' save as/key:')
	5291	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
	5292	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
	5293	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
	5294	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
	5295	Page.canvas.Bind(wx.EVT_KEY_UP, OnKey)
[1951]	5296	Page.canvas.Bind(wx.EVT_KEY_DOWN,OnKeyPressed)
[762]	5297	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
	5298	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
	5299	# Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus)
	5300	Page.camera['position'] = drawingData['cameraPos']
	5301	Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0])
[1559]	5302	Page.camera['backColor'] = backColor/255.
[859]	5303	try:
	5304	Page.canvas.SetCurrent()
	5305	except:
	5306	pass
[762]	5307	Draw('main')
[1381]	5308	if firstCall: Draw('main') # draw twice the first time that graphics are displayed
	5309
[831]	5310	################################################################################
	5311	#### Plot Rigid Body
	5312	################################################################################
	5313
[835]	5314	def PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults):
[831]	5315	'''RB plotting package. Can show rigid body structures as balls & sticks
	5316	'''
	5317
[839]	5318	def FindBonds(XYZ):
[831]	5319	rbTypes = rbData['rbTypes']
	5320	Radii = []
	5321	for Atype in rbTypes:
	5322	Radii.append(AtInfo[Atype][0])
[854]	5323	if Atype == 'H':
	5324	Radii[-1] = 0.5
[831]	5325	Radii = np.array(Radii)
	5326	Bonds = [[] for i in range(len(Radii))]
	5327	for i,xyz in enumerate(XYZ):
	5328	Dx = XYZ-xyz
	5329	dist = np.sqrt(np.sum(Dx**2,axis=1))
	5330	sumR = Radii[i]+Radii
	5331	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
	5332	for j in IndB[0]:
	5333	Bonds[i].append(Dx[j]*Radii[i]/sumR[j])
	5334	Bonds[j].append(-Dx[j]*Radii[j]/sumR[j])
	5335	return Bonds
	5336
	5337	Wt = np.array([255,255,255])
	5338	Rd = np.array([255,0,0])
	5339	Gr = np.array([0,255,0])
	5340	Bl = np.array([0,0,255])
	5341	uBox = np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1]])
	5342	uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]])
	5343	uColors = [Rd,Gr,Bl]
	5344	if rbType == 'Vector':
[836]	5345	atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['rbTypes'])]
[831]	5346	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
	5347	for imag,mag in enumerate(rbData['VectMag']):
	5348	XYZ += mag*rbData['rbVect'][imag]
[835]	5349	Bonds = FindBonds(XYZ)
[831]	5350	elif rbType == 'Residue':
[934]	5351	# atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['atNames'])]
	5352	atNames = rbData['atNames']
[836]	5353	XYZ = np.copy(rbData['rbXYZ']) #don't mess with original!
	5354	Seq = rbData['rbSeq']
[840]	5355	for ia,ib,ang,mv in Seq:
	5356	va = XYZ[ia]-XYZ[ib]
	5357	Q = G2mth.AVdeg2Q(ang,va)
	5358	for im in mv:
	5359	vb = XYZ[im]-XYZ[ib]
	5360	vb = G2mth.prodQVQ(Q,vb)
	5361	XYZ[im] = XYZ[ib]+vb
[836]	5362	Bonds = FindBonds(XYZ)
[831]	5363	elif rbType == 'Z-matrix':
	5364	pass
	5365
[860]	5366	# def SetRBOrigin():
	5367	# page = getSelection()
	5368	# if page:
	5369	# if G2frame.dataDisplay.GetPageText(page) == 'Rigid bodies':
	5370	# G2frame.MapPeaksTable.SetData(mapPeaks)
	5371	# panel = G2frame.dataDisplay.GetPage(page).GetChildren()
	5372	# names = [child.GetName() for child in panel]
	5373	# panel[names.index('grid window')].Refresh()
	5374
[831]	5375	def OnMouseDown(event):
	5376	xy = event.GetPosition()
	5377	defaults['oldxy'] = list(xy)
	5378
	5379	def OnMouseMove(event):
	5380	newxy = event.GetPosition()
	5381
	5382	if event.Dragging():
	5383	if event.LeftIsDown():
	5384	SetRotation(newxy)
	5385	Q = defaults['Quaternion']
	5386	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
[860]	5387	# elif event.RightIsDown():
	5388	# SetRBOrigin(newxy)
[831]	5389	elif event.MiddleIsDown():
	5390	SetRotationZ(newxy)
	5391	Q = defaults['Quaternion']
	5392	G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1)
	5393	Draw('move')
	5394
	5395	def OnMouseWheel(event):
	5396	defaults['cameraPos'] += event.GetWheelRotation()/24
	5397	defaults['cameraPos'] = max(10,min(500,defaults['cameraPos']))
	5398	G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1)
	5399	Draw('wheel')
	5400
	5401	def SetBackground():
	5402	R,G,B,A = Page.camera['backColor']
	5403	glClearColor(R,G,B,A)
	5404	glClear(GL_COLOR_BUFFER_BIT \| GL_DEPTH_BUFFER_BIT)
	5405
	5406	def SetLights():
	5407	glEnable(GL_DEPTH_TEST)
[934]	5408	glShadeModel(GL_FLAT)
[831]	5409	glEnable(GL_LIGHTING)
	5410	glEnable(GL_LIGHT0)
	5411	glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0)
	5412	glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8])
	5413	glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1])
	5414
[860]	5415	# def SetRBOrigin(newxy):
	5416	##first get translation vector in screen coords.
