| 1 | # -*- coding: utf-8 -*- |
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| 2 | ''' |
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| 3 | *GSASIIplot: plotting routines* |
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| 4 | =============================== |
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| 5 | |
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| 6 | ''' |
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| 7 | ########### SVN repository information ################### |
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| 8 | # $Date: 2015-08-31 18:53:11 +0000 (Mon, 31 Aug 2015) $ |
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| 9 | # $Author: vondreele $ |
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| 10 | # $Revision: 1969 $ |
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| 11 | # $URL: trunk/GSASIIplot.py $ |
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| 12 | # $Id: GSASIIplot.py 1969 2015-08-31 18:53:11Z vondreele $ |
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| 13 | ########### SVN repository information ################### |
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| 14 | import math |
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| 15 | import time |
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| 16 | import copy |
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| 17 | import sys |
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| 18 | import os.path |
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| 19 | import numpy as np |
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| 20 | import numpy.ma as ma |
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| 21 | import numpy.linalg as nl |
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| 22 | import wx |
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| 23 | import wx.aui |
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| 24 | import wx.glcanvas |
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| 25 | import matplotlib as mpl |
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| 26 | import mpl_toolkits.mplot3d.axes3d as mp3d |
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| 27 | import GSASIIpath |
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| 28 | GSASIIpath.SetVersionNumber("$Revision: 1969 $") |
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| 29 | import GSASIIgrid as G2gd |
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| 30 | import GSASIIimage as G2img |
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| 31 | import GSASIIpwd as G2pwd |
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| 32 | import GSASIIIO as G2IO |
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| 33 | import GSASIIpwdGUI as G2pdG |
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| 34 | import GSASIIimgGUI as G2imG |
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| 35 | import GSASIIphsGUI as G2phG |
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| 36 | import GSASIIlattice as G2lat |
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| 37 | import GSASIIspc as G2spc |
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| 38 | import GSASIImath as G2mth |
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| 39 | import GSASIIctrls as G2G |
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| 40 | import pytexture as ptx |
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| 41 | from OpenGL.GL import * |
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| 42 | from OpenGL.GLU import * |
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| 43 | from OpenGL.GLE import * |
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| 44 | import gltext |
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| 45 | from matplotlib.backends.backend_wx import _load_bitmap |
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| 46 | from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas |
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| 47 | from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar |
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| 48 | |
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| 49 | # useful degree trig functions |
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| 50 | sind = lambda x: math.sin(x*math.pi/180.) |
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| 51 | cosd = lambda x: math.cos(x*math.pi/180.) |
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| 52 | tand = lambda x: math.tan(x*math.pi/180.) |
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| 53 | asind = lambda x: 180.*math.asin(x)/math.pi |
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| 54 | acosd = lambda x: 180.*math.acos(x)/math.pi |
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| 55 | atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi |
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| 56 | atand = lambda x: 180.*math.atan(x)/math.pi |
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| 57 | # numpy versions |
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| 58 | npsind = lambda x: np.sin(x*np.pi/180.) |
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| 59 | npcosd = lambda x: np.cos(x*np.pi/180.) |
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| 60 | nptand = lambda x: np.tan(x*np.pi/180.) |
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| 61 | npacosd = lambda x: 180.*np.arccos(x)/np.pi |
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| 62 | npasind = lambda x: 180.*np.arcsin(x)/np.pi |
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| 63 | npatand = lambda x: 180.*np.arctan(x)/np.pi |
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| 64 | npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi |
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| 65 | GkDelta = unichr(0x0394) |
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| 66 | |
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| 67 | class G2PlotMpl(wx.Panel): |
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| 68 | 'Creates a Matplotlib 2-D plot in the GSAS-II graphics window' |
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| 69 | def __init__(self,parent,id=-1,dpi=None,**kwargs): |
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| 70 | wx.Panel.__init__(self,parent,id=id,**kwargs) |
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| 71 | mpl.rcParams['legend.fontsize'] = 10 |
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| 72 | self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6)) |
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| 73 | self.canvas = Canvas(self,-1,self.figure) |
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| 74 | self.toolbar = GSASIItoolbar(self.canvas) |
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| 75 | |
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| 76 | self.toolbar.Realize() |
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| 77 | |
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| 78 | sizer=wx.BoxSizer(wx.VERTICAL) |
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| 79 | sizer.Add(self.canvas,1,wx.EXPAND) |
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| 80 | sizer.Add(self.toolbar,0,wx.LEFT|wx.EXPAND) |
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| 81 | self.SetSizer(sizer) |
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| 82 | |
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| 83 | class G2PlotOgl(wx.Panel): |
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| 84 | 'Creates an OpenGL plot in the GSAS-II graphics window' |
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| 85 | def __init__(self,parent,id=-1,dpi=None,**kwargs): |
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| 86 | self.figure = wx.Panel.__init__(self,parent,id=id,**kwargs) |
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| 87 | if 'win' in sys.platform: #Windows (& Mac) already double buffered |
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| 88 | self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs) |
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| 89 | else: #fix from Jim Hester for X systems |
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| 90 | attribs = (wx.glcanvas.WX_GL_DOUBLEBUFFER,) |
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| 91 | self.canvas = wx.glcanvas.GLCanvas(self,-1,attribList=attribs,**kwargs) |
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| 92 | # create GL context for wx > 2.8 |
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| 93 | i,j= wx.__version__.split('.')[0:2] |
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| 94 | if int(i)+int(j)/10. > 2.8: |
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| 95 | self.context = wx.glcanvas.GLContext(self.canvas) |
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| 96 | self.canvas.SetCurrent(self.context) |
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| 97 | else: |
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| 98 | self.context = None |
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| 99 | self.camera = {} |
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| 100 | sizer=wx.BoxSizer(wx.VERTICAL) |
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| 101 | sizer.Add(self.canvas,1,wx.EXPAND) |
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| 102 | self.SetSizer(sizer) |
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| 103 | |
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| 104 | class G2Plot3D(wx.Panel): |
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| 105 | 'Creates a 3D Matplotlib plot in the GSAS-II graphics window' |
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| 106 | def __init__(self,parent,id=-1,dpi=None,**kwargs): |
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| 107 | wx.Panel.__init__(self,parent,id=id,**kwargs) |
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| 108 | self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6)) |
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| 109 | self.canvas = Canvas(self,-1,self.figure) |
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| 110 | self.toolbar = GSASIItoolbar(self.canvas) |
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| 111 | |
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| 112 | self.toolbar.Realize() |
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| 113 | |
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| 114 | sizer=wx.BoxSizer(wx.VERTICAL) |
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| 115 | sizer.Add(self.canvas,1,wx.EXPAND) |
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| 116 | sizer.Add(self.toolbar,0,wx.LEFT|wx.EXPAND) |
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| 117 | self.SetSizer(sizer) |
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| 118 | |
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| 119 | class G2PlotNoteBook(wx.Panel): |
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| 120 | 'create a tabbed window for GSAS-II graphics' |
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| 121 | def __init__(self,parent,id=-1): |
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| 122 | wx.Panel.__init__(self,parent,id=id) |
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| 123 | #so one can't delete a plot page!! |
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| 124 | self.nb = wx.aui.AuiNotebook(self, \ |
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| 125 | style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB) |
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| 126 | sizer = wx.BoxSizer() |
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| 127 | sizer.Add(self.nb,1,wx.EXPAND) |
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| 128 | self.SetSizer(sizer) |
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| 129 | self.status = parent.CreateStatusBar() |
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| 130 | self.status.SetFieldsCount(2) |
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| 131 | self.status.SetStatusWidths([150,-1]) |
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| 132 | self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged) |
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| 133 | self.nb.Bind(wx.EVT_KEY_UP,self.OnNotebookKey) |
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| 134 | |
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| 135 | self.plotList = [] |
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| 136 | |
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| 137 | def OnNotebookKey(self,event): |
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| 138 | '''Called when a keystroke event gets picked up by the notebook window |
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| 139 | rather the child. This is not expected, but somehow it does sometimes |
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| 140 | on the Mac and perhaps Linux. |
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| 141 | |
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| 142 | Assume that the page associated with the currently displayed tab |
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| 143 | has a child, .canvas; give that child the focus and pass it the event. |
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| 144 | ''' |
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| 145 | try: |
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| 146 | Page = self.nb.GetPage(self.nb.GetSelection()) |
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| 147 | except ValueError: # occurs with no plot tabs |
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| 148 | return |
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| 149 | try: |
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| 150 | Page.canvas.SetFocus() |
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| 151 | wx.PostEvent(Page.canvas,event) |
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| 152 | except AttributeError: |
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| 153 | pass |
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| 154 | |
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| 155 | def addMpl(self,name=""): |
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| 156 | 'Add a tabbed page with a matplotlib plot' |
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| 157 | page = G2PlotMpl(self.nb) |
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| 158 | self.nb.AddPage(page,name) |
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| 159 | |
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| 160 | self.plotList.append(name) |
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| 161 | |
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| 162 | return page.figure |
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| 163 | |
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| 164 | def add3D(self,name=""): |
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| 165 | 'Add a tabbed page with a 3D plot' |
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| 166 | page = G2Plot3D(self.nb) |
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| 167 | self.nb.AddPage(page,name) |
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| 168 | |
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| 169 | self.plotList.append(name) |
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| 170 | |
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| 171 | return page.figure |
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| 172 | |
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| 173 | def addOgl(self,name=""): |
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| 174 | 'Add a tabbed page with an openGL plot' |
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| 175 | page = G2PlotOgl(self.nb) |
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| 176 | self.nb.AddPage(page,name) |
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| 177 | |
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| 178 | self.plotList.append(name) |
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| 179 | |
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| 180 | return page.figure |
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| 181 | |
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| 182 | def Delete(self,name): |
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| 183 | 'delete a tabbed page' |
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| 184 | try: |
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| 185 | item = self.plotList.index(name) |
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| 186 | del self.plotList[item] |
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| 187 | self.nb.DeletePage(item) |
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| 188 | except ValueError: #no plot of this name - do nothing |
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| 189 | return |
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| 190 | |
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| 191 | def clear(self): |
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| 192 | 'clear all pages from plot window' |
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| 193 | while self.nb.GetPageCount(): |
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| 194 | self.nb.DeletePage(0) |
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| 195 | self.plotList = [] |
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| 196 | self.status.DestroyChildren() |
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| 197 | |
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| 198 | def Rename(self,oldName,newName): |
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| 199 | 'rename a tab' |
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| 200 | try: |
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| 201 | item = self.plotList.index(oldName) |
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| 202 | self.plotList[item] = newName |
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| 203 | self.nb.SetPageText(item,newName) |
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| 204 | except ValueError: #no plot of this name - do nothing |
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| 205 | return |
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| 206 | |
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| 207 | def OnPageChanged(self,event): |
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| 208 | 'respond to someone pressing a tab on the plot window' |
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| 209 | if self.plotList: |
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| 210 | self.status.SetStatusText('Better to select this from GSAS-II data tree',1) |
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| 211 | self.status.DestroyChildren() #get rid of special stuff on status bar |
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| 212 | |
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| 213 | class GSASIItoolbar(Toolbar): |
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| 214 | 'Override the matplotlib toolbar so we can add more icons' |
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| 215 | ON_MPL_HELP = wx.NewId() |
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| 216 | ON_MPL_KEY = wx.NewId() |
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| 217 | arrows = {} |
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| 218 | for direc in ('left','right','up','down','Expand X', |
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| 219 | 'Shrink X','Expand Y','Shrink Y'): |
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| 220 | arrows[direc] = wx.NewId() |
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| 221 | def __init__(self,plotCanvas): |
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| 222 | '''Adds additional icons to toolbar''' |
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| 223 | Toolbar.__init__(self,plotCanvas) |
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| 224 | self.plotCanvas = plotCanvas |
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| 225 | POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6 # remove one button, nos. start at 1! |
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| 226 | self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN) #doesn't work in miniconda |
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| 227 | self.parent = self.GetParent() |
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| 228 | key = os.path.join(os.path.split(__file__)[0],'key.ico') |
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| 229 | self.AddSimpleTool(self.ON_MPL_KEY,_load_bitmap(key),'Key press','Select key press') |
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| 230 | wx.EVT_TOOL(self,self.ON_MPL_KEY,self.OnKey) |
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| 231 | help = os.path.join(os.path.split(__file__)[0],'help.ico') |
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| 232 | self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on') |
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| 233 | wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp) |
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| 234 | # add arrow keys to control zooming |
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| 235 | for direc in ('left','right','up','down'): |
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| 236 | wx.EVT_TOOL(self,self.arrows[direc],self.OnArrow) |
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| 237 | icon = os.path.join(os.path.split(__file__)[0],direc[0]+'arrow.ico') |
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| 238 | self.AddSimpleTool(self.arrows[direc],_load_bitmap(icon), |
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| 239 | 'Shift '+direc,'Shift plot '+direc) |
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| 240 | for direc in ('Expand X','Shrink X','Expand Y','Shrink Y'): |
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| 241 | fil = ''.join([i[0].lower() for i in direc.split()]+['arrow.ico']) |
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| 242 | wx.EVT_TOOL(self,self.arrows[direc],self.OnArrow) |
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| 243 | icon = os.path.join(os.path.split(__file__)[0],fil) |
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| 244 | self.AddSimpleTool(self.arrows[direc],_load_bitmap(icon), |
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| 245 | direc,'Zoom: '+direc) |
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| 246 | def OnArrow(self,event): |
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| 247 | 'reposition limits to scan or zoom by button press' |
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| 248 | ax = self.plotCanvas.figure.get_axes()[0] |
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| 249 | xmin,xmax,ymin,ymax = ax.axis() |
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| 250 | #print xmin,xmax,ymin,ymax |
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| 251 | if event.Id == self.arrows['right']: |
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| 252 | delta = (xmax-xmin)/10. |
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| 253 | xmin -= delta |
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| 254 | xmax -= delta |
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| 255 | elif event.Id == self.arrows['left']: |
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| 256 | delta = (xmax-xmin)/10. |
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| 257 | xmin += delta |
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| 258 | xmax += delta |
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| 259 | elif event.Id == self.arrows['up']: |
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| 260 | delta = (ymax-ymin)/10. |
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| 261 | ymin -= delta |
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| 262 | ymax -= delta |
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| 263 | elif event.Id == self.arrows['down']: |
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| 264 | delta = (ymax-ymin)/10. |
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| 265 | ymin += delta |
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| 266 | ymax += delta |
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| 267 | elif event.Id == self.arrows['Expand X']: |
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| 268 | delta = (xmax-xmin)/10. |
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| 269 | xmin += delta |
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| 270 | xmax -= delta |
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| 271 | elif event.Id == self.arrows['Expand Y']: |
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| 272 | delta = (ymax-ymin)/10. |
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| 273 | ymin += delta |
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| 274 | ymax -= delta |
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| 275 | elif event.Id == self.arrows['Shrink X']: |
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| 276 | delta = (xmax-xmin)/10. |
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| 277 | xmin -= delta |
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| 278 | xmax += delta |
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| 279 | elif event.Id == self.arrows['Shrink Y']: |
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| 280 | delta = (ymax-ymin)/10. |
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| 281 | ymin -= delta |
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| 282 | ymax += delta |
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| 283 | else: |
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| 284 | # should not happen! |
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| 285 | GSASIIpath.IPyBreak() |
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| 286 | self.parent.toolbar.push_current() |
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| 287 | ax.axis((xmin,xmax,ymin,ymax)) |
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| 288 | #print xmin,xmax,ymin,ymax |
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| 289 | self.plotCanvas.figure.canvas.draw() |
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| 290 | self.parent.toolbar.draw() |
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| 291 | # self.parent.toolbar.push_current() |
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| 292 | |
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| 293 | def OnHelp(self,event): |
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| 294 | 'Respond to press of help button on plot toolbar' |
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| 295 | Page = self.GetParent().GetParent() |
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| 296 | pageNo = Page.GetSelection() |
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| 297 | bookmark = Page.GetPageText(pageNo) |
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| 298 | bookmark = bookmark.strip(')').replace('(','_') |
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| 299 | G2G.ShowHelp(bookmark,self.TopLevelParent) |
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| 300 | def OnKey(self,event): |
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| 301 | '''Provide user with list of keystrokes defined for plot as well as an |