	5417	# oldxy = defaults['oldxy']
	5418	# if not len(oldxy): oldxy = list(newxy)
	5419	# dxy = newxy-oldxy
	5420	# defaults['oldxy'] = list(newxy)
	5421	# V = np.array([dxy[0],-dxy[1],0.])/100.
	5422	# Q = defaults['Quaternion']
	5423	# V = G2mth.prodQVQ(G2mth.invQ(Q),V)
	5424	# rbData['rbXYZ'] += V
	5425	# PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults)
	5426	#
[831]	5427	def SetRotation(newxy):
	5428	#first get rotation vector in screen coords. & angle increment
	5429	oldxy = defaults['oldxy']
	5430	if not len(oldxy): oldxy = list(newxy)
	5431	dxy = newxy-oldxy
	5432	defaults['oldxy'] = list(newxy)
	5433	V = np.array([dxy[1],dxy[0],0.])
	5434	A = 0.25np.sqrt(dxy[0]2+dxy[1]*2)
	5435	# next transform vector back to xtal coordinates via inverse quaternion
	5436	# & make new quaternion
	5437	Q = defaults['Quaternion']
	5438	V = G2mth.prodQVQ(G2mth.invQ(Q),V)
	5439	DQ = G2mth.AVdeg2Q(A,V)
	5440	Q = G2mth.prodQQ(Q,DQ)
	5441	defaults['Quaternion'] = Q
	5442	# finally get new view vector - last row of rotation matrix
	5443	VD = G2mth.Q2Mat(Q)[2]
	5444	VD /= np.sqrt(np.sum(VD**2))
	5445	defaults['viewDir'] = VD
	5446
	5447	def SetRotationZ(newxy):
	5448	#first get rotation vector (= view vector) in screen coords. & angle increment
	5449	View = glGetIntegerv(GL_VIEWPORT)
	5450	cent = [View[2]/2,View[3]/2]
	5451	oldxy = defaults['oldxy']
	5452	if not len(oldxy): oldxy = list(newxy)
	5453	dxy = newxy-oldxy
	5454	defaults['oldxy'] = list(newxy)
	5455	V = defaults['viewDir']
	5456	A = [0,0]
	5457	A[0] = dxy[1]*.25
	5458	A[1] = dxy[0]*.25
	5459	if newxy[0] > cent[0]:
	5460	A[0] *= -1
	5461	if newxy[1] < cent[1]:
	5462	A[1] *= -1
	5463	# next transform vector back to xtal coordinates & make new quaternion
	5464	Q = defaults['Quaternion']
	5465	Qx = G2mth.AVdeg2Q(A[0],V)
	5466	Qy = G2mth.AVdeg2Q(A[1],V)
	5467	Q = G2mth.prodQQ(Q,Qx)
	5468	Q = G2mth.prodQQ(Q,Qy)
	5469	defaults['Quaternion'] = Q
	5470
	5471	def RenderUnitVectors(x,y,z):
	5472	xyz = np.array([x,y,z])
	5473	glEnable(GL_COLOR_MATERIAL)
	5474	glLineWidth(1)
	5475	glPushMatrix()
	5476	glTranslate(x,y,z)
	5477	glBegin(GL_LINES)
	5478	for line,color in zip(uEdges,uColors):
	5479	glColor3ubv(color)
	5480	glVertex3fv(-line[1])
	5481	glVertex3fv(line[1])
	5482	glEnd()
	5483	glPopMatrix()
	5484	glColor4ubv([0,0,0,0])
	5485	glDisable(GL_COLOR_MATERIAL)
	5486
	5487	def RenderSphere(x,y,z,radius,color):
	5488	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	5489	glPushMatrix()
	5490	glTranslate(x,y,z)
	5491	q = gluNewQuadric()
	5492	gluSphere(q,radius,20,10)
	5493	glPopMatrix()
	5494
	5495	def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
	5496	glMaterialfv(GL_FRONT_AND_BACK,GL_DIFFUSE,color)
	5497	glPushMatrix()
	5498	glTranslate(x,y,z)
	5499	for Dx in Bonds:
	5500	glPushMatrix()
	5501	Z = np.sqrt(np.sum(Dx**2))
	5502	if Z:
	5503	azm = atan2d(-Dx[1],-Dx[0])
	5504	phi = acosd(Dx[2]/Z)