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| 302 | alternate way to access the same functionality |
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| 303 | ''' |
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| 304 | parent = self.GetParent() |
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| 305 | if parent.Choice: |
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| 306 | dlg = wx.SingleChoiceDialog(parent,'Select','Key press',list(parent.Choice)) |
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| 307 | if dlg.ShowModal() == wx.ID_OK: |
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| 308 | sel = dlg.GetSelection() |
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| 309 | event.key = parent.Choice[sel][0] |
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| 310 | parent.keyPress(event) |
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| 311 | dlg.Destroy() |
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| 312 | |
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| 313 | ################################################################################ |
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| 314 | ##### PlotSngl |
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| 315 | ################################################################################ |
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| 316 | |
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| 317 | def PlotSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=''): |
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| 318 | '''Structure factor plotting package - displays zone of reflections as rings proportional |
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| 319 | to F, F**2, etc. as requested |
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| 320 | ''' |
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| 321 | from matplotlib.patches import Circle,CirclePolygon |
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| 322 | global HKL,HKLF |
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| 323 | |
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| 324 | def OnSCKeyPress(event): |
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| 325 | i = zones.index(Data['Zone']) |
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| 326 | newPlot = False |
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| 327 | pwdrChoice = {'f':'Fo','s':'Fosq','u':'Unit Fc'} |
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| 328 | hklfChoice = {'1':'|DFsq|>sig','3':'|DFsq|>3sig','w':'|DFsq|/sig','f':'Fo','s':'Fosq','i':'Unit Fc'} |
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| 329 | if event.key == 'h': |
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| 330 | Data['Zone'] = '100' |
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| 331 | newPlot = True |
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| 332 | elif event.key == 'k': |
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| 333 | Data['Zone'] = '010' |
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| 334 | newPlot = True |
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| 335 | elif event.key == 'l': |
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| 336 | Data['Zone'] = '001' |
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| 337 | newPlot = True |
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| 338 | elif event.key == 'i': |
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| 339 | Data['Scale'] *= 1.1 |
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| 340 | elif event.key == 'd': |
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| 341 | Data['Scale'] /= 1.1 |
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| 342 | elif event.key in ['+','=']: |
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| 343 | Data['Layer'] = min(Data['Layer']+1,HKLmax[i]) |
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| 344 | elif event.key == '-': |
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| 345 | Data['Layer'] = max(Data['Layer']-1,HKLmin[i]) |
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| 346 | elif event.key == '0': |
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| 347 | Data['Layer'] = 0 |
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| 348 | Data['Scale'] = 1.0 |
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| 349 | elif event.key in hklfChoice and 'HKLF' in Name: |
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| 350 | Data['Type'] = hklfChoice[event.key] |
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| 351 | newPlot = True |
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| 352 | elif event.key in pwdrChoice and 'PWDR' in Name: |
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| 353 | Data['Type'] = pwdrChoice[event.key] |
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| 354 | newPlot = True |
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| 355 | PlotSngl(G2frame,newPlot,Data,hklRef,Title) |
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| 356 | |
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| 357 | def OnSCMotion(event): |
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| 358 | xpos = event.xdata |
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| 359 | if xpos: |
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| 360 | xpos = round(xpos) #avoid out of frame mouse position |
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| 361 | ypos = round(event.ydata) |
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| 362 | zpos = Data['Layer'] |
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| 363 | if '100' in Data['Zone']: |
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| 364 | HKLtxt = '(%3d,%3d,%3d)'%(zpos,xpos,ypos) |
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| 365 | elif '010' in Data['Zone']: |
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| 366 | HKLtxt = '(%3d,%3d,%3d)'%(xpos,zpos,ypos) |
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| 367 | elif '001' in Data['Zone']: |
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| 368 | HKLtxt = '(%3d,%3d,%3d)'%(xpos,ypos,zpos) |
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| 369 | Page.canvas.SetToolTipString(HKLtxt) |
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| 370 | G2frame.G2plotNB.status.SetStatusText('HKL = '+HKLtxt,0) |
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| 371 | G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1) |
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| 372 | |
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| 373 | def OnSCPress(event): |
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| 374 | zpos = Data['Layer'] |
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| 375 | xpos = event.xdata |
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| 376 | if xpos: |
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| 377 | pos = int(round(event.xdata)),int(round(event.ydata)) |
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| 378 | if '100' in Data['Zone']: |
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| 379 | Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(zpos,pos[0],pos[1])) |
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| 380 | hkl = np.array([zpos,pos[0],pos[1]]) |
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| 381 | elif '010' in Data['Zone']: |
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| 382 | Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],zpos,pos[1])) |
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| 383 | hkl = np.array([pos[0],zpos,pos[1]]) |
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| 384 | elif '001' in Data['Zone']: |
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| 385 | Page.canvas.SetToolTipString('(picked:(%3d,%3d,%3d))'%(pos[0],pos[1],zpos)) |
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| 386 | hkl = np.array([pos[0],pos[1],zpos]) |
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| 387 | h,k,l = hkl |
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| 388 | hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))] |
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| 389 | if len(hklf): |
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| 390 | Fosq,sig,Fcsq = hklf[0] |
|---|
| 391 | HKLtxt = '( %.2f %.3f %.2f %.2f)'%(Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig)) |
|---|
| 392 | G2frame.G2plotNB.status.SetStatusText('Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt,1) |
|---|
| 393 | |
|---|
| 394 | Name = G2frame.PatternTree.GetItemText(G2frame.PatternId) |
|---|
| 395 | if not Title: |
|---|
| 396 | Title = Name |
|---|
| 397 | try: |
|---|
| 398 | plotNum = G2frame.G2plotNB.plotList.index('Structure Factors') |
|---|
| 399 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 400 | if not newPlot: |
|---|
| 401 | Plot = Page.figure.gca() #get previous powder plot & get limits |
|---|
| 402 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 403 | Page.figure.clf() |
|---|
| 404 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 405 | except ValueError: |
|---|
| 406 | Plot = G2frame.G2plotNB.addMpl('Structure Factors').gca() |
|---|
| 407 | plotNum = G2frame.G2plotNB.plotList.index('Structure Factors') |
|---|
| 408 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 409 | Page.canvas.mpl_connect('button_press_event', OnSCPress) |
|---|
| 410 | Page.canvas.mpl_connect('motion_notify_event', OnSCMotion) |
|---|
| 411 | Page.canvas.mpl_connect('key_press_event', OnSCKeyPress) |
|---|
| 412 | Page.keyPress = OnSCKeyPress |
|---|
| 413 | Page.Choice = (' key press','i: increase scale','d: decrease scale', |
|---|
| 414 | 'h: select 100 zone','k: select 010 zone','l: select 001 zone', |
|---|
| 415 | 'f: select Fo','s: select Fosq','u: select unit Fc', |
|---|
| 416 | '+: increase index','-: decrease index','0: zero layer',) |
|---|
| 417 | if 'HKLF' in Name: |
|---|
| 418 | Page.Choice += ('w: select |DFsq|/sig','1: select |DFsq|>sig','3: select |DFsq|>3sig',) |
|---|
| 419 | Page.SetFocus() |
|---|
| 420 | |
|---|
| 421 | G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1) |
|---|
| 422 | Plot.set_aspect(aspect='equal') |
|---|
| 423 | |
|---|
| 424 | Type = Data['Type'] |
|---|
| 425 | scale = Data['Scale'] |
|---|
| 426 | HKLmax = Data['HKLmax'] |
|---|
| 427 | HKLmin = Data['HKLmin'] |
|---|
| 428 | FosqMax = Data['FoMax'] |
|---|
| 429 | Super = Data['Super'] |
|---|
| 430 | SuperVec = [] |
|---|
| 431 | if Super: |
|---|
| 432 | SuperVec = np.array(Data['SuperVec'][0]) |
|---|
| 433 | FoMax = math.sqrt(FosqMax) |
|---|
| 434 | xlabel = ['k, h=','h, k=','h, l='] |
|---|
| 435 | ylabel = ['l','l','k'] |
|---|
| 436 | zones = ['100','010','001'] |
|---|
| 437 | pzone = [[1,2],[0,2],[0,1]] |
|---|
| 438 | izone = zones.index(Data['Zone']) |
|---|
| 439 | Plot.set_title(Data['Type']+' for '+Title) |
|---|
| 440 | HKL = [] |
|---|
| 441 | HKLF = [] |
|---|
| 442 | time0 = time.time() |
|---|
| 443 | for refl in hklRef: |
|---|
| 444 | H = refl[:3] |
|---|
| 445 | if 'HKLF' in Name: |
|---|
| 446 | Fosq,sig,Fcsq = refl[5+Super:8+Super] |
|---|
| 447 | else: |
|---|
| 448 | Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super] |
|---|
| 449 | if Super: |
|---|
| 450 | HKL.append(H+SuperVec*refl[3]) |
|---|
| 451 | else: |
|---|
| 452 | HKL.append(H) |
|---|
| 453 | HKLF.append([Fosq,sig,Fcsq]) |
|---|
| 454 | if H[izone] == Data['Layer']: |
|---|
| 455 | A = 0 |
|---|
| 456 | B = 0 |
|---|
| 457 | if Type == 'Fosq': |
|---|
| 458 | A = scale*Fosq/FosqMax |
|---|
| 459 | B = scale*Fcsq/FosqMax |
|---|
| 460 | C = abs(A-B) |
|---|
| 461 | elif Type == 'Fo': |
|---|
| 462 | A = scale*math.sqrt(max(0,Fosq))/FoMax |
|---|
| 463 | B = scale*math.sqrt(max(0,Fcsq))/FoMax |
|---|
| 464 | C = abs(A-B) |
|---|
| 465 | elif Type == 'Unit Fc': |
|---|
| 466 | A = scale/2 |
|---|
| 467 | B = scale/2 |
|---|
| 468 | C = 0.0 |
|---|
| 469 | if Fcsq and Fosq > 0: |
|---|
| 470 | A *= min(1.0,Fosq/Fcsq) |
|---|
| 471 | C = abs(A-B) |
|---|
| 472 | elif Type == '|DFsq|/sig': |
|---|
| 473 | if sig > 0.: |
|---|
| 474 | A = (Fosq-Fcsq)/(3*sig) |
|---|
| 475 | B = 0 |
|---|
| 476 | elif Type == '|DFsq|>sig': |
|---|
| 477 | if sig > 0.: |
|---|
| 478 | A = (Fosq-Fcsq)/(3*sig) |
|---|
| 479 | if abs(A) < 1.0: A = 0 |
|---|
| 480 | B = 0 |
|---|
| 481 | elif Type == '|DFsq|>3sig': |
|---|
| 482 | if sig > 0.: |
|---|
| 483 | A = (Fosq-Fcsq)/(3*sig) |
|---|
| 484 | if abs(A) < 3.0: A = 0 |
|---|
| 485 | B = 0 |
|---|
| 486 | if Super: |
|---|
| 487 | h = H+SuperVec*refl[3] |
|---|
| 488 | else: |
|---|
| 489 | h = H |
|---|
| 490 | xy = (h[pzone[izone][0]],h[pzone[izone][1]]) |
|---|
| 491 | if Type in ['|DFsq|/sig','|DFsq|>sig','|DFsq|>3sig']: |
|---|
| 492 | if A > 0.0: |
|---|
| 493 | Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w')) |
|---|
| 494 | else: |
|---|
| 495 | Plot.add_artist(Circle(xy,radius=-A,ec='r',fc='w')) |
|---|
| 496 | else: |
|---|
| 497 | if A > 0.0 and A > B: |
|---|
| 498 | Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w')) |
|---|
| 499 | if B: |
|---|
| 500 | Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w')) |
|---|
| 501 | if A < B: |
|---|
| 502 | Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w')) |
|---|
| 503 | radius = C |
|---|
| 504 | if radius > 0: |
|---|
| 505 | if A > B: |
|---|
| 506 | Plot.add_artist(Circle(xy,radius=radius,ec='g',fc='g')) |
|---|
| 507 | else: |
|---|
| 508 | Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r')) |
|---|
| 509 | # print 'plot time: %.3f'%(time.time()-time0) |
|---|
| 510 | HKL = np.array(HKL) |
|---|
| 511 | HKLF = np.array(HKLF) |
|---|
| 512 | Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12) |
|---|
| 513 | Plot.set_ylabel(ylabel[izone],fontsize=12) |
|---|
| 514 | if not newPlot: |
|---|
| 515 | Page.toolbar.push_current() |
|---|
| 516 | Plot.set_xlim(xylim[0]) |
|---|
| 517 | Plot.set_ylim(xylim[1]) |
|---|
| 518 | # xylim = [] |
|---|
| 519 | Page.toolbar.push_current() |
|---|
| 520 | Page.toolbar.draw() |
|---|
| 521 | else: |
|---|
| 522 | Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]])) |
|---|
| 523 | Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]])) |
|---|
| 524 | Page.canvas.draw() |
|---|
| 525 | |
|---|
| 526 | ################################################################################ |
|---|
| 527 | ##### Plot3DSngl |
|---|
| 528 | ################################################################################ |
|---|
| 529 | |
|---|
| 530 | def Plot3DSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=False): |
|---|
| 531 | '''3D Structure factor plotting package - displays reflections as rings proportional |
|---|
| 532 | to F, F**2, etc. as requested as 3D array |
|---|
| 533 | ''' |
|---|
| 534 | |
|---|
| 535 | global ifBox |
|---|
| 536 | ifBox = False |
|---|
| 537 | def OnKeyBox(event): |
|---|
| 538 | mode = cb.GetValue() |
|---|
| 539 | if mode in ['jpeg','bmp','tiff',]: |
|---|
| 540 | try: |
|---|
| 541 | import Image as Im |
|---|
| 542 | except ImportError: |
|---|
| 543 | try: |
|---|
| 544 | from PIL import Image as Im |
|---|
| 545 | except ImportError: |
|---|
| 546 | print "PIL/pillow Image module not present. Cannot save images without this" |
|---|
| 547 | raise Exception("PIL/pillow Image module not found") |
|---|
| 548 | try: |
|---|
| 549 | Fname = os.path.join(Mydir,generalData['Name']+'.'+mode) |
|---|
| 550 | except NameError: #for when generalData doesn't exist! |
|---|
| 551 | Fname = os.path.join(Mydir,'unknown'+'.'+mode) |
|---|
| 552 | print Fname+' saved' |
|---|
| 553 | size = Page.canvas.GetSize() |
|---|
| 554 | glPixelStorei(GL_UNPACK_ALIGNMENT, 1) |
|---|
| 555 | if mode in ['jpeg',]: |
|---|
| 556 | Pix = glReadPixels(0,0,size[0],size[1],GL_RGBA, GL_UNSIGNED_BYTE) |
|---|
| 557 | im = Im.new("RGBA", (size[0],size[1])) |
|---|
| 558 | else: |
|---|
| 559 | Pix = glReadPixels(0,0,size[0],size[1],GL_RGB, GL_UNSIGNED_BYTE) |
|---|
| 560 | im = Im.new("RGB", (size[0],size[1])) |
|---|
| 561 | im.fromstring(Pix) |
|---|
| 562 | im.save(Fname,mode) |
|---|
| 563 | cb.SetValue(' save as/key:') |
|---|
| 564 | G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1) |
|---|
| 565 | else: |
|---|
| 566 | event.key = cb.GetValue()[0] |
|---|
| 567 | cb.SetValue(' save as/key:') |
|---|
| 568 | wx.CallAfter(OnKey,event) |
|---|
| 569 | Page.canvas.SetFocus() # redirect the Focus from the button back to the plot |
|---|
| 570 | |
|---|
| 571 | def OnKey(event): #on key UP!! |
|---|
| 572 | global ifBox |
|---|
| 573 | Choice = {'F':'Fo','S':'Fosq','U':'Unit','D':'dFsq','W':'dFsq/sig'} |
|---|
| 574 | 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]]} |
|---|
| 575 | try: |
|---|
| 576 | keyCode = event.GetKeyCode() |
|---|
| 577 | if keyCode > 255: |
|---|
| 578 | keyCode = 0 |
|---|
| 579 | key = chr(keyCode) |
|---|
| 580 | except AttributeError: #if from OnKeyBox above |
|---|
| 581 | key = str(event.key).upper() |
|---|
| 582 | if key in ['C','H','K','L']: |
|---|
| 583 | if key == 'C': |
|---|
| 584 | Data['Zone'] = False |
|---|
| 585 | key = 'L' |
|---|
| 586 | Data['viewKey'] = key |
|---|
| 587 | drawingData['viewPoint'][0] = drawingData['default'] |
|---|
| 588 | drawingData['viewDir'] = np.array(viewChoice[key][0]) |
|---|
| 589 | drawingData['viewUp'] = np.array(viewChoice[key][1]) |
|---|
| 590 | drawingData['oldxy'] = [] |
|---|
| 591 | if Data['Zone']: |
|---|
| 592 | if key == 'L': |
|---|
| 593 | Q = [-1,0,0,0] |
|---|
| 594 | else: |
|---|
| 595 | V0 = np.array(viewChoice[key][0]) |
|---|
| 596 | V1 = np.array(viewChoice[key][1]) |
|---|
| 597 | V0 = np.inner(Amat,V0) |
|---|
| 598 | V1 = np.inner(Amat,V1) |
|---|
| 599 | V0 /= nl.norm(V0) |
|---|
| 600 | V1 /= nl.norm(V1) |
|---|
| 601 | A = np.arccos(np.sum(V1*V0)) |
|---|
| 602 | Q = G2mth.AV2Q(-A,viewChoice[key][2]) |
|---|
| 603 | else: |
|---|
| 604 | V0 = np.array(viewChoice[key][0]) |
|---|
| 605 | V = np.inner(Bmat,V0) |
|---|
| 606 | V /= np.sqrt(np.sum(V**2)) |
|---|
| 607 | V *= np.array([0,0,1]) |
|---|
| 608 | A = np.arccos(np.sum(V*V0)) |
|---|
| 609 | Q = G2mth.AV2Q(-A,viewChoice[key][2]) |
|---|
| 610 | drawingData['Quaternion'] = Q |
|---|
| 611 | elif key in 'Z': |
|---|
| 612 | Data['Zone'] = not Data['Zone'] |
|---|
| 613 | elif key in 'B': |
|---|
| 614 | ifBox = not ifBox |
|---|
| 615 | elif key in ['+','=']: |
|---|
| 616 | Data['Scale'] *= 1.25 |
|---|
| 617 | elif key == '-': |
|---|
| 618 | Data['Scale'] /= 1.25 |
|---|
| 619 | elif key == 'P': |
|---|
| 620 | vec = viewChoice[Data['viewKey']][0] |
|---|
| 621 | drawingData['viewPoint'][0] -= vec |
|---|
| 622 | elif key == 'N': |
|---|
| 623 | vec = viewChoice[Data['viewKey']][0] |
|---|
| 624 | drawingData['viewPoint'][0] += vec |
|---|
| 625 | elif key == '0': |
|---|
| 626 | drawingData['viewPoint'][0] = [0,0,0] |
|---|
| 627 | Data['Scale'] = 1.0 |
|---|
| 628 | elif key == 'I': |
|---|
| 629 | Data['Iscale'] = not Data['Iscale'] |
|---|
| 630 | elif key in Choice: |
|---|
| 631 | Data['Type'] = Choice[key] |
|---|
| 632 | Draw('key') |
|---|
| 633 | |
|---|
| 634 | Name = G2frame.PatternTree.GetItemText(G2frame.PatternId) |
|---|
| 635 | if Title and Title in G2frame.GetPhaseData(): #NB: save image as e.g. jpeg will fail if False; MyDir is unknown |
|---|
| 636 | generalData = G2frame.GetPhaseData()[Title]['General'] |
|---|
| 637 | cell = generalData['Cell'][1:7] |
|---|
| 638 | Mydir = generalData['Mydir'] |
|---|
| 639 | else: |
|---|
| 640 | Title = 'Unknown' |
|---|
| 641 | cell = [10,10,10,90,90,90] |
|---|
| 642 | Mydir = G2frame.dirname |
|---|
| 643 | drawingData = Data['Drawing'] |
|---|
| 644 | Super = Data['Super'] |
|---|
| 645 | SuperVec = [] |
|---|
| 646 | if Super: |
|---|
| 647 | SuperVec = np.array(Data['SuperVec'][0]) |
|---|
| 648 | defaultViewPt = copy.copy(drawingData['viewPoint']) |
|---|
| 649 | Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse |
|---|
| 650 | Gmat,gmat = G2lat.cell2Gmat(cell) |
|---|
| 651 | invcell = G2lat.Gmat2cell(Gmat) |
|---|
| 652 | A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) |
|---|
| 653 | B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) |
|---|
| 654 | drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Bmat,[0,0,1])) |
|---|
| 655 | Wt = np.array([255,255,255]) |
|---|
| 656 | Rd = np.array([255,0,0]) |
|---|
| 657 | Gr = np.array([0,255,0]) |
|---|
| 658 | wxGreen = wx.Colour(0,255,0) |
|---|
| 659 | Bl = np.array([0,0,255]) |
|---|
| 660 | Or = np.array([255,128,0]) |
|---|
| 661 | wxOrange = wx.Colour(255,128,0) |
|---|
| 662 | 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]]) |
|---|
| 663 | uEdges = np.array([ |
|---|
| 664 | [uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]], |
|---|
| 665 | [uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]], |
|---|
| 666 | [uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]]) |
|---|
| 667 | uColors = [Rd,Gr,Bl, Wt,Wt,Wt, Wt,Wt,Wt, Wt,Wt,Wt] |
|---|
| 668 | def FillHKLRC(): |
|---|
| 669 | R = np.zeros(len(hklRef)) |
|---|
| 670 | C = [] |
|---|
| 671 | HKL = [] |
|---|
| 672 | RC = [] |
|---|
| 673 | for i,refl in enumerate(hklRef): |
|---|
| 674 | H = refl[:3] |
|---|
| 675 | if 'HKLF' in Name: |
|---|
| 676 | Fosq,sig,Fcsq = refl[5+Super:8+Super] |
|---|
| 677 | if refl[3+Super] < 0: |
|---|
| 678 | Fosq,sig,Fcsq = [0,1,0] |
|---|
| 679 | else: |
|---|
| 680 | Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super] |
|---|
| 681 | if Super: |
|---|
| 682 | HKL.append(H+SuperVec*refl[3]) |
|---|
| 683 | else: |
|---|
| 684 | HKL.append(H) |
|---|
| 685 | if Data['Type'] == 'Unit': |
|---|
| 686 | R[i] = 0.1 |
|---|
| 687 | C.append(Gr) |
|---|
| 688 | elif Data['Type'] == 'Fosq': |
|---|
| 689 | if Fosq > 0: |
|---|
| 690 | R[i] = Fosq |
|---|
| 691 | C.append(Gr) |
|---|
| 692 | else: |
|---|
| 693 | R[i] = -Fosq |
|---|
| 694 | C.append(Rd) |
|---|
| 695 | elif Data['Type'] == 'Fo': |
|---|
| 696 | if Fosq > 0: |
|---|
| 697 | R[i] = np.sqrt(Fosq) |
|---|
| 698 | C.append(Gr) |
|---|
| 699 | else: |
|---|
| 700 | R[i] = np.sqrt(-Fosq) |
|---|
| 701 | C.append(Rd) |
|---|
| 702 | elif Data['Type'] == 'dFsq/sig': |
|---|
| 703 | dFsig = (Fosq-Fcsq)/sig |
|---|
| 704 | if dFsig > 0: |
|---|
| 705 | R[i] = dFsig |
|---|
| 706 | C.append(Gr) |
|---|
| 707 | else: |
|---|
| 708 | R[i] = -dFsig |
|---|
| 709 | C.append(Rd) |
|---|
| 710 | elif Data['Type'] == 'dFsq': |
|---|
| 711 | dF = Fosq-Fcsq |
|---|
| 712 | if dF > 0: |
|---|
| 713 | R[i] = dF |
|---|
| 714 | C.append(Gr) |
|---|
| 715 | else: |
|---|
| 716 | R[i] = -dF |
|---|
| 717 | C.append(Rd) |
|---|
| 718 | R /= np.max(R) |
|---|
| 719 | R *= Data['Scale'] |
|---|
| 720 | R = np.where(R<1.e-5,1.e-5,R) |
|---|
| 721 | if Data['Iscale']: |
|---|
| 722 | R = np.where(R<=1.,R,1.) |
|---|
| 723 | C = np.array(C) |
|---|
| 724 | C = (C.T*R).T |
|---|
| 725 | R = np.ones_like(R)*0.05 |
|---|
| 726 | return HKL,zip(list(R),C) |
|---|
| 727 | |
|---|
| 728 | def GetTruePosition(xy): |
|---|
| 729 | View = glGetIntegerv(GL_VIEWPORT) |
|---|
| 730 | Proj = glGetDoublev(GL_PROJECTION_MATRIX) |
|---|
| 731 | Model = glGetDoublev(GL_MODELVIEW_MATRIX) |
|---|
| 732 | Zmax = 1. |
|---|
| 733 | xy = [int(xy[0]),int(View[3]-xy[1])] |
|---|
| 734 | for i,ref in enumerate(hklRef): |
|---|
| 735 | h,k,l = ref[:3] |
|---|
| 736 | X,Y,Z = gluProject(h,k,l,Model,Proj,View) |
|---|
| 737 | XY = [int(X),int(Y)] |
|---|
| 738 | if np.allclose(xy,XY,atol=10) and Z < Zmax: |
|---|
| 739 | Zmax = Z |
|---|
| 740 | return [int(h),int(k),int(l)] |
|---|
| 741 | |
|---|
| 742 | def SetTranslation(newxy): |
|---|
| 743 | #first get translation vector in screen coords. |
|---|
| 744 | oldxy = drawingData['oldxy'] |
|---|
| 745 | if not len(oldxy): oldxy = list(newxy) |
|---|
| 746 | dxy = newxy-oldxy |
|---|
| 747 | drawingData['oldxy'] = list(newxy) |
|---|
| 748 | V = np.array([-dxy[0],dxy[1],0.]) |
|---|
| 749 | #then transform to rotated crystal coordinates & apply to view point |
|---|
| 750 | Q = drawingData['Quaternion'] |
|---|
| 751 | V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V)) |
|---|
| 752 | Tx,Ty,Tz = drawingData['viewPoint'][0] |
|---|
| 753 | Tx += V[0]*0.1 |
|---|
| 754 | Ty += V[1]*0.1 |
|---|
| 755 | Tz += V[2]*0.1 |
|---|
| 756 | drawingData['viewPoint'][0] = Tx,Ty,Tz |
|---|
| 757 | |
|---|
| 758 | def SetRotation(newxy): |
|---|
| 759 | 'Perform a rotation in x-y space due to a left-mouse drag' |
|---|
| 760 | #first get rotation vector in screen coords. & angle increment |
|---|
| 761 | oldxy = drawingData['oldxy'] |
|---|
| 762 | if not len(oldxy): oldxy = list(newxy) |
|---|
| 763 | dxy = newxy-oldxy |
|---|
| 764 | drawingData['oldxy'] = list(newxy) |
|---|
| 765 | V = np.array([dxy[1],dxy[0],0.]) |
|---|
| 766 | A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) |
|---|
| 767 | if not A: return # nothing changed, nothing to do |
|---|
| 768 | # next transform vector back to xtal coordinates via inverse quaternion |
|---|
| 769 | # & make new quaternion |
|---|
| 770 | Q = drawingData['Quaternion'] |
|---|
| 771 | V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V)) |
|---|
| 772 | DQ = G2mth.AVdeg2Q(A,V) |
|---|
| 773 | Q = G2mth.prodQQ(Q,DQ) |
|---|
| 774 | drawingData['Quaternion'] = Q |
|---|
| 775 | # finally get new view vector - last row of rotation matrix |
|---|
| 776 | VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2]) |
|---|
| 777 | VD /= np.sqrt(np.sum(VD**2)) |
|---|
| 778 | drawingData['viewDir'] = VD |
|---|
| 779 | |
|---|
| 780 | def SetRotationZ(newxy): |
|---|
| 781 | #first get rotation vector (= view vector) in screen coords. & angle increment |
|---|
| 782 | View = glGetIntegerv(GL_VIEWPORT) |
|---|
| 783 | cent = [View[2]/2,View[3]/2] |
|---|
| 784 | oldxy = drawingData['oldxy'] |
|---|
| 785 | if not len(oldxy): oldxy = list(newxy) |
|---|
| 786 | dxy = newxy-oldxy |
|---|
| 787 | drawingData['oldxy'] = list(newxy) |
|---|
| 788 | V = drawingData['viewDir'] |
|---|
| 789 | A = [0,0] |
|---|
| 790 | A[0] = dxy[1]*.25 |
|---|
| 791 | A[1] = dxy[0]*.25 |
|---|
| 792 | if newxy[0] > cent[0]: |
|---|
| 793 | A[0] *= -1 |
|---|
| 794 | if newxy[1] < cent[1]: |
|---|
| 795 | A[1] *= -1 |
|---|
| 796 | # next transform vector back to xtal coordinates & make new quaternion |
|---|
| 797 | Q = drawingData['Quaternion'] |
|---|
| 798 | V = np.inner(Amat,V) |
|---|
| 799 | Qx = G2mth.AVdeg2Q(A[0],V) |
|---|
| 800 | Qy = G2mth.AVdeg2Q(A[1],V) |
|---|
| 801 | Q = G2mth.prodQQ(Q,Qx) |
|---|
| 802 | Q = G2mth.prodQQ(Q,Qy) |
|---|
| 803 | drawingData['Quaternion'] = Q |
|---|
| 804 | |
|---|
| 805 | def OnMouseDown(event): |
|---|
| 806 | xy = event.GetPosition() |
|---|
| 807 | drawingData['oldxy'] = list(xy) |
|---|
| 808 | |
|---|
| 809 | def OnMouseMove(event): |
|---|
| 810 | if event.ShiftDown(): #don't want any inadvertant moves when picking |
|---|
| 811 | return |
|---|
| 812 | newxy = event.GetPosition() |
|---|
| 813 | |
|---|
| 814 | if event.Dragging(): |
|---|
| 815 | if event.LeftIsDown(): |
|---|
| 816 | SetRotation(newxy) |
|---|
| 817 | Q = drawingData['Quaternion'] |
|---|
| 818 | elif event.RightIsDown(): |
|---|
| 819 | SetTranslation(newxy) |
|---|
| 820 | Tx,Ty,Tz = drawingData['viewPoint'][0] |
|---|
| 821 | elif event.MiddleIsDown(): |
|---|
| 822 | SetRotationZ(newxy) |
|---|
| 823 | Q = drawingData['Quaternion'] |
|---|
| 824 | Draw('move') |
|---|
| 825 | else: |
|---|
| 826 | hkl = GetTruePosition(newxy) |
|---|
| 827 | if hkl: |
|---|
| 828 | h,k,l = hkl |
|---|
| 829 | Page.canvas.SetToolTipString('%d,%d,%d'%(h,k,l)) |
|---|
| 830 | G2frame.G2plotNB.status.SetStatusText('hkl = %d,%d,%d'%(h,k,l),1) |
|---|
| 831 | |
|---|
| 832 | def OnMouseWheel(event): |
|---|
| 833 | if event.ShiftDown(): |
|---|
| 834 | return |
|---|
| 835 | drawingData['cameraPos'] += event.GetWheelRotation()/120. |
|---|
| 836 | drawingData['cameraPos'] = max(0.1,min(20.00,drawingData['cameraPos'])) |
|---|
| 837 | Draw('wheel') |
|---|
| 838 | |
|---|
| 839 | def SetBackground(): |
|---|
| 840 | R,G,B,A = Page.camera['backColor'] |
|---|
| 841 | glClearColor(R,G,B,A) |
|---|
| 842 | glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT) |
|---|
| 843 | |
|---|
| 844 | def SetLights(): |
|---|
| 845 | glEnable(GL_DEPTH_TEST) |
|---|
| 846 | glShadeModel(GL_SMOOTH) |
|---|
| 847 | glEnable(GL_LIGHTING) |
|---|
| 848 | glEnable(GL_LIGHT0) |
|---|
| 849 | glLightModeli(GL_LIGHT_MODEL_TWO_SIDE,0) |
|---|
| 850 | glLightfv(GL_LIGHT0,GL_AMBIENT,[1,1,1,.8]) |
|---|
| 851 | glLightfv(GL_LIGHT0,GL_DIFFUSE,[1,1,1,1]) |
|---|
| 852 | |
|---|
| 853 | def RenderBox(x,y,z): |
|---|
| 854 | xyz = np.array([x,y,z]) |
|---|
| 855 | glEnable(GL_COLOR_MATERIAL) |
|---|
| 856 | glLineWidth(1) |
|---|
| 857 | glPushMatrix() |
|---|
| 858 | glTranslate(x,y,z) |
|---|
| 859 | glColor4ubv([0,0,0,0]) |
|---|
| 860 | glBegin(GL_LINES) |
|---|
| 861 | for line,color in zip(uEdges,uColors): |
|---|
| 862 | glColor3ubv(color) |
|---|
| 863 | glVertex3fv(line[0]) |
|---|
| 864 | glVertex3fv(line[1]) |
|---|
| 865 | glEnd() |
|---|
| 866 | glPopMatrix() |
|---|
| 867 | glColor4ubv([0,0,0,0]) |
|---|
| 868 | glDisable(GL_COLOR_MATERIAL) |
|---|
| 869 | |
|---|
| 870 | def RenderUnitVectors(x,y,z): |
|---|
| 871 | xyz = np.array([x,y,z]) |
|---|
| 872 | glEnable(GL_COLOR_MATERIAL) |
|---|
| 873 | glLineWidth(1) |
|---|
| 874 | glPushMatrix() |
|---|
| 875 | glTranslate(x,y,z) |
|---|
| 876 | glBegin(GL_LINES) |
|---|
| 877 | for line,color in zip(uEdges,uColors)[:3]: |
|---|
| 878 | glColor3ubv(color) |
|---|
| 879 | glVertex3fv([0,0,0]) |
|---|
| 880 | # glVertex3fv(-line[1]) |
|---|
| 881 | glVertex3fv(line[1]) |
|---|
| 882 | glEnd() |
|---|
| 883 | glPopMatrix() |
|---|
| 884 | glColor4ubv([0,0,0,0]) |
|---|
| 885 | glDisable(GL_COLOR_MATERIAL) |
|---|
| 886 | |
|---|
| 887 | def RenderDots(XYZ,RC): |
|---|
| 888 | glEnable(GL_COLOR_MATERIAL) |
|---|
| 889 | XYZ = np.array(XYZ) |
|---|
| 890 | glPushMatrix() |
|---|
| 891 | for xyz,rc in zip(XYZ,RC): |
|---|
| 892 | x,y,z = xyz |
|---|
| 893 | r,c = rc |
|---|
| 894 | glColor3ubv(c) |
|---|
| 895 | glPointSize(r*50) |
|---|
| 896 | glBegin(GL_POINTS) |
|---|
| 897 | glVertex3fv(xyz) |
|---|
| 898 | glEnd() |
|---|
| 899 | glPopMatrix() |
|---|
| 900 | glColor4ubv([0,0,0,0]) |
|---|
| 901 | glDisable(GL_COLOR_MATERIAL) |
|---|
| 902 | |
|---|
| 903 | def Draw(caller=''): |
|---|
| 904 | #useful debug? |
|---|
| 905 | # if caller: |
|---|
| 906 | # print caller |
|---|
| 907 | # end of useful debug |
|---|
| 908 | G2frame.G2plotNB.status.SetStatusText('Plot type = %s for %s'%(Data['Type'],Name),1) |
|---|
| 909 | VS = np.array(Page.canvas.GetSize()) |
|---|
| 910 | aspect = float(VS[0])/float(VS[1]) |
|---|
| 911 | cPos = drawingData['cameraPos'] |
|---|
| 912 | Zclip = drawingData['Zclip']*cPos/20. |
|---|
| 913 | if Data['Zone']: |
|---|
| 914 | Zclip = 0.1 |
|---|
| 915 | Q = drawingData['Quaternion'] |
|---|
| 916 | Tx,Ty,Tz = drawingData['viewPoint'][0] |
|---|
| 917 | G,g = G2lat.cell2Gmat(cell) |
|---|
| 918 | GS = G |
|---|
| 919 | GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1]) |
|---|
| 920 | GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2]) |
|---|
| 921 | GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2]) |
|---|
| 922 | |
|---|
| 923 | HKL,RC = FillHKLRC() |
|---|
| 924 | |
|---|
| 925 | SetBackground() |
|---|
| 926 | glInitNames() |
|---|
| 927 | glPushName(0) |
|---|
| 928 | |
|---|
| 929 | glMatrixMode(GL_PROJECTION) |
|---|
| 930 | glLoadIdentity() |
|---|
| 931 | glViewport(0,0,VS[0],VS[1]) |
|---|
| 932 | gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip) |
|---|
| 933 | gluLookAt(0,0,cPos,0,0,0,0,1,0) |
|---|
| 934 | SetLights() |
|---|
| 935 | |
|---|
| 936 | glMatrixMode(GL_MODELVIEW) |
|---|
| 937 | glLoadIdentity() |
|---|
| 938 | matRot = G2mth.Q2Mat(Q) |
|---|
| 939 | matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) |
|---|
| 940 | glMultMatrixf(matRot.T) |
|---|
| 941 | glMultMatrixf(B4mat.T) |
|---|
| 942 | glTranslate(-Tx,-Ty,-Tz) |
|---|
| 943 | x,y,z = drawingData['viewPoint'][0] |
|---|
| 944 | if ifBox: |
|---|
| 945 | RenderBox(x,y,z) |
|---|
| 946 | else: |
|---|
| 947 | RenderUnitVectors(x,y,z) |
|---|
| 948 | RenderUnitVectors(0,0,0) |
|---|
| 949 | RenderDots(HKL,RC) |
|---|
| 950 | time0 = time.time() |
|---|
| 951 | if Page.context: Page.canvas.SetCurrent(Page.context) # wx 2.9 fix |
|---|
| 952 | Page.canvas.SwapBuffers() |
|---|
| 953 | |
|---|
| 954 | # PlotStructure execution starts here (N.B. initialization above) |
|---|
| 955 | try: |
|---|
| 956 | plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors') |
|---|
| 957 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 958 | except ValueError: |
|---|
| 959 | Plot = G2frame.G2plotNB.addOgl('3D Structure Factors') |
|---|
| 960 | plotNum = G2frame.G2plotNB.plotList.index('3D Structure Factors') |
|---|
| 961 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 962 | Page.views = False |
|---|
| 963 | view = False |
|---|
| 964 | altDown = False |
|---|
| 965 | Font = Page.GetFont() |
|---|
| 966 | Page.SetFocus() |
|---|
| 967 | Page.Choice = None |
|---|
| 968 | choice = [' save as/key:','jpeg','tiff','bmp','h: view down h','k: view down k','l: view down l', |
|---|
| 969 | 'z: zero zone toggle','c: reset to default','b: toggle box ','+: increase scale','-: decrease scale', |
|---|
| 970 | 'f: Fobs','s: Fobs**2','u: unit','d: Fo-Fc','w: DF/sig','i: toggle intensity scaling'] |
|---|
| 971 | cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice) |
|---|
| 972 | cb.Bind(wx.EVT_COMBOBOX, OnKeyBox) |
|---|
| 973 | cb.SetValue(' save as/key:') |
|---|
| 974 | Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel) |
|---|
| 975 | Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown) |
|---|
| 976 | Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown) |
|---|
| 977 | Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown) |
|---|
| 978 | Page.canvas.Bind(wx.EVT_KEY_UP, OnKey) |
|---|
| 979 | Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove) |
|---|
| 980 | # Page.canvas.Bind(wx.EVT_SIZE, OnSize) |
|---|
| 981 | Page.camera['position'] = drawingData['cameraPos'] |
|---|
| 982 | Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0]) |
|---|
| 983 | Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255. |
|---|
| 984 | Page.controls = Data |
|---|
| 985 | try: |
|---|
| 986 | Page.canvas.SetCurrent() |
|---|
| 987 | except: |
|---|
| 988 | pass |
|---|
| 989 | Draw('main') |
|---|
| 990 | # if firstCall: Draw('main') # draw twice the first time that graphics are displayed |
|---|
| 991 | |
|---|
| 992 | |
|---|
| 993 | ################################################################################ |
|---|
| 994 | ##### PlotPatterns |
|---|
| 995 | ################################################################################ |
|---|
| 996 | |
|---|
| 997 | def PlotPatterns(G2frame,newPlot=False,plotType='PWDR'): |
|---|
| 998 | '''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs |
|---|
| 999 | 2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I |
|---|
| 1000 | plotting available. |
|---|
| 1001 | ''' |
|---|
| 1002 | global exclLines |
|---|
| 1003 | global DifLine |
|---|
| 1004 | global Ymax |
|---|
| 1005 | plottype = plotType |
|---|
| 1006 | #patch |
|---|
| 1007 | data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId) |
|---|
| 1008 | if 'Offset' not in data[0] and plotType in ['PWDR','SASD']: #plot offset data |
|---|
| 1009 | data[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0, |
|---|
| 1010 | 'refDelt':0.01,}) |
|---|
| 1011 | G2frame.PatternTree.SetItemPyData(G2frame.PickId,data) |
|---|
| 1012 | #end patch |
|---|
| 1013 | def OnPlotKeyPress(event): |
|---|
| 1014 | try: #one way to check if key stroke will work on plot |
|---|
| 1015 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1016 | except TypeError: |
|---|
| 1017 | G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1) |
|---|
| 1018 | return |
|---|
| 1019 | newPlot = False |
|---|
| 1020 | if event.key == 'w': |
|---|
| 1021 | G2frame.Weight = not G2frame.Weight |
|---|
| 1022 | if not G2frame.Weight and 'PWDR' in plottype: |
|---|
| 1023 | G2frame.SinglePlot = True |
|---|
| 1024 | newPlot = True |
|---|
| 1025 | elif event.key == 'e' and 'SASD' in plottype: |
|---|
| 1026 | G2frame.ErrorBars = not G2frame.ErrorBars |
|---|
| 1027 | elif event.key == 'b': |
|---|
| 1028 | G2frame.SubBack = not G2frame.SubBack |
|---|
| 1029 | if not G2frame.SubBack: |
|---|
| 1030 | G2frame.SinglePlot = True |
|---|
| 1031 | elif event.key == 'n': |
|---|
| 1032 | if G2frame.Contour: |
|---|
| 1033 | pass |
|---|
| 1034 | else: |
|---|
| 1035 | G2frame.logPlot = not G2frame.logPlot |
|---|
| 1036 | if not G2frame.logPlot: |
|---|
| 1037 | Pattern[0]['Offset'][0] = 0 |
|---|
| 1038 | newPlot = True |
|---|
| 1039 | elif event.key == 's' and 'PWDR' in plottype: |
|---|
| 1040 | if G2frame.Contour: |
|---|
| 1041 | choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")] |
|---|
| 1042 | choice.sort() |
|---|
| 1043 | dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) |
|---|
| 1044 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 1045 | sel = dlg.GetSelection() |
|---|
| 1046 | G2frame.ContourColor = choice[sel] |
|---|
| 1047 | else: |
|---|
| 1048 | G2frame.ContourColor = 'Paired' |
|---|
| 1049 | dlg.Destroy() |
|---|
| 1050 | elif G2frame.SinglePlot: |
|---|
| 1051 | G2frame.plotStyle['sqrtPlot'] = not G2frame.plotStyle['sqrtPlot'] |
|---|
| 1052 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1053 | Pattern[0]['delOffset'] = .002 |
|---|
| 1054 | Pattern[0]['refOffset'] = -1.0 |
|---|
| 1055 | Pattern[0]['refDelt'] = .001 |
|---|
| 1056 | else: |
|---|
| 1057 | Pattern[0]['delOffset'] = .02 |
|---|
| 1058 | Pattern[0]['refOffset'] = -1.0 |
|---|
| 1059 | Pattern[0]['refDelt'] = .01 |
|---|
| 1060 | newPlot = True |
|---|
| 1061 | elif event.key == 'u' and (G2frame.Contour or not G2frame.SinglePlot): |
|---|
| 1062 | if G2frame.Contour: |
|---|
| 1063 | G2frame.Cmax = min(1.0,G2frame.Cmax*1.2) |
|---|
| 1064 | elif Pattern[0]['Offset'][0] < 100.: |
|---|
| 1065 | Pattern[0]['Offset'][0] += 1. |
|---|
| 1066 | elif event.key == 'd' and (G2frame.Contour or not G2frame.SinglePlot): |
|---|
| 1067 | if G2frame.Contour: |
|---|
| 1068 | G2frame.Cmax = max(0.0,G2frame.Cmax*0.8) |
|---|
| 1069 | elif Pattern[0]['Offset'][0] > 0.: |
|---|
| 1070 | Pattern[0]['Offset'][0] -= 1. |
|---|
| 1071 | elif event.key == 'l' and not G2frame.SinglePlot: |
|---|
| 1072 | Pattern[0]['Offset'][1] -= 1. |
|---|
| 1073 | elif event.key == 'r' and not G2frame.SinglePlot: |
|---|
| 1074 | Pattern[0]['Offset'][1] += 1. |
|---|
| 1075 | elif event.key == 'o' and not G2frame.SinglePlot: |
|---|
| 1076 | G2frame.Cmax = 1.0 |
|---|
| 1077 | Pattern[0]['Offset'] = [0,0] |
|---|
| 1078 | elif event.key == 'c' and 'PWDR' in plottype: |
|---|
| 1079 | newPlot = True |
|---|
| 1080 | if not G2frame.Contour: |
|---|
| 1081 | G2frame.SinglePlot = False |
|---|
| 1082 | Pattern[0]['Offset'] = [0.,0.] |
|---|
| 1083 | else: |
|---|
| 1084 | G2frame.SinglePlot = True |
|---|
| 1085 | G2frame.Contour = not G2frame.Contour |
|---|
| 1086 | elif event.key == 'q': |
|---|
| 1087 | if 'PWDR' in plottype: |
|---|
| 1088 | newPlot = True |
|---|
| 1089 | G2frame.plotStyle['qPlot'] = not G2frame.plotStyle['qPlot'] |
|---|
| 1090 | G2frame.plotStyle['dPlot'] = False |
|---|
| 1091 | elif 'SASD' in plottype: |
|---|
| 1092 | newPlot = True |
|---|
| 1093 | G2frame.plotStyle['sqPlot'] = not G2frame.plotStyle['sqPlot'] |
|---|
| 1094 | elif event.key == 't' and 'PWDR' in plottype: |
|---|
| 1095 | G2frame.plotStyle['dPlot'] = not G2frame.plotStyle['dPlot'] |
|---|
| 1096 | G2frame.plotStyle['qPlot'] = False |
|---|
| 1097 | newPlot = True |
|---|
| 1098 | elif event.key == 'm': |
|---|
| 1099 | G2frame.plotStyle['sqrtPlot'] = False |
|---|
| 1100 | G2frame.SinglePlot = not G2frame.SinglePlot |
|---|
| 1101 | newPlot = True |
|---|
| 1102 | elif event.key in ['+','=']: |
|---|
| 1103 | if G2frame.PickId: |
|---|
| 1104 | G2frame.PickId = False |
|---|
| 1105 | elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot |
|---|
| 1106 | choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning', |
|---|
| 1107 | 'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel', |
|---|
| 1108 | 'mitchell','sinc','lanczos'] |
|---|
| 1109 | dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice) |
|---|
| 1110 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 1111 | sel = dlg.GetSelection() |
|---|
| 1112 | G2frame.Interpolate = choice[sel] |
|---|
| 1113 | else: |
|---|
| 1114 | G2frame.Interpolate = 'nearest' |
|---|
| 1115 | dlg.Destroy() |
|---|
| 1116 | else: |
|---|
| 1117 | # print 'no binding for key',event.key |
|---|
| 1118 | #GSASIIpath.IPyBreak() |
|---|
| 1119 | return |
|---|
| 1120 | wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype) |
|---|
| 1121 | |
|---|
| 1122 | def OnMotion(event): |
|---|
| 1123 | xpos = event.xdata |
|---|
| 1124 | if xpos: #avoid out of frame mouse position |
|---|
| 1125 | ypos = event.ydata |
|---|
| 1126 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 1127 | try: |
|---|
| 1128 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1129 | if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype: |
|---|
| 1130 | q = xpos |
|---|
| 1131 | dsp = 2.*np.pi/q |
|---|
| 1132 | try: |
|---|
| 1133 | xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos) |
|---|
| 1134 | except ValueError: #avoid bad value in asin beyond upper limit |
|---|
| 1135 | pass |
|---|
| 1136 | elif 'SASD' in plottype: |
|---|
| 1137 | q = xpos |
|---|
| 1138 | dsp = 2.*np.pi/q |
|---|
| 1139 | elif G2frame.plotStyle['dPlot']: |
|---|
| 1140 | dsp = xpos |
|---|
| 1141 | q = 2.*np.pi/dsp |
|---|
| 1142 | xpos = G2lat.Dsp2pos(Parms,xpos) |
|---|
| 1143 | elif G2frame.Contour and 'T' in Parms['Type'][0]: |
|---|
| 1144 | xpos = X[xpos] |
|---|
| 1145 | dsp = G2lat.Pos2dsp(Parms,xpos) |
|---|
| 1146 | q = 2.*np.pi/dsp |
|---|
| 1147 | else: |
|---|
| 1148 | dsp = G2lat.Pos2dsp(Parms,xpos) |
|---|
| 1149 | q = 2.*np.pi/dsp |
|---|
| 1150 | if G2frame.Contour: #PWDR only |
|---|
| 1151 | if 'C' in Parms['Type'][0]: |
|---|
| 1152 | G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1) |
|---|
| 1153 | else: |
|---|
| 1154 | G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1) |
|---|
| 1155 | else: |
|---|
| 1156 | if 'C' in Parms['Type'][0]: |
|---|
| 1157 | if 'PWDR' in plottype: |
|---|
| 1158 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1159 | G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1) |
|---|
| 1160 | else: |
|---|
| 1161 | G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1) |
|---|
| 1162 | elif 'SASD' in plottype: |
|---|
| 1163 | G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1) |
|---|
| 1164 | else: |
|---|
| 1165 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1166 | G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1) |
|---|
| 1167 | else: |
|---|
| 1168 | G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1) |
|---|
| 1169 | if G2frame.itemPicked: |
|---|
| 1170 | Page.canvas.SetToolTipString('%9.5f'%(xpos)) |
|---|
| 1171 | if G2frame.PickId: |
|---|
| 1172 | found = [] |
|---|
| 1173 | pickIdText = G2frame.PatternTree.GetItemText(G2frame.PickId) |
|---|
| 1174 | if pickIdText in ['Index Peak List','Unit Cells List','Reflection Lists'] or \ |
|---|
| 1175 | 'PWDR' in pickIdText: |
|---|
| 1176 | indx = -1 |
|---|
| 1177 | if pickIdText in ['Index Peak List','Unit Cells List',]: |
|---|
| 1178 | indx = -2 |
|---|
| 1179 | if len(G2frame.HKL): |
|---|
| 1180 | view = Page.toolbar._views.forward()[0][:2] |
|---|
| 1181 | wid = view[1]-view[0] |
|---|
| 1182 | found = G2frame.HKL[np.where(np.fabs(G2frame.HKL.T[indx]-xpos) < 0.002*wid)] |
|---|
| 1183 | if len(found): |
|---|
| 1184 | if len(found[0]) > 6: #SS reflections |
|---|
| 1185 | h,k,l,m = found[0][:4] |
|---|
| 1186 | Page.canvas.SetToolTipString('%d,%d,%d,%d'%(int(h),int(k),int(l),int(m))) |
|---|
| 1187 | else: |
|---|
| 1188 | h,k,l = found[0][:3] |
|---|
| 1189 | Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l))) |
|---|
| 1190 | else: |
|---|
| 1191 | Page.canvas.SetToolTipString('') |
|---|
| 1192 | |
|---|
| 1193 | except TypeError: |
|---|
| 1194 | G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1) |
|---|
| 1195 | |
|---|
| 1196 | def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots |
|---|
| 1197 | olderr = np.seterr(invalid='ignore') |
|---|
| 1198 | |
|---|
| 1199 | def OnPick(event): |
|---|
| 1200 | '''Respond to an item being picked. This usually means that the item |
|---|
| 1201 | will be dragged with the mouse. |
|---|
| 1202 | ''' |
|---|
| 1203 | def OnDragMarker(event): |
|---|
| 1204 | '''Respond to dragging of a plot Marker |
|---|
| 1205 | ''' |
|---|
| 1206 | Page.canvas.restore_region(savedplot) |
|---|
| 1207 | G2frame.itemPicked.set_data([event.xdata], [event.ydata]) |
|---|
| 1208 | Page.figure.gca().draw_artist(G2frame.itemPicked) |
|---|
| 1209 | Page.canvas.blit(Page.figure.gca().bbox) |
|---|
| 1210 | def OnDragLine(event): |
|---|
| 1211 | '''Respond to dragging of a plot line |
|---|
| 1212 | ''' |
|---|
| 1213 | Page.canvas.restore_region(savedplot) |
|---|
| 1214 | coords = G2frame.itemPicked.get_data() |
|---|
| 1215 | coords[0][0] = coords[0][1] = event.xdata |
|---|
| 1216 | coords = G2frame.itemPicked.set_data(coords) |
|---|
| 1217 | Page.figure.gca().draw_artist(G2frame.itemPicked) |
|---|
| 1218 | Page.canvas.blit(Page.figure.gca().bbox) |
|---|
| 1219 | |
|---|
| 1220 | if G2frame.itemPicked is not None: return |
|---|
| 1221 | PatternId = G2frame.PatternId |
|---|
| 1222 | try: |
|---|
| 1223 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1224 | except TypeError: |
|---|
| 1225 | return |
|---|
| 1226 | PickId = G2frame.PickId |
|---|
| 1227 | pick = event.artist |
|---|
| 1228 | mouse = event.mouseevent |
|---|
| 1229 | xpos = pick.get_xdata() |
|---|
| 1230 | ypos = pick.get_ydata() |
|---|
| 1231 | ind = event.ind |
|---|
| 1232 | xy = list(zip(np.take(xpos,ind),np.take(ypos,ind))[0]) |
|---|
| 1233 | # convert from plot units |
|---|
| 1234 | if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta |
|---|
| 1235 | xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0]) |
|---|
| 1236 | elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta |
|---|
| 1237 | xy[0] = G2lat.Dsp2pos(Parms,xy[0]) |
|---|
| 1238 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1239 | xy[1] = xy[1]**2 |
|---|
| 1240 | if G2frame.PatternTree.GetItemText(PickId) == 'Peak List': |
|---|
| 1241 | if ind.all() != [0] and ObsLine[0].get_label() in str(pick): #picked a data point |
|---|
| 1242 | data = G2frame.PatternTree.GetItemPyData(G2frame.PickId) |
|---|
| 1243 | XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1]) |
|---|
| 1244 | data['peaks'].append(XY) |
|---|
| 1245 | data['sigDict'] = {} #now invalid |
|---|
| 1246 | G2pdG.UpdatePeakGrid(G2frame,data) |
|---|
| 1247 | PlotPatterns(G2frame,plotType=plottype) |
|---|
| 1248 | else: #picked a peak list line |
|---|
| 1249 | G2frame.itemPicked = pick |
|---|
| 1250 | elif G2frame.PatternTree.GetItemText(PickId) == 'Limits': |
|---|
| 1251 | if ind.all() != [0]: #picked a data point |
|---|
| 1252 | LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits') |
|---|
| 1253 | data = G2frame.PatternTree.GetItemPyData(LimitId) |
|---|
| 1254 | if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta |
|---|
| 1255 | xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0]) |
|---|
| 1256 | elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta |
|---|
| 1257 | xy[0] = G2lat.Dsp2pos(Parms,xy[0]) |
|---|
| 1258 | if G2frame.ifGetExclude: |
|---|
| 1259 | excl = [0,0] |
|---|
| 1260 | excl[0] = max(data[1][0],min(xy[0],data[1][1])) |
|---|
| 1261 | excl[1] = excl[0]+0.1 |
|---|
| 1262 | data.append(excl) |
|---|
| 1263 | G2frame.ifGetExclude = False |
|---|
| 1264 | else: |
|---|
| 1265 | if mouse.button==1: |
|---|
| 1266 | data[1][0] = min(xy[0],data[1][1]) |
|---|
| 1267 | if mouse.button==3: |
|---|
| 1268 | data[1][1] = max(xy[0],data[1][0]) |
|---|
| 1269 | G2frame.PatternTree.SetItemPyData(LimitId,data) |
|---|
| 1270 | G2pdG.UpdateLimitsGrid(G2frame,data,plottype) |
|---|
| 1271 | wx.CallAfter(PlotPatterns,G2frame,plotType=plottype) |
|---|
| 1272 | else: #picked a limit line |
|---|
| 1273 | # prepare to animate move of line |
|---|
| 1274 | G2frame.itemPicked = pick |
|---|
| 1275 | pick.set_linestyle(':') # set line as dotted |
|---|
| 1276 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1277 | Plot = Page.figure.gca() |
|---|
| 1278 | Page.canvas.draw() # refresh without dotted line & save bitmap |
|---|
| 1279 | savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) |
|---|
| 1280 | G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragLine) |
|---|
| 1281 | pick.set_linestyle('--') # back to dashed |
|---|
| 1282 | |
|---|
| 1283 | elif G2frame.PatternTree.GetItemText(PickId) == 'Models': |
|---|
| 1284 | if ind.all() != [0]: #picked a data point |
|---|
| 1285 | LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits') |
|---|
| 1286 | data = G2frame.PatternTree.GetItemPyData(LimitId) |
|---|
| 1287 | if mouse.button==1: |
|---|
| 1288 | data[1][0] = min(xy[0],data[1][1]) |
|---|
| 1289 | if mouse.button==3: |
|---|
| 1290 | data[1][1] = max(xy[0],data[1][0]) |
|---|
| 1291 | G2frame.PatternTree.SetItemPyData(LimitId,data) |
|---|
| 1292 | wx.CallAfter(PlotPatterns,G2frame,plotType=plottype) |
|---|
| 1293 | else: #picked a limit line |
|---|
| 1294 | G2frame.itemPicked = pick |
|---|
| 1295 | elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or |
|---|
| 1296 | 'PWDR' in G2frame.PatternTree.GetItemText(PickId) |
|---|
| 1297 | ): |
|---|
| 1298 | G2frame.itemPicked = pick |
|---|
| 1299 | pick = str(pick) |
|---|
| 1300 | elif G2frame.PatternTree.GetItemText(PickId) == 'Background': |
|---|
| 1301 | # selected a fixed background point. Can move it or delete it. |
|---|
| 1302 | for mode,id in G2frame.dataFrame.wxID_BackPts.iteritems(): # what menu is selected? |
|---|
| 1303 | if G2frame.dataFrame.BackMenu.FindItemById(id).IsChecked(): |
|---|
| 1304 | break |
|---|
| 1305 | # mode will be 'Add' or 'Move' or 'Del' |
|---|
| 1306 | if pick.get_marker() == 'D': |
|---|
| 1307 | # find the closest point |
|---|
| 1308 | backDict = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Background'))[1] |
|---|
| 1309 | d2 = [(x-xy[0])**2+(y-xy[1])**2 for x,y in backDict['FixedPoints']] |
|---|
| 1310 | G2frame.fixPtMarker = d2.index(min(d2)) |
|---|
| 1311 | if mode == 'Move': |
|---|
| 1312 | # animate move of FixedBkg marker |
|---|
| 1313 | G2frame.itemPicked = pick |
|---|
| 1314 | pick.set_marker('|') # change the point appearance |
|---|
| 1315 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1316 | Plot = Page.figure.gca() |
|---|
| 1317 | Page.canvas.draw() # refresh with changed point & save bitmap |
|---|
| 1318 | savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) |
|---|
| 1319 | G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragMarker) |
|---|
| 1320 | pick.set_marker('D') # put it back |
|---|
| 1321 | elif mode == 'Del': |
|---|
| 1322 | del backDict['FixedPoints'][G2frame.fixPtMarker] |
|---|
| 1323 | wx.CallAfter(PlotPatterns,G2frame,plotType=plottype) |
|---|
| 1324 | return |
|---|
| 1325 | def OnRelease(event): # mouse release from item pick or background pt add/move/del |
|---|
| 1326 | plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns') |
|---|
| 1327 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1328 | if G2frame.cid is not None: # if there is a drag connection, delete it |
|---|
| 1329 | Page.canvas.mpl_disconnect(G2frame.cid) |
|---|
| 1330 | G2frame.cid = None |
|---|
| 1331 | PickId = G2frame.PickId # points to item in tree |
|---|
| 1332 | if G2frame.PatternTree.GetItemText(PickId) == 'Background' and event.xdata: |
|---|
| 1333 | if Page.toolbar._active: # prevent ops. if a toolbar zoom button pressed |
|---|
| 1334 | return |
|---|
| 1335 | # Background page, deal with fixed background points |
|---|
| 1336 | if G2frame.SubBack or G2frame.Weight or G2frame.Contour or not G2frame.SinglePlot: |
|---|
| 1337 | return |
|---|
| 1338 | backDict = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Background'))[1] |
|---|
| 1339 | if 'FixedPoints' not in backDict: backDict['FixedPoints'] = [] |
|---|
| 1340 | try: |
|---|
| 1341 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1342 | except TypeError: |
|---|
| 1343 | return |
|---|
| 1344 | # unit conversions |
|---|
| 1345 | xy = [event.xdata,event.ydata] |
|---|
| 1346 | if G2frame.plotStyle['qPlot']: #qplot - convert back to 2-theta |
|---|
| 1347 | xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0]) |
|---|
| 1348 | elif G2frame.plotStyle['dPlot']: #dplot - convert back to 2-theta |
|---|
| 1349 | xy[0] = G2lat.Dsp2pos(Parms,xy[0]) |
|---|
| 1350 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1351 | xy[1] = xy[1]**2 |
|---|
| 1352 | for mode,id in G2frame.dataFrame.wxID_BackPts.iteritems(): # what menu item is selected? |
|---|
| 1353 | if G2frame.dataFrame.BackMenu.FindItemById(id).IsChecked(): |
|---|
| 1354 | break |
|---|
| 1355 | if mode == 'Add': |
|---|
| 1356 | backDict['FixedPoints'].append(xy) |
|---|
| 1357 | Plot = Page.figure.gca() |
|---|
| 1358 | Plot.plot(event.xdata,event.ydata,'rD',clip_on=False,picker=3.) |
|---|
| 1359 | Page.canvas.draw() |
|---|
| 1360 | return |
|---|
| 1361 | elif G2frame.itemPicked is not None: # end of drag in move |
|---|
| 1362 | backDict['FixedPoints'][G2frame.fixPtMarker] = xy |
|---|
| 1363 | G2frame.itemPicked = None |
|---|
| 1364 | wx.CallAfter(PlotPatterns,G2frame,plotType=plottype) |
|---|
| 1365 | return |
|---|
| 1366 | |
|---|
| 1367 | if G2frame.itemPicked is None: return |
|---|
| 1368 | if str(DifLine[0]) == str(G2frame.itemPicked): |
|---|
| 1369 | data = G2frame.PatternTree.GetItemPyData(PickId) |
|---|
| 1370 | ypos = event.ydata |
|---|
| 1371 | Pattern[0]['delOffset'] = -ypos/Ymax |
|---|
| 1372 | G2frame.itemPicked = None |
|---|
| 1373 | wx.CallAfter(PlotPatterns,G2frame,plotType=plottype) |
|---|
| 1374 | return |
|---|
| 1375 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1376 | xpos = event.xdata |
|---|
| 1377 | if G2frame.PatternTree.GetItemText(PickId) in ['Peak List','Limits'] and xpos: |
|---|
| 1378 | lines = [] |
|---|
| 1379 | for line in G2frame.Lines: |
|---|
| 1380 | lines.append(line.get_xdata()[0]) |
|---|
| 1381 | try: |
|---|
| 1382 | lineNo = lines.index(G2frame.itemPicked.get_xdata()[0]) |
|---|
| 1383 | except ValueError: |
|---|
| 1384 | lineNo = -1 |
|---|
| 1385 | if lineNo in [0,1] or lineNo in exclLines: |
|---|
| 1386 | LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits') |
|---|
| 1387 | limits = G2frame.PatternTree.GetItemPyData(LimitId) |
|---|
| 1388 | id = lineNo/2+1 |
|---|
| 1389 | id2 = lineNo%2 |
|---|
| 1390 | if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype: |
|---|
| 1391 | limits[id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos) |
|---|
| 1392 | elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype: |
|---|
| 1393 | limits[id][id2] = G2lat.Dsp2pos(Parms,xpos) |
|---|
| 1394 | else: |
|---|
| 1395 | limits[id][id2] = xpos |
|---|
| 1396 | if id > 1 and limits[id][0] > limits[id][1]: |
|---|
| 1397 | limits[id].reverse() |
|---|
| 1398 | limits[1][0] = min(max(limits[0][0],limits[1][0]),limits[1][1]) |
|---|
| 1399 | limits[1][1] = max(min(limits[0][1],limits[1][1]),limits[1][0]) |
|---|
| 1400 | if G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Limits': |
|---|
| 1401 | G2pdG.UpdateLimitsGrid(G2frame,limits,plottype) |