	5505	glRotate(-azm,0,0,1)
	5506	glRotate(phi,1,0,0)
	5507	q = gluNewQuadric()
	5508	gluCylinder(q,radius,radius,Z,slice,2)
	5509	glPopMatrix()
	5510	glPopMatrix()
	5511
[987]	5512	def RenderLabel(x,y,z,label,matRot):
[831]	5513	glPushMatrix()
	5514	glTranslate(x,y,z)
	5515	glDisable(GL_LIGHTING)
[935]	5516	glRasterPos3f(0,0,0)
[987]	5517	glMultMatrixf(matRot)
	5518	glRotate(180,1,0,0) #fix to flip about x-axis
	5519	text = gltext.TextElement(text=label,font=Font,foreground=wx.WHITE)
	5520	text.draw_text(scale=0.025)
[831]	5521	glEnable(GL_LIGHTING)
	5522	glPopMatrix()
	5523
	5524	def Draw(caller=''):
	5525	#useful debug?
	5526	# if caller:
	5527	# print caller
	5528	# end of useful debug
	5529	cPos = defaults['cameraPos']
	5530	VS = np.array(Page.canvas.GetSize())
	5531	aspect = float(VS[0])/float(VS[1])
	5532	Zclip = 500.0
	5533	Q = defaults['Quaternion']
	5534	SetBackground()
	5535	glInitNames()
	5536	glPushName(0)
	5537
	5538	glMatrixMode(GL_PROJECTION)
	5539	glLoadIdentity()
	5540	glViewport(0,0,VS[0],VS[1])
[1054]	5541	gluPerspective(20.,aspect,1.,500.)
[831]	5542	gluLookAt(0,0,cPos,0,0,0,0,1,0)
	5543	SetLights()
	5544
	5545	glMatrixMode(GL_MODELVIEW)
	5546	glLoadIdentity()
	5547	matRot = G2mth.Q2Mat(Q)
	5548	matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
	5549	glMultMatrixf(matRot.T)
	5550	RenderUnitVectors(0.,0.,0.)
[934]	5551	radius = 0.2
[831]	5552	for iat,atom in enumerate(XYZ):
	5553	x,y,z = atom
[835]	5554	CL = AtInfo[rbData['rbTypes'][iat]][1]
[831]	5555	color = np.array(CL)/255.
	5556	RenderSphere(x,y,z,radius,color)
[934]	5557	RenderBonds(x,y,z,Bonds[iat],0.05,color)
[987]	5558	RenderLabel(x,y,z,' '+atNames[iat],matRot)
[1379]	5559	if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix
[831]	5560	Page.canvas.SwapBuffers()
	5561
	5562	def OnSize(event):
	5563	Draw('size')
	5564
	5565	try:
[837]	5566	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
[831]	5567	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	5568	except ValueError:
[837]	5569	Plot = G2frame.G2plotNB.addOgl('Rigid body')
	5570	plotNum = G2frame.G2plotNB.plotList.index('Rigid body')
[831]	5571	Page = G2frame.G2plotNB.nb.GetPage(plotNum)
	5572	Page.views = False
	5573	view = False
	5574	altDown = False
	5575	Page.SetFocus()
[985]	5576	Font = Page.GetFont()
[831]	5577	Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel)
	5578	Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown)
	5579	Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown)
	5580	Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown)
	5581	Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove)
	5582	Page.canvas.Bind(wx.EVT_SIZE, OnSize)
	5583	Page.camera['position'] = defaults['cameraPos']
	5584	Page.camera['backColor'] = np.array([0,0,0,0])
	5585	Page.canvas.SetCurrent()
	5586	Draw('main')

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