|---|
| 1402 | elif lineNo > 1: |
|---|
| 1403 | PeakId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Peak List') |
|---|
| 1404 | peaks = G2frame.PatternTree.GetItemPyData(PeakId) |
|---|
| 1405 | if event.button == 3: |
|---|
| 1406 | del peaks['peaks'][lineNo-2] |
|---|
| 1407 | else: |
|---|
| 1408 | if G2frame.plotStyle['qPlot']: |
|---|
| 1409 | peaks['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos) |
|---|
| 1410 | elif G2frame.plotStyle['dPlot']: |
|---|
| 1411 | peaks['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,xpos) |
|---|
| 1412 | else: |
|---|
| 1413 | peaks['peaks'][lineNo-2][0] = xpos |
|---|
| 1414 | peaks['sigDict'] = {} #no longer valid |
|---|
| 1415 | G2pdG.UpdatePeakGrid(G2frame,peaks) |
|---|
| 1416 | elif G2frame.PatternTree.GetItemText(PickId) in ['Models',] and xpos: |
|---|
| 1417 | lines = [] |
|---|
| 1418 | for line in G2frame.Lines: |
|---|
| 1419 | lines.append(line.get_xdata()[0]) |
|---|
| 1420 | try: |
|---|
| 1421 | lineNo = lines.index(G2frame.itemPicked.get_xdata()[0]) |
|---|
| 1422 | except ValueError: |
|---|
| 1423 | lineNo = -1 |
|---|
| 1424 | if lineNo in [0,1]: |
|---|
| 1425 | LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits') |
|---|
| 1426 | data = G2frame.PatternTree.GetItemPyData(LimitId) |
|---|
| 1427 | data[1][lineNo] = xpos |
|---|
| 1428 | data[1][0] = min(max(data[0][0],data[1][0]),data[1][1]) |
|---|
| 1429 | data[1][1] = max(min(data[0][1],data[1][1]),data[1][0]) |
|---|
| 1430 | elif (G2frame.PatternTree.GetItemText(PickId) == 'Reflection Lists' or \ |
|---|
| 1431 | 'PWDR' in G2frame.PatternTree.GetItemText(PickId)) and xpos: |
|---|
| 1432 | Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists')) |
|---|
| 1433 | pick = str(G2frame.itemPicked).split('(')[1].strip(')') |
|---|
| 1434 | if 'line' not in pick: #avoid data points, etc. |
|---|
| 1435 | data = G2frame.PatternTree.GetItemPyData(PatternId) |
|---|
| 1436 | num = Phases.keys().index(pick) |
|---|
| 1437 | if num: |
|---|
| 1438 | data[0]['refDelt'] = -(event.ydata-Pattern[0]['refOffset'])/(num*Ymax) |
|---|
| 1439 | else: #1st row of refl ticks |
|---|
| 1440 | data[0]['refOffset'] = event.ydata |
|---|
| 1441 | PlotPatterns(G2frame,plotType=plottype) |
|---|
| 1442 | G2frame.itemPicked = None |
|---|
| 1443 | |
|---|
| 1444 | # beginning PlotPatterns execution |
|---|
| 1445 | try: |
|---|
| 1446 | plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns') |
|---|
| 1447 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1448 | Plot = Page.figure.gca() #get previous powder plot & get limits |
|---|
| 1449 | G2frame.xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 1450 | Page.figure.clf() |
|---|
| 1451 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 1452 | except ValueError: |
|---|
| 1453 | if plottype == 'SASD': |
|---|
| 1454 | G2frame.logPlot = True |
|---|
| 1455 | G2frame.ErrorBars = True |
|---|
| 1456 | newPlot = True |
|---|
| 1457 | G2frame.Cmax = 1.0 |
|---|
| 1458 | Plot = G2frame.G2plotNB.addMpl('Powder Patterns').gca() |
|---|
| 1459 | plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns') |
|---|
| 1460 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1461 | Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) |
|---|
| 1462 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 1463 | Page.canvas.mpl_connect('pick_event', OnPick) |
|---|
| 1464 | Page.canvas.mpl_connect('button_release_event', OnRelease) |
|---|
| 1465 | Page.canvas.mpl_connect('button_press_event',OnPress) |
|---|
| 1466 | if plottype == 'PWDR': # avoids a very nasty clash with KILL_FOCUS in SASD TextCtrl? |
|---|
| 1467 | Page.SetFocus() |
|---|
| 1468 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 1469 | if G2frame.Contour: |
|---|
| 1470 | Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max', |
|---|
| 1471 | 'i: interpolation method','s: color scheme','c: contour off') |
|---|
| 1472 | else: |
|---|
| 1473 | if G2frame.logPlot: |
|---|
| 1474 | if 'PWDR' in plottype: |
|---|
| 1475 | if G2frame.SinglePlot: |
|---|
| 1476 | Page.Choice = (' key press','n: log(I) off', |
|---|
| 1477 | 'c: contour on','q: toggle q plot','t: toggle d-spacing plot', |
|---|
| 1478 | 'm: toggle multidata plot','w: toggle divide by sig','+: no selection') |
|---|
| 1479 | else: |
|---|
| 1480 | Page.Choice = (' key press','n: log(I) off', |
|---|
| 1481 | 'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset', |
|---|
| 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') |
|---|
| 1484 | elif 'SASD' in plottype: |
|---|
| 1485 | if G2frame.SinglePlot: |
|---|
| 1486 | Page.Choice = (' key press','b: toggle subtract background file','n: semilog on', |
|---|
| 1487 | 'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection') |
|---|
| 1488 | else: |
|---|
| 1489 | Page.Choice = (' key press','b: toggle subtract background file','n: semilog on', |
|---|
| 1490 | 'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset', |
|---|
| 1491 | 'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection') |
|---|
| 1492 | else: |
|---|
| 1493 | if 'PWDR' in plottype: |
|---|
| 1494 | if G2frame.SinglePlot: |
|---|
| 1495 | Page.Choice = (' key press', |
|---|
| 1496 | 'b: toggle subtract background','n: log(I) on','s: toggle sqrt plot','c: contour on', |
|---|
| 1497 | 'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot', |
|---|
| 1498 | 'w: toggle divide by sig','+: no selection') |
|---|
| 1499 | else: |
|---|
| 1500 | Page.Choice = (' key press','l: offset left','r: offset right','d: offset down', |
|---|
| 1501 | 'u: offset up','o: reset offset','b: toggle subtract background','n: log(I) on','c: contour on', |
|---|
| 1502 | 'q: toggle q plot','t: toggle d-spacing plot','m: toggle multidata plot', |
|---|
| 1503 | 'w: toggle divide by sig','+: no selection') |
|---|
| 1504 | elif 'SASD' in plottype: |
|---|
| 1505 | if G2frame.SinglePlot: |
|---|
| 1506 | Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars', |
|---|
| 1507 | 'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection') |
|---|
| 1508 | else: |
|---|
| 1509 | Page.Choice = (' key press','b: toggle subtract background file','n: loglog on','e: toggle error bars', |
|---|
| 1510 | 'd: offset down','l: offset left','r: offset right','u: offset up','o: reset offset', |
|---|
| 1511 | 'q: toggle S(q) plot','m: toggle multidata plot','w: toggle (Io-Ic)/sig plot','+: no selection') |
|---|
| 1512 | G2frame.cid = None |
|---|
| 1513 | Page.keyPress = OnPlotKeyPress |
|---|
| 1514 | PickId = G2frame.PickId |
|---|
| 1515 | PatternId = G2frame.PatternId |
|---|
| 1516 | colors=['b','g','r','c','m','k'] |
|---|
| 1517 | Lines = [] |
|---|
| 1518 | exclLines = [] |
|---|
| 1519 | if G2frame.SinglePlot and PatternId: |
|---|
| 1520 | Pattern = G2frame.PatternTree.GetItemPyData(PatternId) |
|---|
| 1521 | Pattern.append(G2frame.PatternTree.GetItemText(PatternId)) |
|---|
| 1522 | PlotList = [Pattern,] |
|---|
| 1523 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, |
|---|
| 1524 | G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1525 | Sample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters')) |
|---|
| 1526 | ParmList = [Parms,] |
|---|
| 1527 | SampleList = [Sample,] |
|---|
| 1528 | Title = Pattern[-1] |
|---|
| 1529 | else: |
|---|
| 1530 | Title = os.path.split(G2frame.GSASprojectfile)[1] |
|---|
| 1531 | PlotList = [] |
|---|
| 1532 | ParmList = [] |
|---|
| 1533 | SampleList = [] |
|---|
| 1534 | item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root) |
|---|
| 1535 | while item: |
|---|
| 1536 | if plottype in G2frame.PatternTree.GetItemText(item): |
|---|
| 1537 | Pattern = G2frame.PatternTree.GetItemPyData(item) |
|---|
| 1538 | if len(Pattern) < 3: # put name on end if needed |
|---|
| 1539 | Pattern.append(G2frame.PatternTree.GetItemText(item)) |
|---|
| 1540 | if 'Offset' not in Pattern[0]: #plot offset data |
|---|
| 1541 | Pattern[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,}) |
|---|
| 1542 | PlotList.append(Pattern) |
|---|
| 1543 | ParmList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, |
|---|
| 1544 | item,'Instrument Parameters'))[0]) |
|---|
| 1545 | SampleList.append(G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, |
|---|
| 1546 | item, 'Sample Parameters'))) |
|---|
| 1547 | item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie) |
|---|
| 1548 | lenX = 0 |
|---|
| 1549 | Ymax = None |
|---|
| 1550 | for Pattern in PlotList: |
|---|
| 1551 | xye = Pattern[1] |
|---|
| 1552 | if xye[1] is None: continue |
|---|
| 1553 | if Ymax is None: Ymax = max(xye[1]) |
|---|
| 1554 | Ymax = max(Ymax,max(xye[1])) |
|---|
| 1555 | if Ymax is None: return # nothing to plot |
|---|
| 1556 | offsetX = Pattern[0]['Offset'][1] |
|---|
| 1557 | offsetY = Pattern[0]['Offset'][0] |
|---|
| 1558 | if G2frame.logPlot: |
|---|
| 1559 | Title = 'log('+Title+')' |
|---|
| 1560 | Plot.set_title(Title) |
|---|
| 1561 | if G2frame.plotStyle['qPlot'] or 'SASD' in plottype and not G2frame.Contour: |
|---|
| 1562 | Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=16) |
|---|
| 1563 | elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype and not G2frame.Contour: |
|---|
| 1564 | Plot.set_xlabel(r'$d, \AA$',fontsize=16) |
|---|
| 1565 | else: |
|---|
| 1566 | if 'C' in ParmList[0]['Type'][0]: |
|---|
| 1567 | Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=16) |
|---|
| 1568 | else: |
|---|
| 1569 | if G2frame.Contour: |
|---|
| 1570 | Plot.set_xlabel(r'Channel no.',fontsize=16) |
|---|
| 1571 | else: |
|---|
| 1572 | Plot.set_xlabel(r'$TOF, \mathsf{\mu}$s',fontsize=16) |
|---|
| 1573 | if G2frame.Weight: |
|---|
| 1574 | if 'PWDR' in plottype: |
|---|
| 1575 | Plot.set_ylabel(r'$\mathsf{I/\sigma(I)}$',fontsize=16) |
|---|
| 1576 | elif 'SASD' in plottype: |
|---|
| 1577 | Plot.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16) |
|---|
| 1578 | else: |
|---|
| 1579 | if 'C' in ParmList[0]['Type'][0]: |
|---|
| 1580 | if 'PWDR' in plottype: |
|---|
| 1581 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1582 | Plot.set_ylabel(r'$\sqrt{Intensity}$',fontsize=16) |
|---|
| 1583 | else: |
|---|
| 1584 | Plot.set_ylabel(r'$Intensity$',fontsize=16) |
|---|
| 1585 | elif 'SASD' in plottype: |
|---|
| 1586 | if G2frame.sqPlot: |
|---|
| 1587 | Plot.set_ylabel(r'$S(Q)=I*Q^{4}$',fontsize=16) |
|---|
| 1588 | else: |
|---|
| 1589 | Plot.set_ylabel(r'$Intensity, cm^{-1}$',fontsize=16) |
|---|
| 1590 | else: |
|---|
| 1591 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1592 | Plot.set_ylabel(r'$\sqrt{Normalized\ intensity}$',fontsize=16) |
|---|
| 1593 | else: |
|---|
| 1594 | Plot.set_ylabel(r'$Normalized\ intensity$',fontsize=16) |
|---|
| 1595 | if G2frame.Contour: |
|---|
| 1596 | ContourZ = [] |
|---|
| 1597 | ContourY = [] |
|---|
| 1598 | Nseq = 0 |
|---|
| 1599 | for N,Pattern in enumerate(PlotList): |
|---|
| 1600 | Parms = ParmList[N] |
|---|
| 1601 | Sample = SampleList[N] |
|---|
| 1602 | if 'C' in Parms['Type'][0]: |
|---|
| 1603 | wave = G2mth.getWave(Parms) |
|---|
| 1604 | else: |
|---|
| 1605 | difC = Parms['difC'][1] |
|---|
| 1606 | ifpicked = False |
|---|
| 1607 | LimitId = 0 |
|---|
| 1608 | if Pattern[1] is None: continue # skip over uncomputed simulations |
|---|
| 1609 | xye = ma.array(ma.getdata(Pattern[1])) |
|---|
| 1610 | Zero = Parms.get('Zero',[0.,0.])[1] |
|---|
| 1611 | if PickId: |
|---|
| 1612 | ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId) |
|---|
| 1613 | LimitId = G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId,'Limits') |
|---|
| 1614 | limits = G2frame.PatternTree.GetItemPyData(LimitId) |
|---|
| 1615 | excls = limits[2:] |
|---|
| 1616 | for excl in excls: |
|---|
| 1617 | xye[0] = ma.masked_inside(xye[0],excl[0],excl[1]) |
|---|
| 1618 | if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype: |
|---|
| 1619 | Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2]) |
|---|
| 1620 | X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye[0]) |
|---|
| 1621 | elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype: |
|---|
| 1622 | Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2]) |
|---|
| 1623 | X = G2lat.Pos2dsp(Parms,xye[0]) |
|---|
| 1624 | else: |
|---|
| 1625 | X = xye[0] |
|---|
| 1626 | if not lenX: |
|---|
| 1627 | lenX = len(X) |
|---|
| 1628 | if 'PWDR' in plottype: |
|---|
| 1629 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1630 | olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error |
|---|
| 1631 | Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1])) |
|---|
| 1632 | np.seterr(invalid=olderr['invalid']) |
|---|
| 1633 | else: |
|---|
| 1634 | Y = xye[1]+offsetY*N*Ymax/100.0 |
|---|
| 1635 | elif 'SASD' in plottype: |
|---|
| 1636 | B = xye[5] |
|---|
| 1637 | if G2frame.sqPlot: |
|---|
| 1638 | Y = xye[1]*Sample['Scale'][0]*(1.05)**(offsetY*N)*X**4 |
|---|
| 1639 | else: |
|---|
| 1640 | Y = xye[1]*Sample['Scale'][0]*(1.05)**(offsetY*N) |
|---|
| 1641 | if LimitId and ifpicked: |
|---|
| 1642 | limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId)) |
|---|
| 1643 | lims = limits[1] |
|---|
| 1644 | if G2frame.plotStyle['qPlot'] and 'PWDR' in plottype: |
|---|
| 1645 | lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims) |
|---|
| 1646 | elif G2frame.plotStyle['dPlot'] and 'PWDR' in plottype: |
|---|
| 1647 | lims = G2lat.Pos2dsp(Parms,lims) |
|---|
| 1648 | Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.)) |
|---|
| 1649 | Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.)) |
|---|
| 1650 | for i,item in enumerate(limits[2:]): |
|---|
| 1651 | Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.)) |
|---|
| 1652 | Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.)) |
|---|
| 1653 | exclLines += [2*i+2,2*i+3] |
|---|
| 1654 | if G2frame.Contour: |
|---|
| 1655 | if lenX == len(X): |
|---|
| 1656 | ContourY.append(N) |
|---|
| 1657 | ContourZ.append(Y) |
|---|
| 1658 | if 'C' in ParmList[0]['Type'][0]: |
|---|
| 1659 | ContourX = X |
|---|
| 1660 | else: #'T'OF |
|---|
| 1661 | ContourX = range(lenX) |
|---|
| 1662 | Nseq += 1 |
|---|
| 1663 | Plot.set_ylabel('Data sequence',fontsize=12) |
|---|
| 1664 | else: |
|---|
| 1665 | if 'SASD' in plottype and G2frame.logPlot: |
|---|
| 1666 | X *= (1.01)**(offsetX*N) |
|---|
| 1667 | else: |
|---|
| 1668 | X += offsetX*.005*N |
|---|
| 1669 | Xum = ma.getdata(X) |
|---|
| 1670 | DifLine = [''] |
|---|
| 1671 | if ifpicked: |
|---|
| 1672 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1673 | olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error |
|---|
| 1674 | Z = np.where(xye[3]>=0.,np.sqrt(xye[3]),-np.sqrt(-xye[3])) |
|---|
| 1675 | np.seterr(invalid=olderr['invalid']) |
|---|
| 1676 | else: |
|---|
| 1677 | Z = xye[3]+offsetY*N*Ymax/100.0 |
|---|
| 1678 | if 'PWDR' in plottype: |
|---|
| 1679 | if G2frame.plotStyle['sqrtPlot']: |
|---|
| 1680 | olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error |
|---|
| 1681 | W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4])) |
|---|
| 1682 | np.seterr(invalid=olderr['invalid']) |
|---|
| 1683 | D = np.where(xye[5],(Y-Z),0.)-Ymax*Pattern[0]['delOffset'] |
|---|
| 1684 | else: |
|---|
| 1685 | W = xye[4]+offsetY*N*Ymax/100.0 |
|---|
| 1686 | D = xye[5]-Ymax*Pattern[0]['delOffset'] #powder background |
|---|
| 1687 | elif 'SASD' in plottype: |
|---|
| 1688 | if G2frame.sqPlot: |
|---|
| 1689 | W = xye[4]*X**4 |
|---|
| 1690 | Z = xye[3]*X**4 |
|---|
| 1691 | B = B*X**4 |
|---|
| 1692 | else: |
|---|
| 1693 | W = xye[4] |
|---|
| 1694 | if G2frame.SubBack: |
|---|
| 1695 | YB = Y-B |
|---|
| 1696 | ZB = Z |
|---|
| 1697 | else: |
|---|
| 1698 | YB = Y |
|---|
| 1699 | ZB = Z+B |
|---|
| 1700 | Plot.set_yscale("log",nonposy='mask') |
|---|
| 1701 | if np.any(W>0.): |
|---|
| 1702 | Plot.set_ylim(bottom=np.min(np.trim_zeros(W))/2.,top=np.max(Y)*2.) |
|---|
| 1703 | else: |
|---|
| 1704 | Plot.set_ylim(bottom=np.min(np.trim_zeros(YB))/2.,top=np.max(Y)*2.) |
|---|
| 1705 | if G2frame.logPlot: |
|---|
| 1706 | if 'PWDR' in plottype: |
|---|
| 1707 | Plot.set_yscale("log",nonposy='mask') |
|---|
| 1708 | Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False) |
|---|
| 1709 | Plot.plot(X,Z,colors[(N+1)%6],picker=False) |
|---|
| 1710 | Plot.plot(X,W,colors[(N+2)%6],picker=False) #background |
|---|
| 1711 | elif 'SASD' in plottype: |
|---|
| 1712 | Plot.set_xscale("log",nonposx='mask') |
|---|
| 1713 | Ibeg = np.searchsorted(X,limits[1][0]) |
|---|
| 1714 | Ifin = np.searchsorted(X,limits[1][1]) |
|---|
| 1715 | if G2frame.Weight: |
|---|
| 1716 | Plot.set_yscale("linear") |
|---|
| 1717 | DS = (YB-ZB)*np.sqrt(xye[2]) |
|---|
| 1718 | Plot.plot(X[Ibeg:Ifin],DS[Ibeg:Ifin],colors[(N+3)%6],picker=False) |
|---|
| 1719 | Plot.axhline(0.,color=wx.BLACK) |
|---|
| 1720 | Plot.set_ylim(bottom=np.min(DS[Ibeg:Ifin])*1.2,top=np.max(DS[Ibeg:Ifin])*1.2) |
|---|
| 1721 | else: |
|---|
| 1722 | Plot.set_yscale("log",nonposy='mask') |
|---|
| 1723 | if G2frame.ErrorBars: |
|---|
| 1724 | if G2frame.sqPlot: |
|---|
| 1725 | Plot.errorbar(X,YB,yerr=X**4*Sample['Scale'][0]*np.sqrt(1./(Pattern[0]['wtFactor']*xye[2])), |
|---|
| 1726 | ecolor=colors[N%6],picker=3.,clip_on=False) |
|---|
| 1727 | else: |
|---|
| 1728 | Plot.errorbar(X,YB,yerr=Sample['Scale'][0]*np.sqrt(1./(Pattern[0]['wtFactor']*xye[2])), |
|---|
| 1729 | ecolor=colors[N%6],picker=3.,clip_on=False) |
|---|
| 1730 | else: |
|---|
| 1731 | Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False) |
|---|
| 1732 | Plot.plot(X,W,colors[(N+2)%6],picker=False) #const. background |
|---|
| 1733 | Plot.plot(X,ZB,colors[(N+1)%6],picker=False) |
|---|
| 1734 | elif G2frame.Weight and 'PWDR' in plottype: |
|---|
| 1735 | DY = xye[1]*np.sqrt(xye[2]) |
|---|
| 1736 | Ymax = max(DY) |
|---|
| 1737 | DZ = xye[3]*np.sqrt(xye[2]) |
|---|
| 1738 | DS = xye[5]*np.sqrt(xye[2])-Ymax*Pattern[0]['delOffset'] |
|---|
| 1739 | ObsLine = Plot.plot(X,DY,colors[N%6]+'+',picker=3.,clip_on=False) #Io/sig(Io) |
|---|
| 1740 | Plot.plot(X,DZ,colors[(N+1)%6],picker=False) #Ic/sig(Io) |
|---|
| 1741 | DifLine = Plot.plot(X,DS,colors[(N+3)%6],picker=1.) #(Io-Ic)/sig(Io) |
|---|
| 1742 | Plot.axhline(0.,color=wx.BLACK) |
|---|
| 1743 | else: |
|---|
| 1744 | if G2frame.SubBack: |
|---|
| 1745 | if 'PWDR' in plottype: |
|---|
| 1746 | Plot.plot(Xum,Y-W,colors[N%6]+'+',picker=False,clip_on=False) #Io-Ib |
|---|
| 1747 | Plot.plot(X,Z-W,colors[(N+1)%6],picker=False) #Ic-Ib |
|---|
| 1748 | else: |
|---|
| 1749 | Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False) |
|---|
| 1750 | Plot.plot(X,ZB,colors[(N+1)%6],picker=False) |
|---|
| 1751 | else: |
|---|
| 1752 | if 'PWDR' in plottype: |
|---|
| 1753 | ObsLine = Plot.plot(Xum,Y,colors[N%6]+'+',picker=3.,clip_on=False) #Io |
|---|
| 1754 | Plot.plot(X,Z,colors[(N+1)%6],picker=False) #Ic |
|---|
| 1755 | else: |
|---|
| 1756 | Plot.plot(X,YB,colors[N%6]+'+',picker=3.,clip_on=False) |
|---|
| 1757 | Plot.plot(X,ZB,colors[(N+1)%6],picker=False) |
|---|
| 1758 | if 'PWDR' in plottype: |
|---|
| 1759 | Plot.plot(X,W,colors[(N+2)%6],picker=False) #Ib |
|---|
| 1760 | DifLine = Plot.plot(X,D,colors[(N+3)%6],picker=1.) #Io-Ic |
|---|
| 1761 | Plot.axhline(0.,color=wx.BLACK) |
|---|
| 1762 | Page.canvas.SetToolTipString('') |
|---|
| 1763 | if PickId: |
|---|
| 1764 | if G2frame.PatternTree.GetItemText(PickId) == 'Peak List': |
|---|
| 1765 | tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete' |
|---|
| 1766 | Page.canvas.SetToolTipString(tip) |
|---|
| 1767 | data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List')) |
|---|
| 1768 | for item in data['peaks']: |
|---|
| 1769 | if G2frame.plotStyle['qPlot']: |
|---|
| 1770 | Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.)) |
|---|
| 1771 | elif G2frame.plotStyle['dPlot']: |
|---|
| 1772 | Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.)) |
|---|
| 1773 | else: |
|---|
| 1774 | Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.)) |
|---|
| 1775 | if G2frame.PatternTree.GetItemText(PickId) == 'Limits': |
|---|
| 1776 | tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move' |
|---|
| 1777 | Page.canvas.SetToolTipString(tip) |
|---|
| 1778 | data = G2frame.LimitsTable.GetData() |
|---|
| 1779 | |
|---|
| 1780 | else: #not picked |
|---|
| 1781 | if G2frame.logPlot: |
|---|
| 1782 | if 'PWDR' in plottype: |
|---|
| 1783 | Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask') |
|---|
| 1784 | elif 'SASD' in plottype: |
|---|
| 1785 | Plot.semilogy(X,Y,colors[N%6],picker=False,nonposy='mask') |
|---|
| 1786 | else: |
|---|
| 1787 | if 'PWDR' in plottype: |
|---|
| 1788 | Plot.plot(X,Y,colors[N%6],picker=False) |
|---|
| 1789 | elif 'SASD' in plottype: |
|---|
| 1790 | Plot.loglog(X,Y,colors[N%6],picker=False,nonposy='mask') |
|---|
| 1791 | Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.) |
|---|
| 1792 | |
|---|
| 1793 | if G2frame.logPlot and 'PWDR' in plottype: |
|---|
| 1794 | Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.) |
|---|
| 1795 | if PickId and not G2frame.Contour: |
|---|
| 1796 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters')) |
|---|
| 1797 | if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']: |
|---|
| 1798 | peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List')) |
|---|
| 1799 | if not len(peaks): return # are there any peaks? |
|---|
| 1800 | for peak in peaks[0]: |
|---|
| 1801 | if peak[2]: |
|---|
| 1802 | if G2frame.plotStyle['qPlot']: |
|---|
| 1803 | Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b') |
|---|
| 1804 | if G2frame.plotStyle['dPlot']: |
|---|
| 1805 | Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b') |
|---|
| 1806 | else: |
|---|
| 1807 | Plot.axvline(peak[0],color='b') |
|---|
| 1808 | for hkl in G2frame.HKL: |
|---|
| 1809 | clr = 'r' |
|---|
| 1810 | if len(hkl) > 6 and hkl[3]: |
|---|
| 1811 | clr = 'g' |
|---|
| 1812 | if G2frame.plotStyle['qPlot']: |
|---|
| 1813 | Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5)) |
|---|
| 1814 | if G2frame.plotStyle['dPlot']: |
|---|
| 1815 | Plot.axvline(G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(5,5)) |
|---|
| 1816 | else: |
|---|
| 1817 | Plot.axvline(hkl[-2],color=clr,dashes=(5,5)) |
|---|
| 1818 | elif G2frame.PatternTree.GetItemText(PickId) in ['Reflection Lists'] or \ |
|---|
| 1819 | 'PWDR' in G2frame.PatternTree.GetItemText(PickId): |
|---|
| 1820 | refColors=['b','r','c','g','m','k'] |
|---|
| 1821 | Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists')) |
|---|
| 1822 | for pId,phase in enumerate(Phases): |
|---|
| 1823 | peaks = Phases[phase].get('RefList',[]) |
|---|
| 1824 | if not len(peaks): |
|---|
| 1825 | continue |
|---|
| 1826 | if Phases[phase].get('Super',False): |
|---|
| 1827 | peak = np.array([[peak[5],peak[6]] for peak in peaks]) |
|---|
| 1828 | else: |
|---|
| 1829 | peak = np.array([[peak[4],peak[5]] for peak in peaks]) |
|---|
| 1830 | pos = Pattern[0]['refOffset']-pId*Ymax*Pattern[0]['refDelt']*np.ones_like(peak) |
|---|
| 1831 | if G2frame.plotStyle['qPlot']: |
|---|
| 1832 | Plot.plot(2*np.pi/peak.T[0],pos,refColors[pId%6]+'|',mew=1,ms=8,picker=3.,label=phase) |
|---|
| 1833 | elif G2frame.plotStyle['dPlot']: |
|---|
| 1834 | Plot.plot(peak.T[0],pos,refColors[pId%6]+'|',mew=1,ms=8,picker=3.,label=phase) |
|---|
| 1835 | else: |
|---|
| 1836 | Plot.plot(peak.T[1],pos,refColors[pId%6]+'|',mew=1,ms=8,picker=3.,label=phase) |
|---|
| 1837 | if len(Phases): |
|---|
| 1838 | handles,legends = Plot.get_legend_handles_labels() #got double entries in the legends for some reason |
|---|
| 1839 | if handles: |
|---|
| 1840 | Plot.legend(handles[::2],legends[::2],title='Phases',loc='best') #skip every other one |
|---|
| 1841 | |
|---|
| 1842 | if G2frame.Contour: |
|---|
| 1843 | acolor = mpl.cm.get_cmap(G2frame.ContourColor) |
|---|
| 1844 | Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate, |
|---|
| 1845 | extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower') |
|---|
| 1846 | Page.figure.colorbar(Img) |
|---|
| 1847 | else: |
|---|
| 1848 | G2frame.Lines = Lines |
|---|
| 1849 | if G2frame.PatternTree.GetItemText(PickId) == 'Background': |
|---|
| 1850 | # plot fixed background points |
|---|
| 1851 | backDict = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Background'))[1] |
|---|
| 1852 | try: |
|---|
| 1853 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) |
|---|
| 1854 | except TypeError: |
|---|
| 1855 | Parms = None |
|---|
| 1856 | for x,y in backDict.get('FixedPoints',[]): |
|---|
| 1857 | # "normal" intensity modes only! |
|---|
| 1858 | if G2frame.SubBack or G2frame.Weight or G2frame.Contour or not G2frame.SinglePlot: |
|---|
| 1859 | break |
|---|
| 1860 | if y < 0 and (G2frame.plotStyle['sqrtPlot'] or G2frame.logPlot): |
|---|
| 1861 | y = Page.figure.gca().get_ylim()[0] # put out of range point at bottom of plot |
|---|
| 1862 | elif G2frame.plotStyle['sqrtPlot']: |
|---|
| 1863 | y = math.sqrt(y) |
|---|
| 1864 | if G2frame.plotStyle['qPlot']: #Q - convert from 2-theta |
|---|
| 1865 | if Parms: |
|---|
| 1866 | x = 2*np.pi/G2lat.Pos2dsp(Parms,x) |
|---|
| 1867 | else: |
|---|
| 1868 | break |
|---|
| 1869 | elif G2frame.plotStyle['dPlot']: #d - convert from 2-theta |
|---|
| 1870 | if Parms: |
|---|
| 1871 | x = G2lat.Dsp2pos(Parms,x) |
|---|
| 1872 | else: |
|---|
| 1873 | break |
|---|
| 1874 | Plot.plot(x,y,'rD',clip_on=False,picker=3.) |
|---|
| 1875 | if not newPlot: |
|---|
| 1876 | Page.toolbar.push_current() |
|---|
| 1877 | Plot.set_xlim(G2frame.xylim[0]) |
|---|
| 1878 | Plot.set_ylim(G2frame.xylim[1]) |
|---|
| 1879 | # xylim = [] |
|---|
| 1880 | Page.toolbar.push_current() |
|---|
| 1881 | Page.toolbar.draw() |
|---|
| 1882 | else: |
|---|
| 1883 | G2frame.xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 1884 | Page.canvas.draw() |
|---|
| 1885 | olderr = np.seterr(invalid='ignore') #ugh - this removes a matplotlib error for mouse clicks in log plots |
|---|
| 1886 | # and sqrt(-ve) in np.where usage |
|---|
| 1887 | # G2frame.Pwdr = True |
|---|
| 1888 | |
|---|
| 1889 | ################################################################################ |
|---|
| 1890 | ##### PlotDeltSig |
|---|
| 1891 | ################################################################################ |
|---|
| 1892 | |
|---|
| 1893 | def PlotDeltSig(G2frame,kind): |
|---|
| 1894 | 'needs a doc string' |
|---|
| 1895 | try: |
|---|
| 1896 | plotNum = G2frame.G2plotNB.plotList.index('Error analysis') |
|---|
| 1897 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1898 | Page.figure.clf() |
|---|
| 1899 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 1900 | except ValueError: |
|---|
| 1901 | newPlot = True |
|---|
| 1902 | G2frame.Cmax = 1.0 |
|---|
| 1903 | Plot = G2frame.G2plotNB.addMpl('Error analysis').gca() |
|---|
| 1904 | plotNum = G2frame.G2plotNB.plotList.index('Error analysis') |
|---|
| 1905 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 1906 | Page.Choice = None |
|---|
| 1907 | PatternId = G2frame.PatternId |
|---|
| 1908 | Pattern = G2frame.PatternTree.GetItemPyData(PatternId) |
|---|
| 1909 | Pattern.append(G2frame.PatternTree.GetItemText(PatternId)) |
|---|
| 1910 | wtFactor = Pattern[0]['wtFactor'] |
|---|
| 1911 | if kind == 'PWDR': |
|---|
| 1912 | limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits'))[1] |
|---|
| 1913 | xye = np.array(Pattern[1]) |
|---|
| 1914 | xmin = np.searchsorted(xye[0],limits[0]) |
|---|
| 1915 | xmax = np.searchsorted(xye[0],limits[1]) |
|---|
| 1916 | DS = xye[5][xmin:xmax]*np.sqrt(wtFactor*xye[2][xmin:xmax]) |
|---|
| 1917 | elif kind == 'HKLF': |
|---|
| 1918 | refl = Pattern[1]['RefList'] |
|---|
| 1919 | im = 0 |
|---|
| 1920 | if Pattern[1]['Super']: |
|---|
| 1921 | im = 1 |
|---|
| 1922 | DS = [] |
|---|
| 1923 | for ref in refl: |
|---|
| 1924 | if ref[6+im] > 0.: |
|---|
| 1925 | DS.append((ref[5+im]-ref[7+im])/ref[6+im]) |
|---|
| 1926 | Page.SetFocus() |
|---|
| 1927 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 1928 | DS.sort() |
|---|
| 1929 | EDS = np.zeros_like(DS) |
|---|
| 1930 | DX = np.linspace(0.,1.,num=len(DS),endpoint=True) |
|---|
| 1931 | oldErr = np.seterr(invalid='ignore') #avoid problem at DX==0 |
|---|
| 1932 | T = np.sqrt(np.log(1.0/DX**2)) |
|---|
| 1933 | top = 2.515517+0.802853*T+0.010328*T**2 |
|---|
| 1934 | bot = 1.0+1.432788*T+0.189269*T**2+0.001308*T**3 |
|---|
| 1935 | EDS = np.where(DX>0,-(T-top/bot),(T-top/bot)) |
|---|
| 1936 | low1 = np.searchsorted(EDS,-1.) |
|---|
| 1937 | hi1 = np.searchsorted(EDS,1.) |
|---|
| 1938 | slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1) |
|---|
| 1939 | frac = 100.*(hi1-low1)/len(DS) |
|---|
| 1940 | G2frame.G2plotNB.status.SetStatusText( \ |
|---|
| 1941 | 'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1) |
|---|
| 1942 | Plot.set_title('Normal probability for '+Pattern[-1]) |
|---|
| 1943 | Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14) |
|---|
| 1944 | Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14) |
|---|
| 1945 | Plot.plot(EDS,DS,'r+',label='result') |
|---|
| 1946 | Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal') |
|---|
| 1947 | Plot.legend(loc='upper left') |
|---|
| 1948 | np.seterr(invalid='warn') |
|---|
| 1949 | Page.canvas.draw() |
|---|
| 1950 | |
|---|
| 1951 | ################################################################################ |
|---|
| 1952 | ##### PlotISFG |
|---|
| 1953 | ################################################################################ |
|---|
| 1954 | |
|---|
| 1955 | def PlotISFG(G2frame,newPlot=False,type=''): |
|---|
| 1956 | ''' Plotting package for PDF analysis; displays I(q), S(q), F(q) and G(r) as single |
|---|
| 1957 | or multiple plots with waterfall and contour plots as options |
|---|
| 1958 | ''' |
|---|
| 1959 | if not type: |
|---|
| 1960 | type = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()] |
|---|
| 1961 | if type not in ['I(Q)','S(Q)','F(Q)','G(R)']: |
|---|
| 1962 | return |
|---|
| 1963 | superMinusOne = unichr(0xaf)+unichr(0xb9) |
|---|
| 1964 | |
|---|
| 1965 | def OnPlotKeyPress(event): |
|---|
| 1966 | newPlot = False |
|---|
| 1967 | if event.key == 'u': |
|---|
| 1968 | if G2frame.Contour: |
|---|
| 1969 | G2frame.Cmax = min(1.0,G2frame.Cmax*1.2) |
|---|
| 1970 | elif Pattern[0]['Offset'][0] < 100.: |
|---|
| 1971 | Pattern[0]['Offset'][0] += 1. |
|---|
| 1972 | elif event.key == 'd': |
|---|
| 1973 | if G2frame.Contour: |
|---|
| 1974 | G2frame.Cmax = max(0.0,G2frame.Cmax*0.8) |
|---|
| 1975 | elif Pattern[0]['Offset'][0] > 0.: |
|---|
| 1976 | Pattern[0]['Offset'][0] -= 1. |
|---|
| 1977 | elif event.key == 'l': |
|---|
| 1978 | Pattern[0]['Offset'][1] -= 1. |
|---|
| 1979 | elif event.key == 'r': |
|---|
| 1980 | Pattern[0]['Offset'][1] += 1. |
|---|
| 1981 | elif event.key == 'o': |
|---|
| 1982 | Pattern[0]['Offset'] = [0,0] |
|---|
| 1983 | elif event.key == 'c': |
|---|
| 1984 | newPlot = True |
|---|
| 1985 | G2frame.Contour = not G2frame.Contour |
|---|
| 1986 | if not G2frame.Contour: |
|---|
| 1987 | G2frame.SinglePlot = False |
|---|
| 1988 | Pattern[0]['Offset'] = [0.,0.] |
|---|
| 1989 | elif event.key == 's': |
|---|
| 1990 | if G2frame.Contour: |
|---|
| 1991 | choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")] |
|---|
| 1992 | choice.sort() |
|---|
| 1993 | dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) |
|---|
| 1994 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 1995 | sel = dlg.GetSelection() |
|---|
| 1996 | G2frame.ContourColor = choice[sel] |
|---|
| 1997 | else: |
|---|
| 1998 | G2frame.ContourColor = 'Paired' |
|---|
| 1999 | dlg.Destroy() |
|---|
| 2000 | else: |
|---|
| 2001 | G2frame.SinglePlot = not G2frame.SinglePlot |
|---|
| 2002 | elif event.key == 'i': #for smoothing contour plot |
|---|
| 2003 | choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning', |
|---|
| 2004 | 'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel', |
|---|
| 2005 | 'mitchell','sinc','lanczos'] |
|---|
| 2006 | dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice) |
|---|
| 2007 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 2008 | sel = dlg.GetSelection() |
|---|
| 2009 | G2frame.Interpolate = choice[sel] |
|---|
| 2010 | else: |
|---|
| 2011 | G2frame.Interpolate = 'nearest' |
|---|
| 2012 | dlg.Destroy() |
|---|
| 2013 | elif event.key == 't' and not G2frame.Contour: |
|---|
| 2014 | G2frame.Legend = not G2frame.Legend |
|---|
| 2015 | PlotISFG(G2frame,newPlot=newPlot,type=type) |
|---|
| 2016 | |
|---|
| 2017 | def OnKeyBox(event): |
|---|
| 2018 | if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index(type): |
|---|
| 2019 | event.key = cb.GetValue()[0] |
|---|
| 2020 | cb.SetValue(' key press') |
|---|
| 2021 | wx.CallAfter(OnPlotKeyPress,event) |
|---|
| 2022 | Page.canvas.SetFocus() # redirect the Focus from the button back to the plot |
|---|
| 2023 | |
|---|
| 2024 | def OnMotion(event): |
|---|
| 2025 | xpos = event.xdata |
|---|
| 2026 | if xpos: #avoid out of frame mouse position |
|---|
| 2027 | ypos = event.ydata |
|---|
| 2028 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2029 | try: |
|---|
| 2030 | if G2frame.Contour: |
|---|
| 2031 | G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1) |
|---|
| 2032 | else: |
|---|
| 2033 | G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,type,ypos),1) |
|---|
| 2034 | except TypeError: |
|---|
| 2035 | G2frame.G2plotNB.status.SetStatusText('Select '+type+' pattern first',1) |
|---|
| 2036 | |
|---|
| 2037 | xylim = [] |
|---|
| 2038 | try: |
|---|
| 2039 | plotNum = G2frame.G2plotNB.plotList.index(type) |
|---|
| 2040 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2041 | if not newPlot: |
|---|
| 2042 | Plot = Page.figure.gca() #get previous plot & get limits |
|---|
| 2043 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 2044 | Page.figure.clf() |
|---|
| 2045 | Plot = Page.figure.gca() |
|---|
| 2046 | except ValueError: |
|---|
| 2047 | newPlot = True |
|---|
| 2048 | G2frame.Cmax = 1.0 |
|---|
| 2049 | Plot = G2frame.G2plotNB.addMpl(type).gca() |
|---|
| 2050 | plotNum = G2frame.G2plotNB.plotList.index(type) |
|---|
| 2051 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2052 | Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) |
|---|
| 2053 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2054 | |
|---|
| 2055 | Page.SetFocus() |
|---|
| 2056 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 2057 | if G2frame.Contour: |
|---|
| 2058 | Page.Choice = (' key press','d: lower contour max','u: raise contour max', |
|---|
| 2059 | 'i: interpolation method','s: color scheme','c: contour off') |
|---|
| 2060 | else: |
|---|
| 2061 | Page.Choice = (' key press','l: offset left','r: offset right','d: offset down','u: offset up', |
|---|
| 2062 | 'o: reset offset','t: toggle legend','c: contour on','s: toggle single plot') |
|---|
| 2063 | Page.keyPress = OnPlotKeyPress |
|---|
| 2064 | PatternId = G2frame.PatternId |
|---|
| 2065 | PickId = G2frame.PickId |
|---|
| 2066 | Plot.set_title(type) |
|---|
| 2067 | if type == 'G(R)': |
|---|
| 2068 | Plot.set_xlabel(r'$R,\AA$',fontsize=14) |
|---|
| 2069 | else: |
|---|
| 2070 | Plot.set_xlabel(r'$Q,\AA$'+superMinusOne,fontsize=14) |
|---|
| 2071 | Plot.set_ylabel(r''+type,fontsize=14) |
|---|
| 2072 | colors=['b','g','r','c','m','k'] |
|---|
| 2073 | name = G2frame.PatternTree.GetItemText(PatternId)[4:] |
|---|
| 2074 | Pattern = [] |
|---|
| 2075 | if G2frame.SinglePlot: |
|---|
| 2076 | name = G2frame.PatternTree.GetItemText(PatternId) |
|---|
| 2077 | name = type+name[4:] |
|---|
| 2078 | Id = G2gd.GetPatternTreeItemId(G2frame,PatternId,name) |
|---|
| 2079 | Pattern = G2frame.PatternTree.GetItemPyData(Id) |
|---|
| 2080 | if Pattern: |
|---|
| 2081 | Pattern.append(name) |
|---|
| 2082 | PlotList = [Pattern,] |
|---|
| 2083 | else: |
|---|
| 2084 | PlotList = [] |
|---|
| 2085 | item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root) |
|---|
| 2086 | while item: |
|---|
| 2087 | if 'PDF' in G2frame.PatternTree.GetItemText(item): |
|---|
| 2088 | name = type+G2frame.PatternTree.GetItemText(item)[4:] |
|---|
| 2089 | Id = G2gd.GetPatternTreeItemId(G2frame,item,name) |
|---|
| 2090 | Pattern = G2frame.PatternTree.GetItemPyData(Id) |
|---|
| 2091 | if Pattern: |
|---|
| 2092 | Pattern.append(name) |
|---|
| 2093 | PlotList.append(Pattern) |
|---|
| 2094 | item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie) |
|---|
| 2095 | PDFdata = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'PDF Controls')) |
|---|
| 2096 | numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol']) |
|---|
| 2097 | Xb = [0.,10.] |
|---|
| 2098 | Yb = [0.,-40.*np.pi*numbDen] |
|---|
| 2099 | Ymax = 0.01 |
|---|
| 2100 | lenX = 0 |
|---|
| 2101 | for Pattern in PlotList: |
|---|
| 2102 | try: |
|---|
| 2103 | xye = Pattern[1] |
|---|
| 2104 | except IndexError: |
|---|
| 2105 | return |
|---|
| 2106 | Ymax = max(Ymax,max(xye[1])) |
|---|
| 2107 | offset = Pattern[0]['Offset'][0]*Ymax/100.0 |
|---|
| 2108 | if G2frame.Contour: |
|---|
| 2109 | ContourZ = [] |
|---|
| 2110 | ContourY = [] |
|---|
| 2111 | Nseq = 0 |
|---|
| 2112 | for N,Pattern in enumerate(PlotList): |
|---|
| 2113 | xye = Pattern[1] |
|---|
| 2114 | if PickId: |
|---|
| 2115 | ifpicked = Pattern[2] == G2frame.PatternTree.GetItemText(PatternId) |
|---|
| 2116 | X = xye[0] |
|---|
| 2117 | if not lenX: |
|---|
| 2118 | lenX = len(X) |
|---|
| 2119 | Y = xye[1]+offset*N |
|---|
| 2120 | if G2frame.Contour: |
|---|
| 2121 | if lenX == len(X): |
|---|
| 2122 | ContourY.append(N) |
|---|
| 2123 | ContourZ.append(Y) |
|---|
| 2124 | ContourX = X |
|---|
| 2125 | Nseq += 1 |
|---|
| 2126 | Plot.set_ylabel('Data sequence',fontsize=12) |
|---|
| 2127 | else: |
|---|
| 2128 | X = xye[0]+Pattern[0]['Offset'][1]*.005*N |
|---|
| 2129 | if ifpicked: |
|---|
| 2130 | Plot.plot(X,Y,colors[N%6]+'+',picker=3.,clip_on=False) |
|---|
| 2131 | Page.canvas.SetToolTipString('') |
|---|
| 2132 | else: |
|---|
| 2133 | if G2frame.Legend: |
|---|
| 2134 | Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1]) |
|---|
| 2135 | else: |
|---|
| 2136 | Plot.plot(X,Y,colors[N%6],picker=False) |
|---|
| 2137 | if type == 'G(R)': |
|---|
| 2138 | Plot.plot(Xb,Yb,color='k',dashes=(5,5)) |
|---|
| 2139 | elif type == 'F(Q)': |
|---|
| 2140 | Plot.axhline(0.,color=wx.BLACK) |
|---|
| 2141 | elif type == 'S(Q)': |
|---|
| 2142 | Plot.axhline(1.,color=wx.BLACK) |
|---|
| 2143 | if G2frame.Contour: |
|---|
| 2144 | acolor = mpl.cm.get_cmap(G2frame.ContourColor) |
|---|
| 2145 | Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate, |
|---|
| 2146 | extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower') |
|---|
| 2147 | Page.figure.colorbar(Img) |
|---|
| 2148 | elif G2frame.Legend: |
|---|
| 2149 | Plot.legend(loc='best') |
|---|
| 2150 | if not newPlot: |
|---|
| 2151 | Page.toolbar.push_current() |
|---|
| 2152 | Plot.set_xlim(xylim[0]) |
|---|
| 2153 | Plot.set_ylim(xylim[1]) |
|---|
| 2154 | xylim = [] |
|---|
| 2155 | Page.toolbar.push_current() |
|---|
| 2156 | Page.toolbar.draw() |
|---|
| 2157 | else: |
|---|
| 2158 | Page.canvas.draw() |
|---|
| 2159 | |
|---|
| 2160 | ################################################################################ |
|---|
| 2161 | ##### PlotCalib |
|---|
| 2162 | ################################################################################ |
|---|
| 2163 | |
|---|
| 2164 | def PlotCalib(G2frame,Inst,XY,Sigs,newPlot=False): |
|---|
| 2165 | '''plot of CW or TOF peak calibration |
|---|
| 2166 | ''' |
|---|
| 2167 | def OnMotion(event): |
|---|
| 2168 | xpos = event.xdata |
|---|
| 2169 | if xpos: #avoid out of frame mouse position |
|---|
| 2170 | ypos = event.ydata |
|---|
| 2171 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2172 | try: |
|---|
| 2173 | G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3g'%(xpos,Title,ypos),1) |
|---|
| 2174 | except TypeError: |
|---|
| 2175 | G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1) |
|---|
| 2176 | found = [] |
|---|
| 2177 | wid = 1 |
|---|
| 2178 | view = Page.toolbar._views.forward() |
|---|
| 2179 | if view: |
|---|
| 2180 | view = view[0][:2] |
|---|
| 2181 | wid = view[1]-view[0] |
|---|
| 2182 | found = XY[np.where(np.fabs(XY.T[0]-xpos) < 0.005*wid)] |
|---|
| 2183 | if len(found): |
|---|
| 2184 | pos = found[0][1] |
|---|
| 2185 | if 'C' in Inst['Type'][0]: |
|---|
| 2186 | Page.canvas.SetToolTipString('position=%.4f'%(pos)) |
|---|
| 2187 | else: |
|---|
| 2188 | Page.canvas.SetToolTipString('position=%.2f'%(pos)) |
|---|
| 2189 | else: |
|---|
| 2190 | Page.canvas.SetToolTipString('') |
|---|
| 2191 | |
|---|
| 2192 | Title = 'Position calibration' |
|---|
| 2193 | try: |
|---|
| 2194 | plotNum = G2frame.G2plotNB.plotList.index(Title) |
|---|
| 2195 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2196 | if not newPlot: |
|---|
| 2197 | Plot = Page.figure.gca() |
|---|
| 2198 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 2199 | Page.figure.clf() |
|---|
| 2200 | Plot = Page.figure.gca() |
|---|
| 2201 | except ValueError: |
|---|
| 2202 | newPlot = True |
|---|
| 2203 | Plot = G2frame.G2plotNB.addMpl(Title).gca() |
|---|
| 2204 | plotNum = G2frame.G2plotNB.plotList.index(Title) |
|---|
| 2205 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2206 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2207 | |
|---|
| 2208 | Page.Choice = None |
|---|
| 2209 | Page.SetFocus() |
|---|
| 2210 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 2211 | Plot.set_title(Title) |
|---|
| 2212 | Plot.set_xlabel(r'd-spacing',fontsize=14) |
|---|
| 2213 | if 'C' in Inst['Type'][0]: |
|---|
| 2214 | Plot.set_ylabel(r'$\mathsf{\Delta(2\theta)}$',fontsize=14) |
|---|
| 2215 | else: |
|---|
| 2216 | Plot.set_ylabel(r'$\mathsf{\Delta}T/T$',fontsize=14) |
|---|
| 2217 | for ixy,xyw in enumerate(XY): |
|---|
| 2218 | if len(xyw) > 2: |
|---|
| 2219 | X,Y,W = xyw |
|---|
| 2220 | else: |
|---|
| 2221 | X,Y = xyw |
|---|
| 2222 | W = 0. |
|---|
| 2223 | Yc = G2lat.Dsp2pos(Inst,X) |
|---|
| 2224 | if 'C' in Inst['Type'][0]: |
|---|
| 2225 | Y = Y-Yc |
|---|
| 2226 | E = Sigs[ixy] |
|---|
| 2227 | bin = W/2. |
|---|
| 2228 | else: |
|---|
| 2229 | Y = (Y-Yc)/Yc |
|---|
| 2230 | E = Sigs[ixy]/Yc |
|---|
| 2231 | bin = W/(2.*Yc) |
|---|
| 2232 | if E: |
|---|
| 2233 | Plot.errorbar(X,Y,ecolor='k',yerr=E) |
|---|
| 2234 | if ixy: |
|---|
| 2235 | Plot.plot(X,Y,'kx',picker=3) |
|---|
| 2236 | else: |
|---|
| 2237 | Plot.plot(X,Y,'kx',label='peak') |
|---|
| 2238 | if W: |
|---|
| 2239 | if ixy: |
|---|
| 2240 | Plot.plot(X,bin,'b+') |
|---|
| 2241 | else: |
|---|
| 2242 | Plot.plot(X,bin,'b+',label='bin width') |
|---|
| 2243 | Plot.plot(X,-bin,'b+') |
|---|
| 2244 | Plot.axhline(0.,color='r',linestyle='--') |
|---|
| 2245 | Plot.legend(loc='best') |
|---|
| 2246 | if not newPlot: |
|---|
| 2247 | Page.toolbar.push_current() |
|---|
| 2248 | Plot.set_xlim(xylim[0]) |
|---|
| 2249 | Plot.set_ylim(xylim[1]) |
|---|
| 2250 | # xylim = [] |
|---|
| 2251 | Page.toolbar.push_current() |
|---|
| 2252 | Page.toolbar.draw() |
|---|
| 2253 | else: |
|---|
| 2254 | Page.canvas.draw() |
|---|
| 2255 | |
|---|
| 2256 | ################################################################################ |
|---|
| 2257 | ##### PlotXY |
|---|
| 2258 | ################################################################################ |
|---|
| 2259 | |
|---|
| 2260 | def PlotXY(G2frame,XY,XY2=None,labelX=None,labelY=None,newPlot=False,Title=''): |
|---|
| 2261 | '''simple plot of xy data, used for diagnostic purposes |
|---|
| 2262 | ''' |
|---|
| 2263 | def OnMotion(event): |
|---|
| 2264 | xpos = event.xdata |
|---|
| 2265 | if xpos: #avoid out of frame mouse position |
|---|
| 2266 | ypos = event.ydata |
|---|
| 2267 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2268 | try: |
|---|
| 2269 | G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,Title,ypos),1) |
|---|
| 2270 | except TypeError: |
|---|
| 2271 | G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1) |
|---|
| 2272 | |
|---|
| 2273 | try: |
|---|
| 2274 | plotNum = G2frame.G2plotNB.plotList.index(Title) |
|---|
| 2275 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2276 | if not newPlot: |
|---|
| 2277 | Plot = Page.figure.gca() |
|---|
| 2278 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 2279 | Page.figure.clf() |
|---|
| 2280 | Plot = Page.figure.gca() |
|---|
| 2281 | except ValueError: |
|---|
| 2282 | newPlot = True |
|---|
| 2283 | Plot = G2frame.G2plotNB.addMpl(Title).gca() |
|---|
| 2284 | plotNum = G2frame.G2plotNB.plotList.index(Title) |
|---|
| 2285 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2286 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2287 | |
|---|
| 2288 | Page.Choice = None |
|---|
| 2289 | Page.SetFocus() |
|---|
| 2290 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 2291 | Plot.set_title(Title) |
|---|
| 2292 | if labelX: |
|---|
| 2293 | Plot.set_xlabel(r''+labelX,fontsize=14) |
|---|
| 2294 | else: |
|---|
| 2295 | Plot.set_xlabel(r'X',fontsize=14) |
|---|
| 2296 | if labelY: |
|---|
| 2297 | Plot.set_ylabel(r''+labelY,fontsize=14) |
|---|
| 2298 | else: |
|---|
| 2299 | Plot.set_ylabel(r'Y',fontsize=14) |
|---|
| 2300 | colors=['b','g','r','c','m','k'] |
|---|
| 2301 | for ixy,xy in enumerate(XY): |
|---|
| 2302 | X,Y = xy |
|---|
| 2303 | Plot.plot(X,Y,colors[ixy%6]+'+',picker=False) |
|---|
| 2304 | if len(XY2): |
|---|
| 2305 | for ixy,xy in enumerate(XY2): |
|---|
| 2306 | X,Y = xy |
|---|
| 2307 | Plot.plot(X,Y,colors[ixy%6],picker=False) |
|---|
| 2308 | if not newPlot: |
|---|
| 2309 | Page.toolbar.push_current() |
|---|
| 2310 | Plot.set_xlim(xylim[0]) |
|---|
| 2311 | Plot.set_ylim(xylim[1]) |
|---|
| 2312 | xylim = [] |
|---|
| 2313 | Page.toolbar.push_current() |
|---|
| 2314 | Page.toolbar.draw() |
|---|
| 2315 | else: |
|---|
| 2316 | Page.canvas.draw() |
|---|
| 2317 | |
|---|
| 2318 | ################################################################################ |
|---|
| 2319 | ##### PlotStrain |
|---|
| 2320 | ################################################################################ |
|---|
| 2321 | |
|---|
| 2322 | def PlotStrain(G2frame,data,newPlot=False): |
|---|
| 2323 | '''plot of strain data, used for diagnostic purposes |
|---|
| 2324 | ''' |
|---|
| 2325 | def OnMotion(event): |
|---|
| 2326 | xpos = event.xdata |
|---|
| 2327 | if xpos: #avoid out of frame mouse position |
|---|
| 2328 | ypos = event.ydata |
|---|
| 2329 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2330 | try: |
|---|
| 2331 | G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1) |
|---|
| 2332 | except TypeError: |
|---|
| 2333 | G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1) |
|---|
| 2334 | |
|---|
| 2335 | try: |
|---|
| 2336 | plotNum = G2frame.G2plotNB.plotList.index('Strain') |
|---|
| 2337 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2338 | if not newPlot: |
|---|
| 2339 | Plot = Page.figure.gca() |
|---|
| 2340 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 2341 | Page.figure.clf() |
|---|
| 2342 | Plot = Page.figure.gca() |
|---|
| 2343 | except ValueError: |
|---|
| 2344 | newPlot = True |
|---|
| 2345 | Plot = G2frame.G2plotNB.addMpl('Strain').gca() |
|---|
| 2346 | plotNum = G2frame.G2plotNB.plotList.index('Strain') |
|---|
| 2347 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2348 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2349 | |
|---|
| 2350 | Page.Choice = None |
|---|
| 2351 | Page.SetFocus() |
|---|
| 2352 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 2353 | Plot.set_title('Strain') |
|---|
| 2354 | Plot.set_ylabel(r'd-spacing',fontsize=14) |
|---|
| 2355 | Plot.set_xlabel(r'Azimuth',fontsize=14) |
|---|
| 2356 | colors=['b','g','r','c','m','k'] |
|---|
| 2357 | for N,item in enumerate(data['d-zero']): |
|---|
| 2358 | Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y |
|---|
| 2359 | Plot.plot(X,Y,colors[N%6]+'+',picker=False) |
|---|
| 2360 | Y,X = np.array(item['ImtaCalc']) |
|---|
| 2361 | Plot.plot(X,Y,colors[N%6],picker=False) |
|---|
| 2362 | if not newPlot: |
|---|
| 2363 | Page.toolbar.push_current() |
|---|
| 2364 | Plot.set_xlim(xylim[0]) |
|---|
| 2365 | Plot.set_ylim(xylim[1]) |
|---|
| 2366 | xylim = [] |
|---|
| 2367 | Page.toolbar.push_current() |
|---|
| 2368 | Page.toolbar.draw() |
|---|
| 2369 | else: |
|---|
| 2370 | Page.canvas.draw() |
|---|
| 2371 | |
|---|
| 2372 | ################################################################################ |
|---|
| 2373 | ##### PlotSASDSizeDist |
|---|
| 2374 | ################################################################################ |
|---|
| 2375 | |
|---|
| 2376 | def PlotSASDSizeDist(G2frame): |
|---|
| 2377 | |
|---|
| 2378 | def OnPageChanged(event): |
|---|
| 2379 | PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection()) |
|---|
| 2380 | if 'Powder' in PlotText: |
|---|
| 2381 | PlotPatterns(G2frame,plotType='SASD',newPlot=True) |
|---|
| 2382 | elif 'Size' in PlotText: |
|---|
| 2383 | PlotSASDSizeDist(G2frame) |
|---|
| 2384 | |
|---|
| 2385 | def OnMotion(event): |
|---|
| 2386 | xpos = event.xdata |
|---|
| 2387 | if xpos: #avoid out of frame mouse position |
|---|
| 2388 | ypos = event.ydata |
|---|
| 2389 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2390 | try: |
|---|
| 2391 | G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1) |
|---|
| 2392 | except TypeError: |
|---|
| 2393 | G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1) |
|---|
| 2394 | |
|---|
| 2395 | try: |
|---|
| 2396 | plotNum = G2frame.G2plotNB.plotList.index('Size Distribution') |
|---|
| 2397 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2398 | Page.figure.clf() |
|---|
| 2399 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 2400 | except ValueError: |
|---|
| 2401 | newPlot = True |
|---|
| 2402 | Plot = G2frame.G2plotNB.addMpl('Size Distribution').gca() |
|---|
| 2403 | G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged) |
|---|
| 2404 | plotNum = G2frame.G2plotNB.plotList.index('Size Distribution') |
|---|
| 2405 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2406 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2407 | Page.Choice = None |
|---|
| 2408 | Page.SetFocus() |
|---|
| 2409 | PatternId = G2frame.PatternId |
|---|
| 2410 | data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Models')) |
|---|
| 2411 | Bins,Dbins,BinMag = data['Size']['Distribution'] |
|---|
| 2412 | Plot.set_title('Size Distribution') |
|---|
| 2413 | Plot.set_xlabel(r'$D, \AA$',fontsize=14) |
|---|
| 2414 | Plot.set_ylabel(r'$Volume distribution f(D)$',fontsize=14) |
|---|
| 2415 | if data['Size']['logBins']: |
|---|
| 2416 | Plot.set_xscale("log",nonposy='mask') |
|---|
| 2417 | Plot.set_xlim([np.min(2.*Bins)/2.,np.max(2.*Bins)*2.]) |
|---|
| 2418 | Plot.bar(2.*Bins-Dbins,BinMag,2.*Dbins,facecolor='white') #plot diameters |
|---|
| 2419 | if 'Size Calc' in data: |
|---|
| 2420 | Rbins,Dist = data['Size Calc'] |
|---|
| 2421 | for i in range(len(Rbins)): |
|---|
| 2422 | if len(Rbins[i]): |
|---|
| 2423 | Plot.plot(2.*Rbins[i],Dist[i]) #plot diameters |
|---|
| 2424 | Page.canvas.draw() |
|---|
| 2425 | |
|---|
| 2426 | ################################################################################ |
|---|
| 2427 | ##### PlotPowderLines |
|---|
| 2428 | ################################################################################ |
|---|
| 2429 | |
|---|
| 2430 | def PlotPowderLines(G2frame): |
|---|
| 2431 | ''' plotting of powder lines (i.e. no powder pattern) as sticks |
|---|
| 2432 | ''' |
|---|
| 2433 | |
|---|
| 2434 | def OnMotion(event): |
|---|
| 2435 | xpos = event.xdata |
|---|
| 2436 | if xpos: #avoid out of frame mouse position |
|---|
| 2437 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2438 | G2frame.G2plotNB.status.SetFields(['','2-theta =%9.3f '%(xpos,)]) |
|---|
| 2439 | if G2frame.PickId and G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']: |
|---|
| 2440 | found = [] |
|---|
| 2441 | if len(G2frame.HKL): |
|---|
| 2442 | view = Page.toolbar._views.forward()[0][:2] |
|---|
| 2443 | wid = view[1]-view[0] |
|---|
| 2444 | found = G2frame.HKL[np.where(np.fabs(G2frame.HKL.T[-1]-xpos) < 0.002*wid)] |
|---|
| 2445 | if len(found): |
|---|
| 2446 | h,k,l = found[0][:3] |
|---|
| 2447 | Page.canvas.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l))) |
|---|
| 2448 | else: |
|---|
| 2449 | Page.canvas.SetToolTipString('') |
|---|
| 2450 | |
|---|
| 2451 | try: |
|---|
| 2452 | plotNum = G2frame.G2plotNB.plotList.index('Powder Lines') |
|---|
| 2453 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2454 | Page.figure.clf() |
|---|
| 2455 | Plot = Page.figure.gca() |
|---|
| 2456 | except ValueError: |
|---|
| 2457 | Plot = G2frame.G2plotNB.addMpl('Powder Lines').gca() |
|---|
| 2458 | plotNum = G2frame.G2plotNB.plotList.index('Powder Lines') |
|---|
| 2459 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2460 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2461 | |
|---|
| 2462 | Page.Choice = None |
|---|
| 2463 | Page.SetFocus() |
|---|
| 2464 | Plot.set_title('Powder Pattern Lines') |
|---|
| 2465 | Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14) |
|---|
| 2466 | PickId = G2frame.PickId |
|---|
| 2467 | PatternId = G2frame.PatternId |
|---|
| 2468 | peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))[0] |
|---|
| 2469 | for peak in peaks: |
|---|
| 2470 | Plot.axvline(peak[0],color='b') |
|---|
| 2471 | for hkl in G2frame.HKL: |
|---|
| 2472 | Plot.axvline(hkl[-1],color='r',dashes=(5,5)) |
|---|
| 2473 | xmin = peaks[0][0] |
|---|
| 2474 | xmax = peaks[-1][0] |
|---|
| 2475 | delt = xmax-xmin |
|---|
| 2476 | xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)] |
|---|
| 2477 | Plot.set_xlim(xlim) |
|---|
| 2478 | Page.canvas.draw() |
|---|
| 2479 | Page.toolbar.push_current() |
|---|
| 2480 | |
|---|
| 2481 | ################################################################################ |
|---|
| 2482 | ##### PlotPeakWidths |
|---|
| 2483 | ################################################################################ |
|---|
| 2484 | |
|---|
| 2485 | def PlotPeakWidths(G2frame): |
|---|
| 2486 | ''' Plotting of instrument broadening terms as function of 2-theta |
|---|
| 2487 | Seen when "Instrument Parameters" chosen from powder pattern data tree |
|---|
| 2488 | ''' |
|---|
| 2489 | # sig = lambda Th,U,V,W: 1.17741*math.sqrt(U*tand(Th)**2+V*tand(Th)+W)*math.pi/18000. |
|---|
| 2490 | # gam = lambda Th,X,Y: (X/cosd(Th)+Y*tand(Th))*math.pi/18000. |
|---|
| 2491 | # gamFW = lambda s,g: np.exp(np.log(s**5+2.69269*s**4*g+2.42843*s**3*g**2+4.47163*s**2*g**3+0.07842*s*g**4+g**5)/5.) |
|---|
| 2492 | # gamFW2 = lambda s,g: math.sqrt(s**2+(0.4654996*g)**2)+.5345004*g #Ubaldo Bafile - private communication |
|---|
| 2493 | PatternId = G2frame.PatternId |
|---|
| 2494 | limitID = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits') |
|---|
| 2495 | if limitID: |
|---|
| 2496 | limits = G2frame.PatternTree.GetItemPyData(limitID)[:2] |
|---|
| 2497 | else: |
|---|
| 2498 | return |
|---|
| 2499 | Parms,Parms2 = G2frame.PatternTree.GetItemPyData( \ |
|---|
| 2500 | G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters')) |
|---|
| 2501 | if 'C' in Parms['Type'][0]: |
|---|
| 2502 | lam = G2mth.getWave(Parms) |
|---|
| 2503 | else: |
|---|
| 2504 | difC = Parms['difC'][0] |
|---|
| 2505 | try: # PATCH: deal with older peak lists, before changed to dict to implement TOF |
|---|
| 2506 | peaks = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List'))['peaks'] |
|---|
| 2507 | except TypeError: |
|---|
| 2508 | print "Your peak list needs reformatting...", |
|---|
| 2509 | item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Peak List') |
|---|
| 2510 | G2frame.PatternTree.SelectItem(item) |
|---|
| 2511 | item = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters') |
|---|
| 2512 | G2frame.PatternTree.SelectItem(item) |
|---|
| 2513 | print "done" |
|---|
| 2514 | return |
|---|
| 2515 | try: |
|---|
| 2516 | plotNum = G2frame.G2plotNB.plotList.index('Peak Widths') |
|---|
| 2517 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2518 | Page.figure.clf() |
|---|
| 2519 | Plot = Page.figure.gca() |
|---|
| 2520 | except ValueError: |
|---|
| 2521 | Plot = G2frame.G2plotNB.addMpl('Peak Widths').gca() |
|---|
| 2522 | plotNum = G2frame.G2plotNB.plotList.index('Peak Widths') |
|---|
| 2523 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2524 | Page.Choice = None |
|---|
| 2525 | Page.SetFocus() |
|---|
| 2526 | |
|---|
| 2527 | Page.canvas.SetToolTipString('') |
|---|
| 2528 | colors=['b','g','r','c','m','k'] |
|---|
| 2529 | X = [] |
|---|
| 2530 | Y = [] |
|---|
| 2531 | Z = [] |
|---|
| 2532 | W = [] |
|---|
| 2533 | if 'C' in Parms['Type'][0]: |
|---|
| 2534 | Plot.set_title('Instrument and sample peak widths') |
|---|
| 2535 | Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14) |
|---|
| 2536 | Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14) |
|---|
| 2537 | try: |
|---|
| 2538 | Xmin,Xmax = limits[1] |
|---|
| 2539 | X = np.linspace(Xmin,Xmax,num=101,endpoint=True) |
|---|
| 2540 | Q = 4.*np.pi*npsind(X/2.)/lam |
|---|
| 2541 | Z = np.ones_like(X) |
|---|
| 2542 | data = G2mth.setPeakparms(Parms,Parms2,X,Z) |
|---|
| 2543 | s = 1.17741*np.sqrt(data[4])*np.pi/18000. |
|---|
| 2544 | g = data[6]*np.pi/18000. |
|---|
| 2545 | G = G2pwd.getgamFW(g,s) |
|---|
| 2546 | Y = s/nptand(X/2.) |
|---|
| 2547 | Z = g/nptand(X/2.) |
|---|
| 2548 | W = G/nptand(X/2.) |
|---|
| 2549 | Plot.plot(Q,Y,color='r',label='Gaussian') |
|---|
| 2550 | Plot.plot(Q,Z,color='g',label='Lorentzian') |
|---|
| 2551 | Plot.plot(Q,W,color='b',label='G+L') |
|---|
| 2552 | |
|---|
| 2553 | fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True) |
|---|
| 2554 | sf = 1.17741*np.sqrt(fit[4])*np.pi/18000. |
|---|
| 2555 | gf = fit[6]*np.pi/18000. |
|---|
| 2556 | Gf = G2pwd.getgamFW(gf,sf) |
|---|
| 2557 | Yf = sf/nptand(X/2.) |
|---|
| 2558 | Zf = gf/nptand(X/2.) |
|---|
| 2559 | Wf = Gf/nptand(X/2.) |
|---|
| 2560 | Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit') |
|---|
| 2561 | Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit') |
|---|
| 2562 | Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit') |
|---|
| 2563 | |
|---|
| 2564 | X = [] |
|---|
| 2565 | Y = [] |
|---|
| 2566 | Z = [] |
|---|
| 2567 | W = [] |
|---|
| 2568 | V = [] |
|---|
| 2569 | for peak in peaks: |
|---|
| 2570 | X.append(4.0*math.pi*sind(peak[0]/2.0)/lam) |
|---|
| 2571 | try: |
|---|
| 2572 | s = 1.17741*math.sqrt(peak[4])*math.pi/18000. |
|---|
| 2573 | except ValueError: |
|---|
| 2574 | s = 0.01 |
|---|
| 2575 | g = peak[6]*math.pi/18000. |
|---|
| 2576 | G = G2pwd.getgamFW(g,s) |
|---|
| 2577 | Y.append(s/tand(peak[0]/2.)) |
|---|
| 2578 | Z.append(g/tand(peak[0]/2.)) |
|---|
| 2579 | W.append(G/tand(peak[0]/2.)) |
|---|
| 2580 | if len(peaks): |
|---|
| 2581 | Plot.plot(X,Y,'+',color='r',label='G peak') |
|---|
| 2582 | Plot.plot(X,Z,'+',color='g',label='L peak') |
|---|
| 2583 | Plot.plot(X,W,'+',color='b',label='G+L peak') |
|---|
| 2584 | Plot.legend(loc='best') |
|---|
| 2585 | Page.canvas.draw() |
|---|
| 2586 | except ValueError: |
|---|
| 2587 | print '**** ERROR - default U,V,W profile coefficients yield sqrt of negative value at 2theta =', \ |
|---|
| 2588 | '%.3f'%(2*theta) |
|---|
| 2589 | G2frame.G2plotNB.Delete('Peak Widths') |
|---|
| 2590 | else: #'T'OF |
|---|
| 2591 | Plot.set_title('Instrument and sample peak coefficients') |
|---|
| 2592 | Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14) |
|---|
| 2593 | Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14) |
|---|
| 2594 | Xmin,Xmax = limits[1] |
|---|
| 2595 | T = np.linspace(Xmin,Xmax,num=101,endpoint=True) |
|---|
| 2596 | Z = np.ones_like(T) |
|---|
| 2597 | data = G2mth.setPeakparms(Parms,Parms2,T,Z) |
|---|
| 2598 | ds = T/difC |
|---|
| 2599 | Q = 2.*np.pi/ds |
|---|
| 2600 | A = data[4] |
|---|
| 2601 | B = data[6] |
|---|
| 2602 | S = 1.17741*np.sqrt(data[8])/T |
|---|
| 2603 | G = data[10]/T |
|---|
| 2604 | Plot.plot(Q,A,color='r',label='Alpha') |
|---|
| 2605 | Plot.plot(Q,B,color='g',label='Beta') |
|---|
| 2606 | Plot.plot(Q,S,color='b',label='Gaussian') |
|---|
| 2607 | Plot.plot(Q,G,color='m',label='Lorentzian') |
|---|
| 2608 | |
|---|
| 2609 | fit = G2mth.setPeakparms(Parms,Parms2,T,Z) |
|---|
| 2610 | ds = T/difC |
|---|
| 2611 | Q = 2.*np.pi/ds |
|---|
| 2612 | Af = fit[4] |
|---|
| 2613 | Bf = fit[6] |
|---|
| 2614 | Sf = 1.17741*np.sqrt(fit[8])/T |
|---|
| 2615 | Gf = fit[10]/T |
|---|
| 2616 | Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit') |
|---|
| 2617 | Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit') |
|---|
| 2618 | Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit') |
|---|
| 2619 | Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit') |
|---|
| 2620 | |
|---|
| 2621 | T = [] |
|---|
| 2622 | A = [] |
|---|
| 2623 | B = [] |
|---|
| 2624 | S = [] |
|---|
| 2625 | G = [] |
|---|
| 2626 | W = [] |
|---|
| 2627 | Q = [] |
|---|
| 2628 | V = [] |
|---|
| 2629 | for peak in peaks: |
|---|
| 2630 | T.append(peak[0]) |
|---|
| 2631 | A.append(peak[4]) |
|---|
| 2632 | B.append(peak[6]) |
|---|
| 2633 | Q.append(2.*np.pi*difC/peak[0]) |
|---|
| 2634 | S.append(1.17741*np.sqrt(peak[8])/peak[0]) |
|---|
| 2635 | G.append(peak[10]/peak[0]) |
|---|
| 2636 | |
|---|
| 2637 | |
|---|
| 2638 | Plot.plot(Q,A,'+',color='r',label='Alpha peak') |
|---|
| 2639 | Plot.plot(Q,B,'+',color='g',label='Beta peak') |
|---|
| 2640 | Plot.plot(Q,S,'+',color='b',label='Gaussian peak') |
|---|
| 2641 | Plot.plot(Q,G,'+',color='m',label='Lorentzian peak') |
|---|
| 2642 | Plot.legend(loc='best') |
|---|
| 2643 | Page.canvas.draw() |
|---|
| 2644 | |
|---|
| 2645 | |
|---|
| 2646 | ################################################################################ |
|---|
| 2647 | ##### PlotSizeStrainPO |
|---|
| 2648 | ################################################################################ |
|---|
| 2649 | |
|---|
| 2650 | def PlotSizeStrainPO(G2frame,data,hist='',Start=False): |
|---|
| 2651 | '''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase |
|---|
| 2652 | ''' |
|---|
| 2653 | |
|---|
| 2654 | PatternId = G2frame.PatternId |
|---|
| 2655 | generalData = data['General'] |
|---|
| 2656 | SGData = generalData['SGData'] |
|---|
| 2657 | SGLaue = SGData['SGLaue'] |
|---|
| 2658 | if Start: #initialize the spherical harmonics qlmn arrays |
|---|
| 2659 | ptx.pyqlmninit() |
|---|
| 2660 | Start = False |
|---|
| 2661 | # MuStrKeys = G2spc.MustrainNames(SGData) |
|---|
| 2662 | cell = generalData['Cell'][1:] |
|---|
| 2663 | A,B = G2lat.cell2AB(cell[:6]) |
|---|
| 2664 | Vol = cell[6] |
|---|
| 2665 | useList = data['Histograms'] |
|---|
| 2666 | phase = generalData['Name'] |
|---|
| 2667 | plotType = generalData['Data plot type'] |
|---|
| 2668 | plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'} |
|---|
| 2669 | for ptype in plotDict: |
|---|
| 2670 | G2frame.G2plotNB.Delete(ptype) |
|---|
| 2671 | if plotType in ['None'] or not useList: |
|---|
| 2672 | return |
|---|
| 2673 | if hist == '': |
|---|
| 2674 | hist = useList.keys()[0] |
|---|
| 2675 | numPlots = len(useList) |
|---|
| 2676 | |
|---|
| 2677 | try: |
|---|
| 2678 | plotNum = G2frame.G2plotNB.plotList.index(plotType) |
|---|
| 2679 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2680 | Page.figure.clf() |
|---|
| 2681 | Plot = Page.figure.gca() |
|---|
| 2682 | if not Page.IsShown(): |
|---|
| 2683 | Page.Show() |
|---|
| 2684 | except ValueError: |
|---|
| 2685 | if plotType in ['Mustrain','Size']: |
|---|
| 2686 | Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D(plotType)) |
|---|
| 2687 | else: |
|---|
| 2688 | Plot = G2frame.G2plotNB.addMpl(plotType).gca() |
|---|
| 2689 | plotNum = G2frame.G2plotNB.plotList.index(plotType) |
|---|
| 2690 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2691 | Page.Choice = None |
|---|
| 2692 | G2frame.G2plotNB.status.SetStatusText('',1) |
|---|
| 2693 | |
|---|
| 2694 | PHI = np.linspace(0.,360.,30,True) |
|---|
| 2695 | PSI = np.linspace(0.,180.,30,True) |
|---|
| 2696 | X = np.outer(npsind(PHI),npsind(PSI)) |
|---|
| 2697 | Y = np.outer(npcosd(PHI),npsind(PSI)) |
|---|
| 2698 | Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI)) |
|---|
| 2699 | try: #temp patch instead of 'mustrain' for old files with 'microstrain' |
|---|
| 2700 | coeff = useList[hist][plotDict[plotType]] |
|---|
| 2701 | except KeyError: |
|---|
| 2702 | return |
|---|
| 2703 | if plotType in ['Mustrain','Size']: |
|---|
| 2704 | if coeff[0] == 'isotropic': |
|---|
| 2705 | X *= coeff[1][0] |
|---|
| 2706 | Y *= coeff[1][0] |
|---|
| 2707 | Z *= coeff[1][0] |
|---|
| 2708 | elif coeff[0] == 'uniaxial': |
|---|
| 2709 | |
|---|
| 2710 | def uniaxCalc(xyz,iso,aniso,axes): |
|---|
| 2711 | Z = np.array(axes) |
|---|
| 2712 | cp = abs(np.dot(xyz,Z)) |
|---|
| 2713 | sp = np.sqrt(1.-cp**2) |
|---|
| 2714 | R = iso*aniso/np.sqrt((iso*cp)**2+(aniso*sp)**2) |
|---|
| 2715 | return R*xyz |
|---|
| 2716 | |
|---|
| 2717 | iso,aniso = coeff[1][:2] |
|---|
| 2718 | axes = np.inner(A,np.array(coeff[3])) |
|---|
| 2719 | axes /= nl.norm(axes) |
|---|
| 2720 | Shkl = np.array(coeff[1]) |
|---|
| 2721 | XYZ = np.dstack((X,Y,Z)) |
|---|
| 2722 | XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes)) |
|---|
| 2723 | X,Y,Z = np.dsplit(XYZ,3) |
|---|
| 2724 | X = X[:,:,0] |
|---|
| 2725 | Y = Y[:,:,0] |
|---|
| 2726 | Z = Z[:,:,0] |
|---|
| 2727 | |
|---|
| 2728 | elif coeff[0] == 'ellipsoidal': |
|---|
| 2729 | |
|---|
| 2730 | def ellipseCalc(xyz,E,R): |
|---|
| 2731 | XYZ = xyz*E.T |
|---|
| 2732 | return np.inner(XYZ.T,R) |
|---|
| 2733 | |
|---|
| 2734 | S6 = coeff[4] |
|---|
| 2735 | Sij = G2lat.U6toUij(S6) |
|---|
| 2736 | E,R = nl.eigh(Sij) |
|---|
| 2737 | XYZ = np.dstack((X,Y,Z)) |
|---|
| 2738 | XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R)) |
|---|
| 2739 | X,Y,Z = np.dsplit(XYZ,3) |
|---|
| 2740 | X = X[:,:,0] |
|---|
| 2741 | Y = Y[:,:,0] |
|---|
| 2742 | Z = Z[:,:,0] |
|---|
| 2743 | |
|---|
| 2744 | elif coeff[0] == 'generalized': |
|---|
| 2745 | |
|---|
| 2746 | def genMustrain(xyz,SGData,A,Shkl): |
|---|
| 2747 | uvw = np.inner(A.T,xyz) |
|---|
| 2748 | Strm = np.array(G2spc.MustrainCoeff(uvw,SGData)) |
|---|
| 2749 | Sum = np.sum(np.multiply(Shkl,Strm)) |
|---|
| 2750 | Sum = np.where(Sum > 0.01,Sum,0.01) |
|---|
| 2751 | Sum = np.sqrt(Sum) |
|---|
| 2752 | return Sum*xyz |
|---|
| 2753 | |
|---|
| 2754 | Shkl = np.array(coeff[4]) |
|---|
| 2755 | if np.any(Shkl): |
|---|
| 2756 | XYZ = np.dstack((X,Y,Z)) |
|---|
| 2757 | XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl)) |
|---|
| 2758 | X,Y,Z = np.dsplit(XYZ,3) |
|---|
| 2759 | X = X[:,:,0] |
|---|
| 2760 | Y = Y[:,:,0] |
|---|
| 2761 | Z = Z[:,:,0] |
|---|
| 2762 | |
|---|
| 2763 | if np.any(X) and np.any(Y) and np.any(Z): |
|---|
| 2764 | errFlags = np.seterr(all='ignore') |
|---|
| 2765 | Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1) |
|---|
| 2766 | np.seterr(all='ignore') |
|---|
| 2767 | xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T |
|---|
| 2768 | XYZlim = [min(xyzlim[0]),max(xyzlim[1])] |
|---|
| 2769 | Plot.set_xlim3d(XYZlim) |
|---|
| 2770 | Plot.set_ylim3d(XYZlim) |
|---|
| 2771 | Plot.set_zlim3d(XYZlim) |
|---|
| 2772 | Plot.set_aspect('equal') |
|---|
| 2773 | if plotType == 'Size': |
|---|
| 2774 | Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model') |
|---|
| 2775 | Plot.set_xlabel(r'X, $\mu$m') |
|---|
| 2776 | Plot.set_ylabel(r'Y, $\mu$m') |
|---|
| 2777 | Plot.set_zlabel(r'Z, $\mu$m') |
|---|
| 2778 | else: |
|---|
| 2779 | Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model') |
|---|
| 2780 | Plot.set_xlabel(r'X, $\mu$strain') |
|---|
| 2781 | Plot.set_ylabel(r'Y, $\mu$strain') |
|---|
| 2782 | Plot.set_zlabel(r'Z, $\mu$strain') |
|---|
| 2783 | else: |
|---|
| 2784 | h,k,l = generalData['POhkl'] |
|---|
| 2785 | if coeff[0] == 'MD': |
|---|
| 2786 | print 'March-Dollase preferred orientation plot' |
|---|
| 2787 | |
|---|
| 2788 | else: |
|---|
| 2789 | PH = np.array(generalData['POhkl']) |
|---|
| 2790 | phi,beta = G2lat.CrsAng(PH,cell[:6],SGData) |
|---|
| 2791 | SHCoef = {} |
|---|
| 2792 | for item in coeff[5]: |
|---|
| 2793 | L,N = eval(item.strip('C')) |
|---|
| 2794 | SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item] |
|---|
| 2795 | ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) |
|---|
| 2796 | X = np.linspace(0,90.0,26) |
|---|
| 2797 | Y = G2lat.polfcal(ODFln,'0',X,0.0) |
|---|
| 2798 | Plot.plot(X,Y,color='k',label=str(PH)) |
|---|
| 2799 | Plot.legend(loc='best') |
|---|
| 2800 | Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase+'\n'+hist) |
|---|
| 2801 | Plot.set_xlabel(r'$\psi$',fontsize=16) |
|---|
| 2802 | Plot.set_ylabel('MRD',fontsize=14) |
|---|
| 2803 | Page.canvas.draw() |
|---|
| 2804 | |
|---|
| 2805 | ################################################################################ |
|---|
| 2806 | ##### PlotTexture |
|---|
| 2807 | ################################################################################ |
|---|
| 2808 | |
|---|
| 2809 | def PlotTexture(G2frame,data,Start=False): |
|---|
| 2810 | '''Pole figure, inverse pole figure plotting. |
|---|
| 2811 | dict generalData contains all phase info needed which is in data |
|---|
| 2812 | ''' |
|---|
| 2813 | |
|---|
| 2814 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 2815 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 2816 | PatternId = G2frame.PatternId |
|---|
| 2817 | generalData = data['General'] |
|---|
| 2818 | SGData = generalData['SGData'] |
|---|
| 2819 | pName = generalData['Name'] |
|---|
| 2820 | textureData = generalData['SH Texture'] |
|---|
| 2821 | G2frame.G2plotNB.Delete('Texture') |
|---|
| 2822 | if not textureData['Order']: |
|---|
| 2823 | return #no plot!! |
|---|
| 2824 | SHData = generalData['SH Texture'] |
|---|
| 2825 | SHCoef = SHData['SH Coeff'][1] |
|---|
| 2826 | cell = generalData['Cell'][1:7] |
|---|
| 2827 | Amat,Bmat = G2lat.cell2AB(cell) |
|---|
| 2828 | sq2 = 1.0/math.sqrt(2.0) |
|---|
| 2829 | |
|---|
| 2830 | def rp2xyz(r,p): |
|---|
| 2831 | z = npcosd(r) |
|---|
| 2832 | xy = np.sqrt(1.-z**2) |
|---|
| 2833 | return xy*npsind(p),xy*npcosd(p),z |
|---|
| 2834 | |
|---|
| 2835 | def OnMotion(event): |
|---|
| 2836 | SHData = data['General']['SH Texture'] |
|---|
| 2837 | if event.xdata and event.ydata: #avoid out of frame errors |
|---|
| 2838 | xpos = event.xdata |
|---|
| 2839 | ypos = event.ydata |
|---|
| 2840 | if 'Inverse' in SHData['PlotType']: |
|---|
| 2841 | r = xpos**2+ypos**2 |
|---|
| 2842 | if r <= 1.0: |
|---|
| 2843 | if 'equal' in G2frame.Projection: |
|---|
| 2844 | r,p = 2.*npasind(np.sqrt(r)*sq2),npatan2d(ypos,xpos) |
|---|
| 2845 | else: |
|---|
| 2846 | r,p = 2.*npatand(np.sqrt(r)),npatan2d(ypos,xpos) |
|---|
| 2847 | ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,])) |
|---|
| 2848 | xyz = np.inner(Bmat,np.array([rp2xyz(r,p)])) |
|---|
| 2849 | y,x,z = list(xyz/np.max(np.abs(xyz))) |
|---|
| 2850 | |
|---|
| 2851 | G2frame.G2plotNB.status.SetFields(['', |
|---|
| 2852 | 'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)]) |
|---|
| 2853 | |
|---|
| 2854 | elif 'Axial' in SHData['PlotType']: |
|---|
| 2855 | pass |
|---|
| 2856 | |
|---|
| 2857 | else: #ordinary pole figure |
|---|
| 2858 | z = xpos**2+ypos**2 |
|---|
| 2859 | if z <= 1.0: |
|---|
| 2860 | z = np.sqrt(z) |
|---|
| 2861 | if 'equal' in G2frame.Projection: |
|---|
| 2862 | r,p = 2.*npasind(z*sq2),npatan2d(ypos,xpos) |
|---|
| 2863 | else: |
|---|
| 2864 | r,p = 2.*npatand(z),npatan2d(ypos,xpos) |
|---|
| 2865 | pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,])) |
|---|
| 2866 | G2frame.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)]) |
|---|
| 2867 | |
|---|
| 2868 | try: |
|---|
| 2869 | plotNum = G2frame.G2plotNB.plotList.index('Texture') |
|---|
| 2870 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2871 | Page.figure.clf() |
|---|
| 2872 | Plot = Page.figure.gca() |
|---|
| 2873 | if not Page.IsShown(): |
|---|
| 2874 | Page.Show() |
|---|
| 2875 | except ValueError: |
|---|
| 2876 | if '3D' in SHData['PlotType']: |
|---|
| 2877 | Plot = mp3d.Axes3D(G2frame.G2plotNB.add3D('Texture')) |
|---|
| 2878 | else: |
|---|
| 2879 | Plot = G2frame.G2plotNB.addMpl('Texture').gca() |
|---|
| 2880 | plotNum = G2frame.G2plotNB.plotList.index('Texture') |
|---|
| 2881 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 2882 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 2883 | |
|---|
| 2884 | Page.Choice = None |
|---|
| 2885 | Page.SetFocus() |
|---|
| 2886 | G2frame.G2plotNB.status.SetFields(['','']) |
|---|
| 2887 | PH = np.array(SHData['PFhkl']) |
|---|
| 2888 | phi,beta = G2lat.CrsAng(PH,cell,SGData) |
|---|
| 2889 | ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) |
|---|
| 2890 | if not np.any(ODFln): |
|---|
| 2891 | return |
|---|
| 2892 | PX = np.array(SHData['PFxyz']) |
|---|
| 2893 | gam = atan2d(PX[0],PX[1]) |
|---|
| 2894 | xy = math.sqrt(PX[0]**2+PX[1]**2) |
|---|
| 2895 | xyz = math.sqrt(PX[0]**2+PX[1]**2+PX[2]**2) |
|---|
| 2896 | psi = asind(xy/xyz) |
|---|
| 2897 | IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']]) |
|---|
| 2898 | if 'Axial' in SHData['PlotType']: |
|---|
| 2899 | X = np.linspace(0,90.0,26) |
|---|
| 2900 | Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0) |
|---|
| 2901 | Plot.plot(X,Y,color='k',label=str(SHData['PFhkl'])) |
|---|
| 2902 | Plot.legend(loc='best') |
|---|
| 2903 | h,k,l = SHData['PFhkl'] |
|---|
| 2904 | Plot.set_title('%d %d %d Axial distribution for %s'%(h,k,l,pName)) |
|---|
| 2905 | Plot.set_xlabel(r'$\psi$',fontsize=16) |
|---|
| 2906 | Plot.set_ylabel('MRD',fontsize=14) |
|---|
| 2907 | |
|---|
| 2908 | else: |
|---|
| 2909 | npts = 201 |
|---|
| 2910 | if 'Inverse' in SHData['PlotType']: |
|---|
| 2911 | X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts)) |
|---|
| 2912 | R,P = np.sqrt(X**2+Y**2).flatten(),npatan2d(X,Y).flatten() |
|---|
| 2913 | if 'equal' in G2frame.Projection: |
|---|
| 2914 | R = np.where(R <= 1.,2.*npasind(R*sq2),0.0) |
|---|
| 2915 | else: |
|---|
| 2916 | R = np.where(R <= 1.,2.*npatand(R),0.0) |
|---|
| 2917 | Z = np.zeros_like(R) |
|---|
| 2918 | Z = G2lat.invpolfcal(IODFln,SGData,R,P) |
|---|
| 2919 | Z = np.reshape(Z,(npts,npts)) |
|---|
| 2920 | try: |
|---|
| 2921 | CS = Plot.contour(Y,X,Z,aspect='equal') |
|---|
| 2922 | Plot.clabel(CS,fontsize=9,inline=1) |
|---|
| 2923 | except ValueError: |
|---|
| 2924 | pass |
|---|
| 2925 | Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1]) |
|---|
| 2926 | Page.figure.colorbar(Img) |
|---|
| 2927 | x,y,z = SHData['PFxyz'] |
|---|
| 2928 | Plot.axis('off') |
|---|
| 2929 | Plot.set_title('%d %d %d Inverse pole figure for %s'%(int(x),int(y),int(z),pName)) |
|---|
| 2930 | Plot.set_xlabel(G2frame.Projection.capitalize()+' projection') |
|---|
| 2931 | |
|---|
| 2932 | elif '3D' in SHData['PlotType']: |
|---|
| 2933 | PSI,GAM = np.mgrid[0:31,0:31] |
|---|
| 2934 | PSI = PSI.flatten()*6. |
|---|
| 2935 | GAM = GAM.flatten()*12. |
|---|
| 2936 | P = G2lat.polfcal(ODFln,SamSym[textureData['Model']],PSI,GAM).reshape((31,31)) |
|---|
| 2937 | GAM = np.linspace(0.,360.,31,True) |
|---|
| 2938 | PSI = np.linspace(0.,180.,31,True) |
|---|
| 2939 | X = np.outer(npsind(GAM),npsind(PSI))*P.T |
|---|
| 2940 | Y = np.outer(npcosd(GAM),npsind(PSI))*P.T |
|---|
| 2941 | Z = np.outer(np.ones(np.size(GAM)),npcosd(PSI))*P.T |
|---|
| 2942 | h,k,l = SHData['PFhkl'] |
|---|
| 2943 | |
|---|
| 2944 | if np.any(X) and np.any(Y) and np.any(Z): |
|---|
| 2945 | errFlags = np.seterr(all='ignore') |
|---|
| 2946 | Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1) |
|---|
| 2947 | np.seterr(all='ignore') |
|---|
| 2948 | xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T |
|---|
| 2949 | XYZlim = [min(xyzlim[0]),max(xyzlim[1])] |
|---|
| 2950 | Plot.set_xlim3d(XYZlim) |
|---|
| 2951 | Plot.set_ylim3d(XYZlim) |
|---|
| 2952 | Plot.set_zlim3d(XYZlim) |
|---|
| 2953 | Plot.set_aspect('equal') |
|---|
| 2954 | Plot.set_title('%d %d %d Pole distribution for %s'%(h,k,l,pName)) |
|---|
| 2955 | Plot.set_xlabel(r'X, MRD') |
|---|
| 2956 | Plot.set_ylabel(r'Y, MRD') |
|---|
| 2957 | Plot.set_zlabel(r'Z, MRD') |
|---|
| 2958 | else: |
|---|
| 2959 | PFproj = textureData.get('PFproj','XY') |
|---|
| 2960 | PRrev = textureData.get('PFrev',False) |
|---|
| 2961 | X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts)) |
|---|
| 2962 | R,P = np.sqrt(X**2+Y**2).flatten(),npatan2d(X,Y).flatten() |
|---|
| 2963 | if 'equal' in G2frame.Projection: |
|---|
| 2964 | R = np.where(R <= 1.,2.*npasind(R*sq2),0.0) |
|---|
| 2965 | else: |
|---|
| 2966 | R = np.where(R <= 1.,2.*npatand(R),0.0) |
|---|
| 2967 | Z = np.zeros_like(R) |
|---|
| 2968 | Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P) |
|---|
| 2969 | Z = np.reshape(Z,(npts,npts)) |
|---|
| 2970 | try: |
|---|
| 2971 | CS = Plot.contour(Y,X,Z,aspect='equal') |
|---|
| 2972 | Plot.clabel(CS,fontsize=9,inline=1) |
|---|
| 2973 | except ValueError: |
|---|
| 2974 | pass |
|---|
| 2975 | Img = Plot.imshow(Z.T,aspect='equal',cmap=G2frame.ContourColor,extent=[-1,1,-1,1]) |
|---|
| 2976 | Page.figure.colorbar(Img) |
|---|
| 2977 | h,k,l = SHData['PFhkl'] |
|---|
| 2978 | Plot.axis('off') |
|---|
| 2979 | Plot.set_title('%d %d %d Pole figure for %s'%(h,k,l,pName)) |
|---|
| 2980 | Plot.set_xlabel(G2frame.Projection.capitalize()+' projection') |
|---|
| 2981 | Page.canvas.draw() |
|---|
| 2982 | |
|---|
| 2983 | ################################################################################ |
|---|
| 2984 | ##### Plot Modulation |
|---|
| 2985 | ################################################################################ |
|---|
| 2986 | |
|---|
| 2987 | def ModulationPlot(G2frame,data,atom,ax,off=0): |
|---|
| 2988 | global Off,Atom,Ax |
|---|
| 2989 | Off = off |
|---|
| 2990 | Atom = atom |
|---|
| 2991 | Ax = ax |
|---|
| 2992 | def OnMotion(event): |
|---|
| 2993 | xpos = event.xdata |
|---|
| 2994 | if xpos: #avoid out of frame mouse position |
|---|
| 2995 | ypos = event.ydata |
|---|
| 2996 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 2997 | try: |
|---|
| 2998 | G2frame.G2plotNB.status.SetStatusText('t =%9.3f %s =%9.3f'%(xpos,GkDelta+Ax,ypos),1) |
|---|
| 2999 | except TypeError: |
|---|
| 3000 | G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1) |
|---|
| 3001 | |
|---|
| 3002 | def OnPlotKeyPress(event): |
|---|
| 3003 | global Off,Atom,Ax |
|---|
| 3004 | newPlot = False |
|---|
| 3005 | if event.key == '0': |
|---|
| 3006 | Off = 0 |
|---|
| 3007 | elif event.key in ['+','=']: |
|---|
| 3008 | Off += 1 |
|---|
| 3009 | elif event.key == '-': |
|---|
| 3010 | Off -= 1 |
|---|
| 3011 | elif event.key in ['l','r',] and mapData['Flip']: |
|---|
| 3012 | roll = 1 |
|---|
| 3013 | if event.key == 'l': |
|---|
| 3014 | roll = -1 |
|---|
| 3015 | rho = Map['rho'] |
|---|
| 3016 | Map['rho'] = np.roll(rho,roll,axis=3) |
|---|
| 3017 | wx.CallAfter(ModulationPlot,G2frame,data,Atom,Ax,Off) |
|---|
| 3018 | |
|---|
| 3019 | try: |
|---|
| 3020 | plotNum = G2frame.G2plotNB.plotList.index('Modulation') |
|---|
| 3021 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3022 | Page.figure.clf() |
|---|
| 3023 | Plot = Page.figure.gca() |
|---|
| 3024 | if not Page.IsShown(): |
|---|
| 3025 | Page.Show() |
|---|
| 3026 | except ValueError: |
|---|
| 3027 | Plot = G2frame.G2plotNB.addMpl('Modulation').gca() |
|---|
| 3028 | plotNum = G2frame.G2plotNB.plotList.index('Modulation') |
|---|
| 3029 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3030 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 3031 | Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) |
|---|
| 3032 | |
|---|
| 3033 | Page.SetFocus() |
|---|
| 3034 | General = data['General'] |
|---|
| 3035 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 3036 | mapData = General['Map'] |
|---|
| 3037 | if mapData['Flip']: |
|---|
| 3038 | Page.Choice = ['+: shift up','-: shift down','0: reset shift','l: move left','r: move right'] |
|---|
| 3039 | else: |
|---|
| 3040 | Page.Choice = ['+: shift up','-: shift down','0: reset shift'] |
|---|
| 3041 | Page.keyPress = OnPlotKeyPress |
|---|
| 3042 | Map = General['4DmapData'] |
|---|
| 3043 | MapType = Map['MapType'] |
|---|
| 3044 | rhoSize = np.array(Map['rho'].shape) |
|---|
| 3045 | atxyz = np.array(atom[cx:cx+3]) |
|---|
| 3046 | waveType = atom[-1]['SS1']['waveType'] |
|---|
| 3047 | Spos = atom[-1]['SS1']['Spos'] |
|---|
| 3048 | tau = np.linspace(0.,2.,101) |
|---|
| 3049 | wave = np.zeros((3,101)) |
|---|
| 3050 | if len(Spos): |
|---|
| 3051 | scof = [] |
|---|
| 3052 | ccof = [] |
|---|
| 3053 | for i,spos in enumerate(Spos): |
|---|
| 3054 | if waveType in ['Sawtooth','ZigZag'] and not i: |
|---|
| 3055 | Toff = spos[0][0] |
|---|
| 3056 | slopes = np.array(spos[0][1:]) |
|---|
| 3057 | if waveType == 'Sawtooth': |
|---|
| 3058 | wave = G2mth.posSawtooth(tau,Toff,slopes) |
|---|
| 3059 | elif waveType == 'ZigZag': |
|---|
| 3060 | wave = G2mth.posZigZag(tau,Toff,slopes) |
|---|
| 3061 | else: |
|---|
| 3062 | scof.append(spos[0][:3]) |
|---|
| 3063 | ccof.append(spos[0][3:]) |
|---|
| 3064 | wave += G2mth.posFourier(tau,np.array(scof),np.array(ccof),1) #hmm, why -1 work for Na2CO3? |
|---|
| 3065 | if mapData['Flip']: |
|---|
| 3066 | Title = 'Charge flip' |
|---|
| 3067 | else: |
|---|
| 3068 | Title = MapType |
|---|
| 3069 | Title += ' map for atom '+atom[0]+ \ |
|---|
| 3070 | ' at %.4f %.4f %.4f'%(atxyz[0],atxyz[1],atxyz[2]) |
|---|
| 3071 | ix = -np.array(np.rint(rhoSize[:3]*atxyz),dtype='i') |
|---|
| 3072 | ix += (rhoSize[:3]/2) |
|---|
| 3073 | ix = ix%rhoSize[:3] |
|---|
| 3074 | rho = np.roll(np.roll(np.roll(Map['rho'],ix[0],axis=0),ix[1],axis=1),ix[2],axis=2) |
|---|
| 3075 | ix = rhoSize[:3]/2 |
|---|
| 3076 | ib = 4 |
|---|
| 3077 | if Ax == 'x': |
|---|
| 3078 | slab = np.sum(np.sum(rho[:,ix[1]-ib:ix[1]+ib,ix[2]-ib:ix[2]+ib,:],axis=2),axis=1) |
|---|
| 3079 | Plot.plot(tau,wave[0]) |
|---|
| 3080 | elif Ax == 'y': |
|---|
| 3081 | slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,:,ix[2]-ib:ix[2]+ib,:],axis=2),axis=0) |
|---|
| 3082 | Plot.plot(tau,wave[1]) |
|---|
| 3083 | elif Ax == 'z': |
|---|
| 3084 | slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,ix[1]-ib:ix[1]+ib,:,:],axis=1),axis=0) |
|---|
| 3085 | Plot.plot(tau,wave[2]) |
|---|
| 3086 | Plot.set_title(Title) |
|---|
| 3087 | Plot.set_xlabel('t') |
|---|
| 3088 | Plot.set_ylabel(r'$\mathsf{\Delta}$%s'%(Ax)) |
|---|
| 3089 | Slab = np.hstack((slab,slab,slab)) |
|---|
| 3090 | Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Off*.005,.5+Off*.005)) |
|---|
| 3091 | Page.canvas.draw() |
|---|
| 3092 | |
|---|
| 3093 | ################################################################################ |
|---|
| 3094 | ##### PlotCovariance |
|---|
| 3095 | ################################################################################ |
|---|
| 3096 | |
|---|
| 3097 | def PlotCovariance(G2frame,Data): |
|---|
| 3098 | 'needs a doc string' |
|---|
| 3099 | if not Data: |
|---|
| 3100 | print 'No covariance matrix available' |
|---|
| 3101 | return |
|---|
| 3102 | varyList = Data['varyList'] |
|---|
| 3103 | values = Data['variables'] |
|---|
| 3104 | Xmax = len(varyList) |
|---|
| 3105 | covMatrix = Data['covMatrix'] |
|---|
| 3106 | sig = np.sqrt(np.diag(covMatrix)) |
|---|
| 3107 | xvar = np.outer(sig,np.ones_like(sig)) |
|---|
| 3108 | covArray = np.divide(np.divide(covMatrix,xvar),xvar.T) |
|---|
| 3109 | title = ' for\n'+Data['title'] |
|---|
| 3110 | newAtomDict = Data.get('newAtomDict',{}) |
|---|
| 3111 | G2frame.G2plotNB.Delete('Covariance') |
|---|
| 3112 | |
|---|
| 3113 | |
|---|
| 3114 | def OnPlotKeyPress(event): |
|---|
| 3115 | newPlot = False |
|---|
| 3116 | if event.key == 's': |
|---|
| 3117 | choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")] |
|---|
| 3118 | choice.sort() |
|---|
| 3119 | dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) |
|---|
| 3120 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 3121 | sel = dlg.GetSelection() |
|---|
| 3122 | G2frame.VcovColor = choice[sel] |
|---|
| 3123 | else: |
|---|
| 3124 | G2frame.VcovColor = 'RdYlGn' |
|---|
| 3125 | dlg.Destroy() |
|---|
| 3126 | PlotCovariance(G2frame,Data) |
|---|
| 3127 | |
|---|
| 3128 | def OnMotion(event): |
|---|
| 3129 | if event.button: |
|---|
| 3130 | ytics = imgAx.get_yticks() |
|---|
| 3131 | ytics = np.where(ytics<len(varyList),ytics,-1) |
|---|
| 3132 | ylabs = [np.where(0<=i ,varyList[int(i)],' ') for i in ytics] |
|---|
| 3133 | imgAx.set_yticklabels(ylabs) |
|---|
| 3134 | if event.xdata and event.ydata: #avoid out of frame errors |
|---|
| 3135 | xpos = int(event.xdata+.5) |
|---|
| 3136 | ypos = int(event.ydata+.5) |
|---|
| 3137 | if -1 < xpos < len(varyList) and -1 < ypos < len(varyList): |
|---|
| 3138 | if xpos == ypos: |
|---|
| 3139 | value = values[xpos] |
|---|
| 3140 | name = varyList[xpos] |
|---|
| 3141 | if varyList[xpos] in newAtomDict: |
|---|
| 3142 | name,value = newAtomDict[name] |
|---|
| 3143 | msg = '%s value = %.4g, esd = %.4g'%(name,value,sig[xpos]) |
|---|
| 3144 | else: |
|---|
| 3145 | msg = '%s - %s: %5.3f'%(varyList[xpos],varyList[ypos],covArray[xpos][ypos]) |
|---|
| 3146 | Page.canvas.SetToolTipString(msg) |
|---|
| 3147 | G2frame.G2plotNB.status.SetFields(['',msg]) |
|---|
| 3148 | |
|---|
| 3149 | try: |
|---|
| 3150 | plotNum = G2frame.G2plotNB.plotList.index('Covariance') |
|---|
| 3151 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3152 | Page.figure.clf() |
|---|
| 3153 | Plot = Page.figure.gca() |
|---|
| 3154 | if not Page.IsShown(): |
|---|
| 3155 | Page.Show() |
|---|
| 3156 | except ValueError: |
|---|
| 3157 | Plot = G2frame.G2plotNB.addMpl('Covariance').gca() |
|---|
| 3158 | plotNum = G2frame.G2plotNB.plotList.index('Covariance') |
|---|
| 3159 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3160 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 3161 | Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) |
|---|
| 3162 | Page.Choice = ['s: to change colors'] |
|---|
| 3163 | Page.keyPress = OnPlotKeyPress |
|---|
| 3164 | Page.SetFocus() |
|---|
| 3165 | G2frame.G2plotNB.status.SetFields(['','']) |
|---|
| 3166 | acolor = mpl.cm.get_cmap(G2frame.VcovColor) |
|---|
| 3167 | Img = Plot.imshow(covArray,aspect='equal',cmap=acolor,interpolation='nearest',origin='lower', |
|---|
| 3168 | vmin=-1.,vmax=1.) |
|---|
| 3169 | imgAx = Img.get_axes() |
|---|
| 3170 | ytics = imgAx.get_yticks() |
|---|
| 3171 | ylabs = [varyList[int(i)] for i in ytics[:-1]] |
|---|
| 3172 | imgAx.set_yticklabels(ylabs) |
|---|
| 3173 | colorBar = Page.figure.colorbar(Img) |
|---|
| 3174 | Plot.set_title('V-Cov matrix'+title) |
|---|
| 3175 | Plot.set_xlabel('Variable number') |
|---|
| 3176 | Plot.set_ylabel('Variable name') |
|---|
| 3177 | Page.canvas.draw() |
|---|
| 3178 | |
|---|
| 3179 | ################################################################################ |
|---|
| 3180 | ##### PlotTorsion |
|---|
| 3181 | ################################################################################ |
|---|
| 3182 | |
|---|
| 3183 | def PlotTorsion(G2frame,phaseName,Torsion,TorName,Names=[],Angles=[],Coeff=[]): |
|---|
| 3184 | 'needs a doc string' |
|---|
| 3185 | |
|---|
| 3186 | global names |
|---|
| 3187 | names = Names |
|---|
| 3188 | sum = np.sum(Torsion) |
|---|
| 3189 | torsion = np.log(2*Torsion+1.)/sum |
|---|
| 3190 | tMin = np.min(torsion) |
|---|
| 3191 | tMax = np.max(torsion) |
|---|
| 3192 | torsion = 3.*(torsion-tMin)/(tMax-tMin) |
|---|
| 3193 | X = np.linspace(0.,360.,num=45) |
|---|
| 3194 | |
|---|
| 3195 | def OnPick(event): |
|---|
| 3196 | ind = event.ind[0] |
|---|
| 3197 | msg = 'atoms:'+names[ind] |
|---|
| 3198 | Page.canvas.SetToolTipString(msg) |
|---|
| 3199 | try: |
|---|
| 3200 | page = G2frame.dataDisplay.GetSelection() |
|---|
| 3201 | except: |
|---|
| 3202 | return |
|---|
| 3203 | if G2frame.dataDisplay.GetPageText(page) == 'Torsion restraints': |
|---|
| 3204 | torGrid = G2frame.dataDisplay.GetPage(page).Torsions |
|---|
| 3205 | torGrid.ClearSelection() |
|---|
| 3206 | for row in range(torGrid.GetNumberRows()): |
|---|
| 3207 | if names[ind] in torGrid.GetCellValue(row,0): |
|---|
| 3208 | torGrid.SelectRow(row) |
|---|
| 3209 | torGrid.ForceRefresh() |
|---|
| 3210 | |
|---|
| 3211 | def OnMotion(event): |
|---|
| 3212 | if event.xdata and event.ydata: #avoid out of frame errors |
|---|
| 3213 | xpos = event.xdata |
|---|
| 3214 | ypos = event.ydata |
|---|
| 3215 | msg = 'torsion,energy: %5.3f %5.3f'%(xpos,ypos) |
|---|
| 3216 | Page.canvas.SetToolTipString(msg) |
|---|
| 3217 | |
|---|
| 3218 | try: |
|---|
| 3219 | plotNum = G2frame.G2plotNB.plotList.index('Torsion') |
|---|
| 3220 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3221 | Page.figure.clf() |
|---|
| 3222 | Plot = Page.figure.gca() |
|---|
| 3223 | if not Page.IsShown(): |
|---|
| 3224 | Page.Show() |
|---|
| 3225 | except ValueError: |
|---|
| 3226 | Plot = G2frame.G2plotNB.addMpl('Torsion').gca() |
|---|
| 3227 | plotNum = G2frame.G2plotNB.plotList.index('Torsion') |
|---|
| 3228 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3229 | Page.canvas.mpl_connect('pick_event', OnPick) |
|---|
| 3230 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 3231 | |
|---|
| 3232 | Page.SetFocus() |
|---|
| 3233 | G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify torsion atoms']) |
|---|
| 3234 | Plot.plot(X,torsion,'b+') |
|---|
| 3235 | if len(Coeff): |
|---|
| 3236 | X2 = np.linspace(0.,360.,45) |
|---|
| 3237 | Y2 = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in X2]) |
|---|
| 3238 | Plot.plot(X2,Y2,'r') |
|---|
| 3239 | if len(Angles): |
|---|
| 3240 | Eval = np.array([-G2mth.calcTorsionEnergy(x,Coeff)[1] for x in Angles]) |
|---|
| 3241 | Plot.plot(Angles,Eval,'ro',picker=5) |
|---|
| 3242 | Plot.set_xlim((0.,360.)) |
|---|
| 3243 | Plot.set_title('Torsion angles for '+TorName+' in '+phaseName) |
|---|
| 3244 | Plot.set_xlabel('angle',fontsize=16) |
|---|
| 3245 | Plot.set_ylabel('Energy',fontsize=16) |
|---|
| 3246 | Page.canvas.draw() |
|---|
| 3247 | |
|---|
| 3248 | ################################################################################ |
|---|
| 3249 | ##### PlotRama |
|---|
| 3250 | ################################################################################ |
|---|
| 3251 | |
|---|
| 3252 | def PlotRama(G2frame,phaseName,Rama,RamaName,Names=[],PhiPsi=[],Coeff=[]): |
|---|
| 3253 | 'needs a doc string' |
|---|
| 3254 | |
|---|
| 3255 | global names |
|---|
| 3256 | names = Names |
|---|
| 3257 | rama = np.log(2*Rama+1.) |
|---|
| 3258 | ramaMax = np.max(rama) |
|---|
| 3259 | rama = np.reshape(rama,(45,45)) |
|---|
| 3260 | global Phi,Psi |
|---|
| 3261 | Phi = [] |
|---|
| 3262 | Psi = [] |
|---|
| 3263 | |
|---|
| 3264 | def OnPlotKeyPress(event): |
|---|
| 3265 | newPlot = False |
|---|
| 3266 | if event.key == 's': |
|---|
| 3267 | choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")] |
|---|
| 3268 | choice.sort() |
|---|
| 3269 | dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) |
|---|
| 3270 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 3271 | sel = dlg.GetSelection() |
|---|
| 3272 | G2frame.RamaColor = choice[sel] |
|---|
| 3273 | else: |
|---|
| 3274 | G2frame.RamaColor = 'RdYlGn' |
|---|
| 3275 | dlg.Destroy() |
|---|
| 3276 | PlotRama(G2frame,phaseName,Rama) |
|---|
| 3277 | |
|---|
| 3278 | def OnPick(event): |
|---|
| 3279 | ind = event.ind[0] |
|---|
| 3280 | msg = 'atoms:'+names[ind] |
|---|
| 3281 | Page.canvas.SetToolTipString(msg) |
|---|
| 3282 | try: |
|---|
| 3283 | page = G2frame.dataDisplay.GetSelection() |
|---|
| 3284 | except: |
|---|
| 3285 | return |
|---|
| 3286 | if G2frame.dataDisplay.GetPageText(page) == 'Ramachandran restraints': |
|---|
| 3287 | ramaGrid = G2frame.dataDisplay.GetPage(page).Ramas |
|---|
| 3288 | ramaGrid.ClearSelection() |
|---|
| 3289 | for row in range(ramaGrid.GetNumberRows()): |
|---|
| 3290 | if names[ind] in ramaGrid.GetCellValue(row,0): |
|---|
| 3291 | ramaGrid.SelectRow(row) |
|---|
| 3292 | ramaGrid.ForceRefresh() |
|---|
| 3293 | |
|---|
| 3294 | def OnMotion(event): |
|---|
| 3295 | if event.xdata and event.ydata: #avoid out of frame errors |
|---|
| 3296 | xpos = event.xdata |
|---|
| 3297 | ypos = event.ydata |
|---|
| 3298 | msg = 'phi/psi: %5.3f %5.3f'%(xpos,ypos) |
|---|
| 3299 | Page.canvas.SetToolTipString(msg) |
|---|
| 3300 | |
|---|
| 3301 | try: |
|---|
| 3302 | plotNum = G2frame.G2plotNB.plotList.index('Ramachandran') |
|---|
| 3303 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3304 | Page.figure.clf() |
|---|
| 3305 | Plot = Page.figure.gca() |
|---|
| 3306 | if not Page.IsShown(): |
|---|
| 3307 | Page.Show() |
|---|
| 3308 | except ValueError: |
|---|
| 3309 | Plot = G2frame.G2plotNB.addMpl('Ramachandran').gca() |
|---|
| 3310 | plotNum = G2frame.G2plotNB.plotList.index('Ramachandran') |
|---|
| 3311 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3312 | Page.canvas.mpl_connect('pick_event', OnPick) |
|---|
| 3313 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 3314 | Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) |
|---|
| 3315 | |
|---|
| 3316 | Page.Choice = ['s: to change colors'] |
|---|
| 3317 | Page.keyPress = OnPlotKeyPress |
|---|
| 3318 | Page.SetFocus() |
|---|
| 3319 | G2frame.G2plotNB.status.SetFields(['','Use mouse LB to identify phi/psi atoms']) |
|---|
| 3320 | acolor = mpl.cm.get_cmap(G2frame.RamaColor) |
|---|
| 3321 | if RamaName == 'All' or '-1' in RamaName: |
|---|
| 3322 | if len(Coeff): |
|---|
| 3323 | X,Y = np.meshgrid(np.linspace(-180.,180.,45),np.linspace(-180.,180.,45)) |
|---|
| 3324 | Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())]) |
|---|
| 3325 | Plot.contour(X,Y,np.reshape(Z,(45,45))) |
|---|
| 3326 | Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest', |
|---|
| 3327 | extent=[-180,180,-180,180],origin='lower') |
|---|
| 3328 | if len(PhiPsi): |
|---|
| 3329 | Phi,Psi = PhiPsi.T |
|---|
| 3330 | Phi = np.where(Phi>180.,Phi-360.,Phi) |
|---|
| 3331 | Psi = np.where(Psi>180.,Psi-360.,Psi) |
|---|
| 3332 | Plot.plot(Phi,Psi,'ro',picker=5) |
|---|
| 3333 | Plot.set_xlim((-180.,180.)) |
|---|
| 3334 | Plot.set_ylim((-180.,180.)) |
|---|
| 3335 | else: |
|---|
| 3336 | if len(Coeff): |
|---|
| 3337 | X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45)) |
|---|
| 3338 | Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())]) |
|---|
| 3339 | Plot.contour(X,Y,np.reshape(Z,(45,45))) |
|---|
| 3340 | Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest', |
|---|
| 3341 | extent=[0,360,0,360],origin='lower') |
|---|
| 3342 | if len(PhiPsi): |
|---|
| 3343 | Phi,Psi = PhiPsi.T |
|---|
| 3344 | Plot.plot(Phi,Psi,'ro',picker=5) |
|---|
| 3345 | Plot.set_xlim((0.,360.)) |
|---|
| 3346 | Plot.set_ylim((0.,360.)) |
|---|
| 3347 | Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName) |
|---|
| 3348 | Plot.set_xlabel(r'$\phi$',fontsize=16) |
|---|
| 3349 | Plot.set_ylabel(r'$\psi$',fontsize=16) |
|---|
| 3350 | colorBar = Page.figure.colorbar(Img) |
|---|
| 3351 | Page.canvas.draw() |
|---|
| 3352 | |
|---|
| 3353 | |
|---|
| 3354 | ################################################################################ |
|---|
| 3355 | ##### PlotSeq |
|---|
| 3356 | ################################################################################ |
|---|
| 3357 | def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX,fitnum=None,fitvals=None): |
|---|
| 3358 | '''Plot a result from a sequential refinement |
|---|
| 3359 | |
|---|
| 3360 | :param wx.Frame G2frame: The main GSAS-II tree "window" |
|---|
| 3361 | :param list ColumnList: list of int values corresponding to columns |
|---|
| 3362 | selected as y values |
|---|
| 3363 | :param function TableGet: a function that takes a column number |
|---|
| 3364 | as argument and returns the column label, the values and there ESDs (or None) |
|---|
| 3365 | :param function SelectX: a function that returns a selected column |
|---|
| 3366 | number (or None) as the X-axis selection |
|---|
| 3367 | ''' |
|---|
| 3368 | global Title,xLabel,yLabel |
|---|
| 3369 | xLabel = yLabel = Title = '' |
|---|
| 3370 | def OnMotion(event): |
|---|
| 3371 | if event.xdata and event.ydata: #avoid out of frame errors |
|---|
| 3372 | xpos = event.xdata |
|---|
| 3373 | ypos = event.ydata |
|---|
| 3374 | msg = '%5.3f %.6g'%(xpos,ypos) |
|---|
| 3375 | Page.canvas.SetToolTipString(msg) |
|---|
| 3376 | |
|---|
| 3377 | def OnKeyPress(event): |
|---|
| 3378 | global Title,xLabel,yLabel |
|---|
| 3379 | if event.key == 's': |
|---|
| 3380 | G2frame.seqXaxis = G2frame.seqXselect() |
|---|
| 3381 | Draw() |
|---|
| 3382 | elif event.key == 't': |
|---|
| 3383 | dlg = G2G.MultiStringDialog(G2frame,'Set titles & labels',[' Title ',' x-Label ',' y-Label '], |
|---|
| 3384 | [Title,xLabel,yLabel]) |
|---|
| 3385 | if dlg.Show(): |
|---|
| 3386 | Title,xLabel,yLabel = dlg.GetValues() |
|---|
| 3387 | dlg.Destroy() |
|---|
| 3388 | Draw() |
|---|
| 3389 | elif event.key == 'l': |
|---|
| 3390 | G2frame.seqLines = not G2frame.seqLines |
|---|
| 3391 | wx.CallAfter(Draw) |
|---|
| 3392 | |
|---|
| 3393 | def Draw(): |
|---|
| 3394 | global Title,xLabel,yLabel |
|---|
| 3395 | Page.SetFocus() |
|---|
| 3396 | G2frame.G2plotNB.status.SetStatusText( \ |
|---|
| 3397 | 'press L to toggle lines, S to select X axis, T to change titles (reselect column to show?)',1) |
|---|
| 3398 | Plot.clear() |
|---|
| 3399 | if G2frame.seqXaxis is not None: |
|---|
| 3400 | xName,X,Xsig = Page.seqTableGet(G2frame.seqXaxis) |
|---|
| 3401 | else: |
|---|
| 3402 | X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1) |
|---|
| 3403 | xName = 'Data sequence number' |
|---|
| 3404 | for col in Page.seqYaxisList: |
|---|
| 3405 | name,Y,sig = Page.seqTableGet(col) |
|---|
| 3406 | # deal with missing (None) values |
|---|
| 3407 | Xnew = [] |
|---|
| 3408 | Ynew = [] |
|---|
| 3409 | Ysnew = [] |
|---|
| 3410 | for i in range(len(X)): |
|---|
| 3411 | if X[i] is None or Y[i] is None: continue |
|---|
| 3412 | Xnew.append(X[i]) |
|---|
| 3413 | Ynew.append(Y[i]) |
|---|
| 3414 | if sig: Ysnew.append(sig[i]) |
|---|
| 3415 | if Ysnew: |
|---|
| 3416 | if G2frame.seqReverse and not G2frame.seqXaxis: |
|---|
| 3417 | Ynew = Ynew[::-1] |
|---|
| 3418 | Ysnew = Ysnew[::-1] |
|---|
| 3419 | if G2frame.seqLines: |
|---|
| 3420 | Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name) |
|---|
| 3421 | else: |
|---|
| 3422 | Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name,linestyle='None',marker='x') |
|---|
| 3423 | else: |
|---|
| 3424 | if G2frame.seqReverse and not G2frame.seqXaxis: |
|---|
| 3425 | Ynew = Ynew[::-1] |
|---|
| 3426 | Plot.plot(Xnew,Ynew) |
|---|
| 3427 | Plot.plot(Xnew,Ynew,'o',label=name) |
|---|
| 3428 | if Page.fitvals: # TODO: deal with fitting of None values |
|---|
| 3429 | if G2frame.seqReverse and not G2frame.seqXaxis: |
|---|
| 3430 | Page.fitvals = Page.fitvals[::-1] |
|---|
| 3431 | Plot.plot(X,Page.fitvals,label='Fit') |
|---|
| 3432 | |
|---|
| 3433 | Plot.legend(loc='best') |
|---|
| 3434 | if Title: |
|---|
| 3435 | Plot.set_title(Title) |
|---|
| 3436 | else: |
|---|
| 3437 | Plot.set_title('') |
|---|
| 3438 | if xLabel: |
|---|
| 3439 | Plot.set_xlabel(xLabel) |
|---|
| 3440 | else: |
|---|
| 3441 | Plot.set_xlabel(xName) |
|---|
| 3442 | if yLabel: |
|---|
| 3443 | Plot.set_ylabel(yLabel) |
|---|
| 3444 | else: |
|---|
| 3445 | Plot.set_ylabel('Parameter values') |
|---|
| 3446 | Page.canvas.draw() |
|---|
| 3447 | |
|---|
| 3448 | G2frame.seqXselect = SelectX |
|---|
| 3449 | try: |
|---|
| 3450 | G2frame.seqXaxis |
|---|
| 3451 | except: |
|---|
| 3452 | G2frame.seqXaxis = None |
|---|
| 3453 | |
|---|
| 3454 | if fitnum is None: |
|---|
| 3455 | label = 'Sequential refinement' |
|---|
| 3456 | else: |
|---|
| 3457 | label = 'Parametric fit #'+str(fitnum+1) |
|---|
| 3458 | try: |
|---|
| 3459 | plotNum = G2frame.G2plotNB.plotList.index(label) |
|---|
| 3460 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3461 | Page.figure.clf() |
|---|
| 3462 | Plot = Page.figure.gca() |
|---|
| 3463 | if not Page.IsShown(): |
|---|
| 3464 | Page.Show() |
|---|
| 3465 | except ValueError: |
|---|
| 3466 | Plot = G2frame.G2plotNB.addMpl(label).gca() |
|---|
| 3467 | plotNum = G2frame.G2plotNB.plotList.index(label) |
|---|
| 3468 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3469 | Page.canvas.mpl_connect('key_press_event', OnKeyPress) |
|---|
| 3470 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 3471 | Page.Choice = ['l - toggle lines','s - select x-axis','t - change titles',] |
|---|
| 3472 | Page.keyPress = OnKeyPress |
|---|
| 3473 | Page.seqYaxisList = ColumnList |
|---|
| 3474 | Page.seqTableGet = TableGet |
|---|
| 3475 | Page.fitvals = fitvals |
|---|
| 3476 | |
|---|
| 3477 | Draw() |
|---|
| 3478 | G2frame.G2plotNB.nb.SetSelection(plotNum) # raises plot tab |
|---|
| 3479 | |
|---|
| 3480 | ################################################################################ |
|---|
| 3481 | ##### PlotExposedImage & PlotImage |
|---|
| 3482 | ################################################################################ |
|---|
| 3483 | |
|---|
| 3484 | def PlotExposedImage(G2frame,newPlot=False,event=None): |
|---|
| 3485 | '''General access module for 2D image plotting |
|---|
| 3486 | ''' |
|---|
| 3487 | plotNo = G2frame.G2plotNB.nb.GetSelection() |
|---|
| 3488 | if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image': |
|---|
| 3489 | PlotImage(G2frame,newPlot,event,newImage=True) |
|---|
| 3490 | elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration': |
|---|
| 3491 | PlotIntegration(G2frame,newPlot,event) |
|---|
| 3492 | |
|---|
| 3493 | def OnStartMask(G2frame): |
|---|
| 3494 | '''Initiate the start of a Frame or Polygon map |
|---|
| 3495 | |
|---|
| 3496 | :param wx.Frame G2frame: The main GSAS-II tree "window" |
|---|
| 3497 | :param str eventkey: a single letter ('f' or 'p') that |
|---|
| 3498 | determines what type of mask is created. |
|---|
| 3499 | ''' |
|---|
| 3500 | Masks = G2frame.PatternTree.GetItemPyData( |
|---|
| 3501 | G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks')) |
|---|
| 3502 | if G2frame.MaskKey == 'f': |
|---|
| 3503 | Masks['Frames'] = [] |
|---|
| 3504 | elif G2frame.MaskKey == 'p': |
|---|
| 3505 | Masks['Polygons'].append([]) |
|---|
| 3506 | elif G2frame.MaskKey == 's': |
|---|
| 3507 | Masks['Points'].append([]) |
|---|
| 3508 | elif G2frame.MaskKey == 'a': |
|---|
| 3509 | Masks['Arcs'].append([]) |
|---|
| 3510 | elif G2frame.MaskKey == 'r': |
|---|
| 3511 | Masks['Rings'].append([]) |
|---|
| 3512 | G2imG.UpdateMasks(G2frame,Masks) |
|---|
| 3513 | PlotImage(G2frame,newImage=True) |
|---|
| 3514 | |
|---|
| 3515 | def OnStartNewDzero(G2frame): |
|---|
| 3516 | '''Initiate the start of adding a new d-zero to a strain data set |
|---|
| 3517 | |
|---|
| 3518 | :param wx.Frame G2frame: The main GSAS-II tree "window" |
|---|
| 3519 | :param str eventkey: a single letter ('a') that |
|---|
| 3520 | triggers the addition of a d-zero. |
|---|
| 3521 | ''' |
|---|
| 3522 | G2frame.dataFrame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',0) |
|---|
| 3523 | G2frame.PickId = G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain') |
|---|
| 3524 | data = G2frame.PatternTree.GetItemPyData(G2frame.PickId) |
|---|
| 3525 | return data |
|---|
| 3526 | |
|---|
| 3527 | def PlotImage(G2frame,newPlot=False,event=None,newImage=True): |
|---|
| 3528 | '''Plot of 2D detector images as contoured plot. Also plot calibration ellipses, |
|---|
| 3529 | masks, etc. |
|---|
| 3530 | ''' |
|---|
| 3531 | from matplotlib.patches import Ellipse,Arc,Circle,Polygon |
|---|
| 3532 | import numpy.ma as ma |
|---|
| 3533 | Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.)) |
|---|
| 3534 | global Data,Masks,StrSta |
|---|
| 3535 | colors=['b','g','r','c','m','k'] |
|---|
| 3536 | Data = G2frame.PatternTree.GetItemPyData( |
|---|
| 3537 | G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls')) |
|---|
| 3538 | # patch |
|---|
| 3539 | if 'invert_x' not in Data: |
|---|
| 3540 | Data['invert_x'] = False |
|---|
| 3541 | Data['invert_y'] = True |
|---|
| 3542 | # end patch |
|---|
| 3543 | Masks = G2frame.PatternTree.GetItemPyData( |
|---|
| 3544 | G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Masks')) |
|---|
| 3545 | try: #may be absent |
|---|
| 3546 | StrSta = G2frame.PatternTree.GetItemPyData( |
|---|
| 3547 | G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Stress/Strain')) |
|---|
| 3548 | except TypeError: #is missing |
|---|
| 3549 | StrSta = {} |
|---|
| 3550 | |
|---|
| 3551 | def OnImMotion(event): |
|---|
| 3552 | Page.canvas.SetToolTipString('') |
|---|
| 3553 | sizexy = Data['size'] |
|---|
| 3554 | FlatBkg = Data.get('Flat Bkg',0.) |
|---|
| 3555 | if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors |
|---|
| 3556 | Page.canvas.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata)) |
|---|
| 3557 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 3558 | item = G2frame.itemPicked |
|---|
| 3559 | pixelSize = Data['pixelSize'] |
|---|
| 3560 | scalex = 1000./pixelSize[0] |
|---|
| 3561 | scaley = 1000./pixelSize[1] |
|---|
| 3562 | if item and G2frame.PatternTree.GetItemText(G2frame.PickId) == 'Image Controls': |
|---|
| 3563 | if 'Text' in str(item): |
|---|
| 3564 | Page.canvas.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata)) |
|---|
| 3565 | else: |
|---|
| 3566 | xcent,ycent = Data['center'] |
|---|
| 3567 | xpos = event.xdata-xcent |
|---|
| 3568 | ypos = event.ydata-ycent |
|---|
| 3569 | tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data) |
|---|
| 3570 | if 'line3' in str(item) or 'line4' in str(item) and not Data['fullIntegrate']: |
|---|
| 3571 | Page.canvas.SetToolTipString('%6d deg'%(azm)) |
|---|
| 3572 | elif 'line1' in str(item) or 'line2' in str(item): |
|---|
| 3573 | Page.canvas.SetToolTipString('%8.3f deg'%(tth)) |
|---|
| 3574 | else: |
|---|
| 3575 | xpos = event.xdata |
|---|
| 3576 | ypos = event.ydata |
|---|
| 3577 | xpix = xpos*scalex |
|---|
| 3578 | ypix = ypos*scaley |
|---|
| 3579 | Int = 0 |
|---|
| 3580 | if (0 <= xpix <= sizexy[0]) and (0 <= ypix <= sizexy[1]): |
|---|
| 3581 | Int = G2frame.ImageZ[ypix][xpix]-int(FlatBkg) |
|---|
| 3582 | tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data) |
|---|
| 3583 | Q = 2.*math.pi/dsp |
|---|
| 3584 | fields = ['','Detector 2-th =%9.3fdeg, dsp =%9.3fA, Q = %6.5fA-1, azm = %7.2fdeg, I = %6d'%(tth,dsp,Q,azm,Int)] |
|---|
| 3585 | if G2frame.MaskKey in ['p','f']: |
|---|
| 3586 | fields[1] = 'Polygon/frame mask pick - LB next point, RB close polygon' |
|---|
| 3587 | elif G2frame.StrainKey: |
|---|
| 3588 | fields[0] = 'd-zero pick active' |
|---|
| 3589 | G2frame.G2plotNB.status.SetFields(fields) |
|---|
| 3590 | |
|---|
| 3591 | def OnImPlotKeyPress(event): |
|---|
| 3592 | try: |
|---|
| 3593 | PickName = G2frame.PatternTree.GetItemText(G2frame.PickId) |
|---|
| 3594 | except TypeError: |
|---|
| 3595 | return |
|---|
| 3596 | if PickName == 'Masks': |
|---|
| 3597 | if event.key in ['l','p','f','s','a','r']: |
|---|
| 3598 | G2frame.MaskKey = event.key |
|---|
| 3599 | OnStartMask(G2frame) |
|---|
| 3600 | PlotImage(G2frame,newPlot=False) |
|---|
| 3601 | |
|---|
| 3602 | elif PickName == 'Stress/Strain': |
|---|
| 3603 | if event.key in ['a',]: |
|---|
| 3604 | G2frame.StrainKey = event.key |
|---|
| 3605 | StrSta = OnStartNewDzero(G2frame) |
|---|
| 3606 | PlotImage(G2frame,newPlot=False) |
|---|
| 3607 | |
|---|
| 3608 | elif PickName == 'Image Controls': |
|---|
| 3609 | if event.key in ['c',]: |
|---|
| 3610 | Xpos = event.xdata |
|---|
| 3611 | if not Xpos: #got point out of frame |
|---|
| 3612 | return |
|---|
| 3613 | Ypos = event.ydata |
|---|
| 3614 | dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?', |
|---|
| 3615 | 'Center change',style=wx.OK|wx.CANCEL) |
|---|
| 3616 | try: |
|---|
| 3617 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 3618 | print 'move center to: ',Xpos,Ypos |
|---|
| 3619 | Data['center'] = [Xpos,Ypos] |
|---|
| 3620 | G2imG.UpdateImageControls(G2frame,Data,Masks) |
|---|
| 3621 | PlotImage(G2frame,newPlot=False) |
|---|
| 3622 | finally: |
|---|
| 3623 | dlg.Destroy() |
|---|
| 3624 | return |
|---|
| 3625 | elif event.key == 'l': |
|---|
| 3626 | G2frame.logPlot = not G2frame.logPlot |
|---|
| 3627 | elif event.key in ['x',]: |
|---|
| 3628 | Data['invert_x'] = not Data['invert_x'] |
|---|
| 3629 | elif event.key in ['y',]: |
|---|
| 3630 | Data['invert_y'] = not Data['invert_y'] |
|---|
| 3631 | PlotImage(G2frame,newPlot=True) |
|---|
| 3632 | |
|---|
| 3633 | def OnKeyBox(event): |
|---|
| 3634 | if G2frame.G2plotNB.nb.GetSelection() == G2frame.G2plotNB.plotList.index('2D Powder Image'): |
|---|
| 3635 | event.key = cb.GetValue()[0] |
|---|
| 3636 | cb.SetValue(' key press') |
|---|
| 3637 | if event.key in ['l','s','a','r','p','x','y']: |
|---|
| 3638 | wx.CallAfter(OnImPlotKeyPress,event) |
|---|
| 3639 | Page.canvas.SetFocus() # redirect the Focus from the button back to the plot |
|---|
| 3640 | |
|---|
| 3641 | def OnImPick(event): |
|---|
| 3642 | if G2frame.PatternTree.GetItemText(G2frame.PickId) not in ['Image Controls','Masks']: |
|---|
| 3643 | return |
|---|
| 3644 | if G2frame.itemPicked is not None: return |
|---|
| 3645 | G2frame.itemPicked = event.artist |
|---|
| 3646 | G2frame.mousePicked = event.mouseevent |
|---|
| 3647 | |
|---|
| 3648 | def OnImRelease(event): |
|---|
| 3649 | try: |
|---|
| 3650 | PickName = G2frame.PatternTree.GetItemText(G2frame.PickId) |
|---|
| 3651 | except TypeError: |
|---|
| 3652 | return |
|---|
| 3653 | if PickName not in ['Image Controls','Masks','Stress/Strain']: |
|---|
| 3654 | return |
|---|
| 3655 | pixelSize = Data['pixelSize'] |
|---|
| 3656 | FlatBkg = Data.get('Flat Bkg',0.) |
|---|
| 3657 | scalex = 1000./pixelSize[0] |
|---|
| 3658 | scaley = 1000./pixelSize[1] |
|---|
| 3659 | # pixLimit = Data['pixLimit'] #can be too tight |
|---|
| 3660 | pixLimit = 20 #this makes the search box 40x40 pixels |
|---|
| 3661 | if G2frame.itemPicked is None and PickName == 'Image Controls' and len(G2frame.ImageZ): |
|---|
| 3662 | Xpos = event.xdata |
|---|
| 3663 | if not (Xpos and G2frame.ifGetRing): #got point out of frame |
|---|
| 3664 | return |
|---|
| 3665 | Ypos = event.ydata |
|---|
| 3666 | if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected |
|---|
| 3667 | if event.button == 1: |
|---|
| 3668 | Xpix = Xpos*scalex |
|---|
| 3669 | Ypix = Ypos*scaley |
|---|
| 3670 | xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ-FlatBkg,pixLimit,Xpix,Ypix) |
|---|
| 3671 | if I and J: |
|---|
| 3672 | xpos += .5 #shift to pixel center |
|---|
| 3673 | ypos += .5 |
|---|
| 3674 | xpos /= scalex #convert to mm |
|---|
| 3675 | ypos /= scaley |
|---|
| 3676 | Data['ring'].append([xpos,ypos]) |
|---|
| 3677 | elif event.button == 3: |
|---|
| 3678 | G2frame.dataFrame.GetStatusBar().SetStatusText('Calibrating...',0) |
|---|
| 3679 | if G2img.ImageCalibrate(G2frame,Data): |
|---|
| 3680 | G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check',0) |
|---|
| 3681 | print 'Calibration successful' |
|---|
| 3682 | else: |
|---|
| 3683 | G2frame.dataFrame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose',0) |
|---|
| 3684 | print 'Calibration failed' |
|---|
| 3685 | G2frame.ifGetRing = False |
|---|
| 3686 | G2imG.UpdateImageControls(G2frame,Data,Masks) |
|---|
| 3687 | return |
|---|
| 3688 | PlotImage(G2frame,newImage=False) |
|---|
| 3689 | return |
|---|
| 3690 | elif G2frame.MaskKey and PickName == 'Masks': |
|---|
| 3691 | Xpos,Ypos = [event.xdata,event.ydata] |
|---|
| 3692 | if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected |
|---|
| 3693 | return |
|---|
| 3694 | if G2frame.MaskKey == 's' and event.button == 1: |
|---|
| 3695 | Masks['Points'][-1] = [Xpos,Ypos,1.] |
|---|
| 3696 | G2frame.MaskKey = '' |
|---|
| 3697 | elif G2frame.MaskKey == 'r' and event.button == 1: |
|---|
| 3698 | tth = G2img.GetTth(Xpos,Ypos,Data) |
|---|
| 3699 | Masks['Rings'][-1] = [tth,0.1] |
|---|
| 3700 | G2frame.MaskKey = '' |
|---|
| 3701 | elif G2frame.MaskKey == 'a' and event.button == 1: |
|---|
| 3702 | tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data) |
|---|
| 3703 | azm = int(azm) |
|---|
| 3704 | Masks['Arcs'][-1] = [tth,[azm-5,azm+5],0.1] |
|---|
| 3705 | G2frame.MaskKey = '' |
|---|
| 3706 | elif G2frame.MaskKey =='p': |
|---|
| 3707 | polygon = Masks['Polygons'][-1] |
|---|
| 3708 | if len(polygon) > 2 and event.button == 3: |
|---|
| 3709 | x0,y0 = polygon[0] |
|---|
| 3710 | polygon.append([x0,y0]) |
|---|
| 3711 | G2frame.MaskKey = '' |
|---|
| 3712 | G2frame.G2plotNB.status.SetFields(['','Polygon closed']) |
|---|
| 3713 | else: |
|---|
| 3714 | G2frame.G2plotNB.status.SetFields(['','New polygon point: %.1f,%.1f'%(Xpos,Ypos)]) |
|---|
| 3715 | polygon.append([Xpos,Ypos]) |
|---|
| 3716 | elif G2frame.MaskKey =='f': |
|---|
| 3717 | frame = Masks['Frames'] |
|---|
| 3718 | if len(frame) > 2 and event.button == 3: |
|---|
| 3719 | x0,y0 = frame[0] |
|---|
| 3720 | frame.append([x0,y0]) |
|---|
| 3721 | G2frame.MaskKey = '' |
|---|
| 3722 | G2frame.G2plotNB.status.SetFields(['','Frame closed']) |
|---|
| 3723 | else: |
|---|
| 3724 | G2frame.G2plotNB.status.SetFields(['','New frame point: %.1f,%.1f'%(Xpos,Ypos)]) |
|---|
| 3725 | frame.append([Xpos,Ypos]) |
|---|
| 3726 | G2imG.UpdateMasks(G2frame,Masks) |
|---|
| 3727 | PlotImage(G2frame,newImage=False) |
|---|
| 3728 | elif PickName == 'Stress/Strain' and G2frame.StrainKey: |
|---|
| 3729 | Xpos,Ypos = [event.xdata,event.ydata] |
|---|
| 3730 | if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected |
|---|
| 3731 | return |
|---|
| 3732 | dsp = G2img.GetDsp(Xpos,Ypos,Data) |
|---|
| 3733 | StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':0.5, |
|---|
| 3734 | 'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]}) |
|---|
| 3735 | R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ-FlatBkg,Data) |
|---|
| 3736 | if not len(R): |
|---|
| 3737 | del StrSta['d-zero'][-1] |
|---|
| 3738 | G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection') |
|---|
| 3739 | StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True) |
|---|
| 3740 | G2frame.StrainKey = '' |
|---|
| 3741 | G2imG.UpdateStressStrain(G2frame,StrSta) |
|---|
| 3742 | PlotStrain(G2frame,StrSta) |
|---|
| 3743 | PlotImage(G2frame,newPlot=False) |
|---|
| 3744 | else: |
|---|
| 3745 | Xpos,Ypos = [event.xdata,event.ydata] |
|---|
| 3746 | if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected |
|---|
| 3747 | return |
|---|
| 3748 | if G2frame.ifGetRing: #delete a calibration ring pick |
|---|
| 3749 | xypos = [Xpos,Ypos] |
|---|
| 3750 | rings = Data['ring'] |
|---|
| 3751 | for ring in rings: |
|---|
| 3752 | if np.allclose(ring,xypos,.01,0): |
|---|
| 3753 | rings.remove(ring) |
|---|
| 3754 | else: |
|---|
| 3755 | tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3] |
|---|
| 3756 | itemPicked = str(G2frame.itemPicked) |
|---|
| 3757 | if 'Line2D' in itemPicked and PickName == 'Image Controls': |
|---|
| 3758 | if 'line1' in itemPicked: |
|---|
| 3759 | Data['IOtth'][0] = max(tth,0.001) |
|---|
| 3760 | elif 'line2' in itemPicked: |
|---|
| 3761 | Data['IOtth'][1] = tth |
|---|
| 3762 | elif 'line3' in itemPicked: |
|---|
| 3763 | Data['LRazimuth'][0] = int(azm) |
|---|
| 3764 | elif 'line4' in itemPicked and not Data['fullIntegrate']: |
|---|
| 3765 | Data['LRazimuth'][1] = int(azm) |
|---|
| 3766 | |
|---|
| 3767 | Data['LRazimuth'][0] %= 360 |
|---|
| 3768 | Data['LRazimuth'][1] %= 360 |
|---|
| 3769 | if Data['LRazimuth'][0] > Data['LRazimuth'][1]: |
|---|
| 3770 | Data['LRazimuth'][1] += 360 |
|---|
| 3771 | if Data['fullIntegrate']: |
|---|
| 3772 | Data['LRazimuth'][1] = Data['LRazimuth'][0]+360 |
|---|
| 3773 | |
|---|
| 3774 | if Data['IOtth'][0] > Data['IOtth'][1]: |
|---|
| 3775 | Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0] |
|---|
| 3776 | |
|---|
| 3777 | G2frame.InnerTth.SetValue("%8.2f" % (Data['IOtth'][0])) |
|---|
| 3778 | G2frame.OuterTth.SetValue("%8.2f" % (Data['IOtth'][1])) |
|---|
| 3779 | G2frame.Lazim.SetValue("%6d" % (Data['LRazimuth'][0])) |
|---|
| 3780 | G2frame.Razim.SetValue("%6d" % (Data['LRazimuth'][1])) |
|---|
| 3781 | elif 'Circle' in itemPicked and PickName == 'Masks': |
|---|
| 3782 | spots = Masks['Points'] |
|---|
| 3783 | newPos = itemPicked.split(')')[0].split('(')[2].split(',') |
|---|
| 3784 | newPos = np.array([float(newPos[0]),float(newPos[1])]) |
|---|
| 3785 | for spot in spots: |
|---|
| 3786 | if spot and np.allclose(np.array([spot[:2]]),newPos): |
|---|
| 3787 | spot[:2] = Xpos,Ypos |
|---|
| 3788 | G2imG.UpdateMasks(G2frame,Masks) |
|---|
| 3789 | elif 'Line2D' in itemPicked and PickName == 'Masks': |
|---|
| 3790 | Obj = G2frame.itemPicked.findobj() |
|---|
| 3791 | rings = Masks['Rings'] |
|---|
| 3792 | arcs = Masks['Arcs'] |
|---|
| 3793 | polygons = Masks['Polygons'] |
|---|
| 3794 | frame = Masks['Frames'] |
|---|
| 3795 | for ring in G2frame.ringList: |
|---|
| 3796 | if Obj == ring[0]: |
|---|
| 3797 | rN = ring[1] |
|---|
| 3798 | if ring[2] == 'o': |
|---|
| 3799 | rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)-rings[rN][1]/2. |
|---|
| 3800 | else: |
|---|
| 3801 | rings[rN][0] = G2img.GetTth(Xpos,Ypos,Data)+rings[rN][1]/2. |
|---|
| 3802 | for arc in G2frame.arcList: |
|---|
| 3803 | if Obj == arc[0]: |
|---|
| 3804 | aN = arc[1] |
|---|
| 3805 | if arc[2] == 'o': |
|---|
| 3806 | arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)-arcs[aN][2]/2 |
|---|
| 3807 | elif arc[2] == 'i': |
|---|
| 3808 | arcs[aN][0] = G2img.GetTth(Xpos,Ypos,Data)+arcs[aN][2]/2 |
|---|
| 3809 | elif arc[2] == 'l': |
|---|
| 3810 | arcs[aN][1][0] = int(G2img.GetAzm(Xpos,Ypos,Data)) |
|---|
| 3811 | else: |
|---|
| 3812 | arcs[aN][1][1] = int(G2img.GetAzm(Xpos,Ypos,Data)) |
|---|
| 3813 | for poly in G2frame.polyList: #merging points problem here? |
|---|
| 3814 | if Obj == poly[0]: |
|---|
| 3815 | ind = G2frame.itemPicked.contains(G2frame.mousePicked)[1]['ind'][0] |
|---|
| 3816 | oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata]) |
|---|
| 3817 | pN = poly[1] |
|---|
| 3818 | for i,xy in enumerate(polygons[pN]): |
|---|
| 3819 | if np.allclose(np.array([xy]),oldPos,atol=1.0): |
|---|
| 3820 | if event.button == 1: |
|---|
| 3821 | polygons[pN][i] = Xpos,Ypos |
|---|
| 3822 | elif event.button == 3: |
|---|
| 3823 | polygons[pN].insert(i,[Xpos,Ypos]) |
|---|
| 3824 | break |
|---|
| 3825 | if frame: |
|---|
| 3826 | oldPos = np.array([G2frame.mousePicked.xdata,G2frame.mousePicked.ydata]) |
|---|
| 3827 | for i,xy in enumerate(frame): |
|---|
| 3828 | if np.allclose(np.array([xy]),oldPos,atol=1.0): |
|---|
| 3829 | if event.button == 1: |
|---|
| 3830 | frame[i] = Xpos,Ypos |
|---|
| 3831 | elif event.button == 3: |
|---|
| 3832 | frame.insert(i,[Xpos,Ypos]) |
|---|
| 3833 | break |
|---|
| 3834 | G2imG.UpdateMasks(G2frame,Masks) |
|---|
| 3835 | # else: #keep for future debugging |
|---|
| 3836 | # print str(G2frame.itemPicked),event.xdata,event.ydata,event.button |
|---|
| 3837 | PlotImage(G2frame,newImage=True) |
|---|
| 3838 | G2frame.itemPicked = None |
|---|
| 3839 | |
|---|
| 3840 | try: |
|---|
| 3841 | plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image') |
|---|
| 3842 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3843 | if not newPlot: |
|---|
| 3844 | Plot = Page.figure.gca() #get previous powder plot & get limits |
|---|
| 3845 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 3846 | if newImage: |
|---|
| 3847 | Page.figure.clf() |
|---|
| 3848 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 3849 | except ValueError: |
|---|
| 3850 | Plot = G2frame.G2plotNB.addMpl('2D Powder Image').gca() |
|---|
| 3851 | plotNum = G2frame.G2plotNB.plotList.index('2D Powder Image') |
|---|
| 3852 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 3853 | Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress) |
|---|
| 3854 | Page.canvas.mpl_connect('motion_notify_event', OnImMotion) |
|---|
| 3855 | Page.canvas.mpl_connect('pick_event', OnImPick) |
|---|
| 3856 | Page.canvas.mpl_connect('button_release_event', OnImRelease) |
|---|
| 3857 | xylim = [] |
|---|
| 3858 | Page.Choice = None |
|---|
| 3859 | if not event: #event from GUI TextCtrl - don't want focus to change to plot!!! |
|---|
| 3860 | Page.SetFocus() |
|---|
| 3861 | Title = G2frame.PatternTree.GetItemText(G2frame.Image)[4:] |
|---|
| 3862 | G2frame.G2plotNB.status.DestroyChildren() |
|---|
| 3863 | if G2frame.logPlot: |
|---|
| 3864 | Title = 'log('+Title+')' |
|---|
| 3865 | Plot.set_title(Title) |
|---|
| 3866 | try: |
|---|
| 3867 | if G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Image Controls',]: |
|---|
| 3868 | Page.Choice = (' key press','l: log(I) on','x: flip x','y: flip y',) |
|---|
| 3869 | if G2frame.logPlot: |
|---|
| 3870 | Page.Choice[1] = 'l: log(I) off' |
|---|
| 3871 | Page.keyPress = OnImPlotKeyPress |
|---|
| 3872 | elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Masks',]: |
|---|
| 3873 | Page.Choice = (' key press','l: log(I) on','s: spot mask','a: arc mask','r: ring mask', |
|---|
| 3874 | 'p: polygon mask','f: frame mask',) |
|---|
| 3875 | if G2frame.logPlot: |
|---|
| 3876 | Page.Choice[1] = 'l: log(I) off' |
|---|
| 3877 | Page.keyPress = OnImPlotKeyPress |
|---|
| 3878 | elif G2frame.PatternTree.GetItemText(G2frame.PickId) in ['Stress/Strain',]: |
|---|
| 3879 | Page.Choice = (' key press','a: add new ring',) |
|---|
| 3880 | Page.keyPress = OnImPlotKeyPress |
|---|
| 3881 | except TypeError: |
|---|
| 3882 | pass |
|---|
| 3883 | size,imagefile = G2frame.PatternTree.GetItemPyData(G2frame.Image) |
|---|
| 3884 | dark = Data.get('dark image',[0,'']) |
|---|
| 3885 | if dark[0]: |
|---|
| 3886 | darkfile = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, |
|---|
| 3887 | G2frame.root,dark[0]))[1] |
|---|
| 3888 | if imagefile != G2frame.oldImagefile: |
|---|
| 3889 | imagefile = G2IO.CheckImageFile(G2frame,imagefile) |
|---|
| 3890 | if not imagefile: |
|---|
| 3891 | G2frame.G2plotNB.Delete('2D Powder Image') |
|---|
| 3892 | return |
|---|
| 3893 | G2frame.PatternTree.SetItemPyData(G2frame.Image,[size,imagefile]) |
|---|
| 3894 | G2frame.ImageZ = G2IO.GetImageData(G2frame,imagefile,imageOnly=True) |
|---|
| 3895 | if dark[0]: |
|---|
| 3896 | darkImg = G2IO.GetImageData(G2frame,darkfile,imageOnly=True) |
|---|
| 3897 | G2frame.ImageZ += dark[1]*darkImg |
|---|
| 3898 | G2frame.oldImagefile = imagefile |
|---|
| 3899 | |
|---|
| 3900 | imScale = 1 |
|---|
| 3901 | if len(G2frame.ImageZ) > 1024: |
|---|
| 3902 | imScale = len(G2frame.ImageZ)/1024 |
|---|
| 3903 | sizexy = Data['size'] |
|---|
| 3904 | pixelSize = Data['pixelSize'] |
|---|
| 3905 | scalex = 1000./pixelSize[0] |
|---|
| 3906 | scaley = 1000./pixelSize[1] |
|---|
| 3907 | Xmax = sizexy[0]*pixelSize[0]/1000. |
|---|
| 3908 | Ymax = sizexy[1]*pixelSize[1]/1000. |
|---|
| 3909 | xlim = (0,Xmax) |
|---|
| 3910 | ylim = (Ymax,0) |
|---|
| 3911 | Imin,Imax = Data['range'][1] |
|---|
| 3912 | acolor = mpl.cm.get_cmap(Data['color']) |
|---|
| 3913 | xcent,ycent = Data['center'] |
|---|
| 3914 | Plot.set_xlabel('Image x-axis, mm',fontsize=12) |
|---|
| 3915 | Plot.set_ylabel('Image y-axis, mm',fontsize=12) |
|---|
| 3916 | #do threshold mask - "real" mask - others are just bondaries |
|---|
| 3917 | Zlim = Masks['Thresholds'][1] |
|---|
| 3918 | FlatBkg = Data.get('Flat Bkg',0.0) |
|---|
| 3919 | wx.BeginBusyCursor() |
|---|
| 3920 | try: |
|---|
| 3921 | |
|---|
| 3922 | if newImage: |
|---|
| 3923 | Imin,Imax = Data['range'][1] |
|---|
| 3924 | MA = ma.masked_greater(ma.masked_less(G2frame.ImageZ,Zlim[0]+FlatBkg),Zlim[1]+FlatBkg) |
|---|
| 3925 | MaskA = ma.getmaskarray(MA) |
|---|
| 3926 | A = G2img.ImageCompress(MA,imScale)-FlatBkg |
|---|
| 3927 | AM = G2img.ImageCompress(MaskA,imScale) |
|---|
| 3928 | if G2frame.logPlot: |
|---|
| 3929 | A = np.where(A>Imin,np.where(A<Imax,A,0),0) |
|---|
| 3930 | A = np.where(A>0,np.log(A),0) |
|---|
| 3931 | AM = np.where(AM>0,np.log(AM),0) |
|---|
| 3932 | Imin,Imax = [np.amin(A),np.amax(A)] |
|---|
| 3933 | ImgM = Plot.imshow(AM,aspect='equal',cmap='Reds', |
|---|
| 3934 | interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0]) |
|---|
| 3935 | Img = Plot.imshow(A,aspect='equal',cmap=acolor, |
|---|
| 3936 | interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0]) |
|---|
| 3937 | |
|---|
| 3938 | Plot.plot(xcent,ycent,'x') |
|---|
| 3939 | #G2frame.PatternTree.GetItemText(item) |
|---|
| 3940 | if Data['showLines']: |
|---|
| 3941 | LRAzim = Data['LRazimuth'] #NB: integers |
|---|
| 3942 | Nazm = Data['outAzimuths'] |
|---|
| 3943 | delAzm = float(LRAzim[1]-LRAzim[0])/Nazm |
|---|
| 3944 | AzmthOff = Data['azmthOff'] |
|---|
| 3945 | IOtth = Data['IOtth'] |
|---|
| 3946 | wave = Data['wavelength'] |
|---|
| 3947 | dspI = wave/(2.0*sind(IOtth[0]/2.0)) |
|---|
| 3948 | ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola) |
|---|
| 3949 | dspO = wave/(2.0*sind(IOtth[1]/2.0)) |
|---|
| 3950 | ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse |
|---|
| 3951 | Azm = np.array(range(LRAzim[0],LRAzim[1]+1))-AzmthOff |
|---|
| 3952 | if ellI: |
|---|
| 3953 | xyI = [] |
|---|
| 3954 | for azm in Azm: |
|---|
| 3955 | xy = G2img.GetDetectorXY(dspI,azm,Data) |
|---|
| 3956 | if np.any(xy): |
|---|
| 3957 | xyI.append(xy) |
|---|
| 3958 | if len(xyI): |
|---|
| 3959 | xyI = np.array(xyI) |
|---|
| 3960 | arcxI,arcyI = xyI.T |
|---|
| 3961 | Plot.plot(arcxI,arcyI,picker=3) |
|---|
| 3962 | if ellO: |
|---|
| 3963 | xyO = [] |
|---|
| 3964 | for azm in Azm: |
|---|
| 3965 | xy = G2img.GetDetectorXY(dspO,azm,Data) |
|---|
| 3966 | if np.any(xy): |
|---|
| 3967 | xyO.append(xy) |
|---|
| 3968 | if len(xyO): |
|---|
| 3969 | xyO = np.array(xyO) |
|---|
| 3970 | arcxO,arcyO = xyO.T |
|---|
| 3971 | Plot.plot(arcxO,arcyO,picker=3) |
|---|
| 3972 | if ellO and ellI: |
|---|
| 3973 | Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3) |
|---|
| 3974 | Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3) |
|---|
| 3975 | for i in range(Nazm): |
|---|
| 3976 | cake = LRAzim[0]+i*delAzm-AzmthOff |
|---|
| 3977 | if Data['centerAzm']: |
|---|
| 3978 | cake += delAzm/2. |
|---|
| 3979 | ind = np.searchsorted(Azm,cake) |
|---|
| 3980 | Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5)) |
|---|
| 3981 | |
|---|
| 3982 | if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Image Controls': |
|---|
| 3983 | for xring,yring in Data['ring']: |
|---|
| 3984 | Plot.plot(xring,yring,'r+',picker=3) |
|---|
| 3985 | if Data['setRings']: |
|---|
| 3986 | N = 0 |
|---|
| 3987 | for ring in Data['rings']: |
|---|
| 3988 | xring,yring = np.array(ring).T[:2] |
|---|
| 3989 | Plot.plot(xring,yring,'.',color=colors[N%6]) |
|---|
| 3990 | N += 1 |
|---|
| 3991 | for ellipse in Data['ellipses']: #what about hyperbola? |
|---|
| 3992 | cent,phi,[width,height],col = ellipse |
|---|
| 3993 | if width > 0: #ellipses |
|---|
| 3994 | Plot.add_artist(Ellipse([cent[0],cent[1]],2*width,2*height,phi,ec=col,fc='none')) |
|---|
| 3995 | Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center') |
|---|
| 3996 | if G2frame.PatternTree.GetItemText(G2frame.PickId) in 'Stress/Strain': |
|---|
| 3997 | for N,ring in enumerate(StrSta['d-zero']): |
|---|
| 3998 | xring,yring = ring['ImxyObs'] |
|---|
| 3999 | Plot.plot(xring,yring,colors[N%6]+'.') |
|---|
| 4000 | #masks - mask lines numbered after integration limit lines |
|---|
| 4001 | spots = Masks['Points'] |
|---|
| 4002 | rings = Masks['Rings'] |
|---|
| 4003 | arcs = Masks['Arcs'] |
|---|
| 4004 | polygons = Masks['Polygons'] |
|---|
| 4005 | if 'Frames' not in Masks: |
|---|
| 4006 | Masks['Frames'] = [] |
|---|
| 4007 | frame = Masks['Frames'] |
|---|
| 4008 | for spot in spots: |
|---|
| 4009 | if spot: |
|---|
| 4010 | x,y,d = spot |
|---|
| 4011 | Plot.add_artist(Circle((x,y),radius=d/2,fc='none',ec='r',picker=3)) |
|---|
| 4012 | G2frame.ringList = [] |
|---|
| 4013 | for iring,ring in enumerate(rings): |
|---|
| 4014 | if ring: |
|---|
| 4015 | tth,thick = ring |
|---|
| 4016 | wave = Data['wavelength'] |
|---|
| 4017 | xy1 = [] |
|---|
| 4018 | xy2 = [] |
|---|
| 4019 | Azm = np.linspace(0,362,181) |
|---|
| 4020 | for azm in Azm: |
|---|
| 4021 | xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola |
|---|
| 4022 | xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola |
|---|
| 4023 | x1,y1 = np.array(xy1).T |
|---|
| 4024 | x2,y2 = np.array(xy2).T |
|---|
| 4025 | G2frame.ringList.append([Plot.plot(x1,y1,'r',picker=3),iring,'o']) |
|---|
| 4026 | G2frame.ringList.append([Plot.plot(x2,y2,'r',picker=3),iring,'i']) |
|---|
| 4027 | G2frame.arcList = [] |
|---|
| 4028 | for iarc,arc in enumerate(arcs): |
|---|
| 4029 | if arc: |
|---|
| 4030 | tth,azm,thick = arc |
|---|
| 4031 | wave = Data['wavelength'] |
|---|
| 4032 | xy1 = [] |
|---|
| 4033 | xy2 = [] |
|---|
| 4034 | aR = azm[0],azm[1],azm[1]-azm[0] |
|---|
| 4035 | if azm[1]-azm[0] > 180: |
|---|
| 4036 | aR[2] /= 2 |
|---|
| 4037 | Azm = np.linspace(aR[0],aR[1],aR[2]) |
|---|
| 4038 | for azm in Azm: |
|---|
| 4039 | xy1.append(G2img.GetDetectorXY(Dsp(tth+thick/2.,wave),azm,Data)) #what about hyperbola |
|---|
| 4040 | xy2.append(G2img.GetDetectorXY(Dsp(tth-thick/2.,wave),azm,Data)) #what about hyperbola |
|---|
| 4041 | x1,y1 = np.array(xy1).T |
|---|
| 4042 | x2,y2 = np.array(xy2).T |
|---|
| 4043 | G2frame.arcList.append([Plot.plot(x1,y1,'r',picker=3),iarc,'o']) |
|---|
| 4044 | G2frame.arcList.append([Plot.plot(x2,y2,'r',picker=3),iarc,'i']) |
|---|
| 4045 | G2frame.arcList.append([Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3),iarc,'l']) |
|---|
| 4046 | G2frame.arcList.append([Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3),iarc,'u']) |
|---|
| 4047 | G2frame.polyList = [] |
|---|
| 4048 | for ipoly,polygon in enumerate(polygons): |
|---|
| 4049 | if polygon: |
|---|
| 4050 | x,y = np.hsplit(np.array(polygon),2) |
|---|
| 4051 | G2frame.polyList.append([Plot.plot(x,y,'r+',picker=10),ipoly]) |
|---|
| 4052 | Plot.plot(x,y,'r') |
|---|
| 4053 | G2frame.frameList = [] |
|---|
| 4054 | if frame: |
|---|
| 4055 | x,y = np.hsplit(np.array(frame),2) |
|---|
| 4056 | G2frame.frameList.append([Plot.plot(x,y,'g+',picker=10),0]) |
|---|
| 4057 | Plot.plot(x,y,'g') |
|---|
| 4058 | if newImage: |
|---|
| 4059 | colorBar = Page.figure.colorbar(Img) |
|---|
| 4060 | Plot.set_xlim(xlim) |
|---|
| 4061 | Plot.set_ylim(ylim) |
|---|
| 4062 | if Data['invert_x']: |
|---|
| 4063 | Plot.invert_xaxis() |
|---|
| 4064 | if Data['invert_y']: |
|---|
| 4065 | Plot.invert_yaxis() |
|---|
| 4066 | if not newPlot and xylim: |
|---|
| 4067 | Page.toolbar.push_current() |
|---|
| 4068 | Plot.set_xlim(xylim[0]) |
|---|
| 4069 | Plot.set_ylim(xylim[1]) |
|---|
| 4070 | xylim = [] |
|---|
| 4071 | Page.toolbar.push_current() |
|---|
| 4072 | Page.toolbar.draw() |
|---|
| 4073 | # patch for wx 2.9 on Mac, to force a redraw |
|---|
| 4074 | i,j= wx.__version__.split('.')[0:2] |
|---|
| 4075 | if int(i)+int(j)/10. > 2.8 and 'wxOSX' in wx.PlatformInfo: |
|---|
| 4076 | Page.canvas.draw() |
|---|
| 4077 | else: |
|---|
| 4078 | Page.canvas.draw() |
|---|
| 4079 | finally: |
|---|
| 4080 | wx.EndBusyCursor() |
|---|
| 4081 | |
|---|
| 4082 | ################################################################################ |
|---|
| 4083 | ##### PlotIntegration |
|---|
| 4084 | ################################################################################ |
|---|
| 4085 | |
|---|
| 4086 | def PlotIntegration(G2frame,newPlot=False,event=None): |
|---|
| 4087 | '''Plot of 2D image after image integration with 2-theta and azimuth as coordinates |
|---|
| 4088 | ''' |
|---|
| 4089 | |
|---|
| 4090 | def OnMotion(event): |
|---|
| 4091 | Page.canvas.SetToolTipString('') |
|---|
| 4092 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 4093 | azm = event.ydata |
|---|
| 4094 | tth = event.xdata |
|---|
| 4095 | if azm and tth: |
|---|
| 4096 | G2frame.G2plotNB.status.SetFields(\ |
|---|
| 4097 | ['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)]) |
|---|
| 4098 | |
|---|
| 4099 | try: |
|---|
| 4100 | plotNum = G2frame.G2plotNB.plotList.index('2D Integration') |
|---|
| 4101 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 4102 | if not newPlot: |
|---|
| 4103 | Plot = Page.figure.gca() #get previous plot & get limits |
|---|
| 4104 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 4105 | Page.figure.clf() |
|---|
| 4106 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 4107 | |
|---|
| 4108 | except ValueError: |
|---|
| 4109 | Plot = G2frame.G2plotNB.addMpl('2D Integration').gca() |
|---|
| 4110 | plotNum = G2frame.G2plotNB.plotList.index('2D Integration') |
|---|
| 4111 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 4112 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 4113 | Page.views = False |
|---|
| 4114 | view = False |
|---|
| 4115 | Page.Choice = None |
|---|
| 4116 | if not event: |
|---|
| 4117 | Page.SetFocus() |
|---|
| 4118 | |
|---|
| 4119 | Data = G2frame.PatternTree.GetItemPyData( |
|---|
| 4120 | G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls')) |
|---|
| 4121 | image = G2frame.Integrate[0] |
|---|
| 4122 | xsc = G2frame.Integrate[1] |
|---|
| 4123 | ysc = G2frame.Integrate[2] |
|---|
| 4124 | Imin,Imax = Data['range'][1] |
|---|
| 4125 | acolor = mpl.cm.get_cmap(Data['color']) |
|---|
| 4126 | Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:]) |
|---|
| 4127 | Plot.set_ylabel('azimuth',fontsize=12) |
|---|
| 4128 | Plot.set_xlabel('2-theta',fontsize=12) |
|---|
| 4129 | Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \ |
|---|
| 4130 | extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto') |
|---|
| 4131 | colorBar = Page.figure.colorbar(Img) |
|---|
| 4132 | # if Data['ellipses']: |
|---|
| 4133 | # for ellipse in Data['ellipses']: |
|---|
| 4134 | # x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color |
|---|
| 4135 | # tth,azm = G2img.GetTthAzm(x,y,Data) |
|---|
| 4136 | ## azm = np.where(azm < 0.,azm+360,azm) |
|---|
| 4137 | # Plot.plot(tth,azm,'b,') |
|---|
| 4138 | if not newPlot: |
|---|
| 4139 | Page.toolbar.push_current() |
|---|
| 4140 | Plot.set_xlim(xylim[0]) |
|---|
| 4141 | Plot.set_ylim(xylim[1]) |
|---|
| 4142 | xylim = [] |
|---|
| 4143 | Page.toolbar.push_current() |
|---|
| 4144 | Page.toolbar.draw() |
|---|
| 4145 | else: |
|---|
| 4146 | Page.canvas.draw() |
|---|
| 4147 | |
|---|
| 4148 | ################################################################################ |
|---|
| 4149 | ##### PlotTRImage |
|---|
| 4150 | ################################################################################ |
|---|
| 4151 | |
|---|
| 4152 | def PlotTRImage(G2frame,tax,tay,taz,newPlot=False): |
|---|
| 4153 | '''a test plot routine - not normally used |
|---|
| 4154 | ''' |
|---|
| 4155 | |
|---|
| 4156 | def OnMotion(event): |
|---|
| 4157 | Page.canvas.SetToolTipString('') |
|---|
| 4158 | Page.canvas.SetCursor(wx.CROSS_CURSOR) |
|---|
| 4159 | azm = event.xdata |
|---|
| 4160 | tth = event.ydata |
|---|
| 4161 | if azm and tth: |
|---|
| 4162 | G2frame.G2plotNB.status.SetFields(\ |
|---|
| 4163 | ['','Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm)]) |
|---|
| 4164 | |
|---|
| 4165 | try: |
|---|
| 4166 | plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image') |
|---|
| 4167 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 4168 | if not newPlot: |
|---|
| 4169 | Plot = Page.figure.gca() #get previous plot & get limits |
|---|
| 4170 | xylim = Plot.get_xlim(),Plot.get_ylim() |
|---|
| 4171 | Page.figure.clf() |
|---|
| 4172 | Plot = Page.figure.gca() #get a fresh plot after clf() |
|---|
| 4173 | |
|---|
| 4174 | except ValueError: |
|---|
| 4175 | Plot = G2frame.G2plotNB.addMpl('2D Transformed Powder Image').gca() |
|---|
| 4176 | plotNum = G2frame.G2plotNB.plotList.index('2D Transformed Powder Image') |
|---|
| 4177 | Page = G2frame.G2plotNB.nb.GetPage(plotNum) |
|---|
| 4178 | Page.canvas.mpl_connect('motion_notify_event', OnMotion) |
|---|
| 4179 | Page.views = False |
|---|
| 4180 | view = False |
|---|
| 4181 | Page.Choice = None |
|---|
| 4182 | Page.SetFocus() |
|---|
| 4183 | |
|---|
| 4184 | Data = G2frame.PatternTree.GetItemPyData( |
|---|
| 4185 | G2gd.GetPatternTreeItemId(G2frame,G2frame.Image, 'Image Controls')) |
|---|
| 4186 | Imin,Imax = Data['range'][1] |
|---|
| 4187 | step = (Imax-Imin)/5. |
|---|
| 4188 | V = np.arange(Imin,Imax,step) |
|---|
| 4189 | acolor = mpl.cm.get_cmap(Data['color']) |
|---|
| 4190 | Plot.set_title(G2frame.PatternTree.GetItemText(G2frame.Image)[4:]) |
|---|
| 4191 | Plot.set_xlabel('azimuth',fontsize=12) |
|---|
| 4192 | Plot.set_ylabel('2-theta',fontsize=12) |
|---|
| 4193 | Plot.contour(tax,tay,taz,V,cmap=acolor) |
|---|
| 4194 | if Data['showLines']: |
|---|
| 4195 | IOtth = Data['IOtth'] |
|---|
| 4196 | if Data['fullIntegrate']: |
|---|
| 4197 | LRAzim = [-180,180] |
|---|
| 4198 | else: |
|---|
| 4199 | LRAzim = Data['LRazimuth'] #NB: integers |
|---|
| 4200 | Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True) |
|---|
| 4201 | Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True) |
|---|
| 4202 | if not Data['fullIntegrate']: |
|---|
| 4203 | Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True) |
|---|
| 4204 | Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True) |
|---|
| 4205 | if Data['setRings']: |
|---|
| 4206 | rings = np.concatenate((Data['rings']),axis=0) |
|---|
| 4207 | for xring,yring,dsp in rings: |
|---|
| 4208 | x,y = G2img.GetTthAzm(xring,yring,Data) |
|---|
| 4209 | Plot.plot(y,x,'r+') |
|---|
| 4210 | if Data['ellipses']: |
|---|
| 4211 | for ellipse in Data['ellipses']: |
|---|
| 4212 | ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color |
|---|
| 4213 | x,y = np.hsplit(ring,2) |
|---|
| 4214 | tth,azm = G2img.GetTthAzm(x,y,Data) |
|---|
| 4215 | Plot.plot(azm,tth,'b,') |
|---|
| 4216 | if not newPlot: |
|---|
| 4217 | Page.toolbar.push_current() |
|---|
| 4218 | Plot.set_xlim(xylim[0]) |
|---|
| 4219 | Plot.set_ylim(xylim[1]) |
|---|
| 4220 | xylim = [] |
|---|
| 4221 | Page.toolbar.push_current() |
|---|
| 4222 | Page.toolbar.draw() |
|---|
| 4223 | else: |
|---|
| 4224 | Page.canvas.draw() |
|---|
| 4225 | |
|---|
| 4226 | ################################################################################ |
|---|
| 4227 | ##### PlotStructure |
|---|
| 4228 | ################################################################################ |
|---|
| 4229 | |
|---|
| 4230 | def PlotStructure(G2frame,data,firstCall=False): |
|---|
| 4231 | '''Crystal structure plotting package. Can show structures as balls, sticks, lines, |
|---|
| 4232 | thermal motion ellipsoids and polyhedra |
|---|
| 4233 | ''' |
|---|
| 4234 | |
|---|
| 4235 | def FindPeaksBonds(XYZ): |
|---|
| 4236 | rFact = data['Drawing'].get('radiusFactor',0.85) #data['Drawing'] could be empty! |
|---|
| 4237 | Bonds = [[] for x in XYZ] |
|---|
| 4238 | for i,xyz in enumerate(XYZ): |
|---|
| 4239 | Dx = XYZ-xyz |
|---|
| 4240 | dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1)) |
|---|
| 4241 | IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2)) |
|---|
| 4242 | for j in IndB[0]: |
|---|
| 4243 | Bonds[i].append(Dx[j]/2.) |
|---|
| 4244 | Bonds[j].append(-Dx[j]/2.) |
|---|
| 4245 | return Bonds |
|---|
| 4246 | |
|---|
| 4247 | # PlotStructure initialization here |
|---|
| 4248 | ForthirdPI = 4.0*math.pi/3.0 |
|---|
| 4249 | generalData = data['General'] |
|---|
| 4250 | cell = generalData['Cell'][1:7] |
|---|
| 4251 | Vol = generalData['Cell'][7:8][0] |
|---|
| 4252 | Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse |
|---|
| 4253 | Gmat,gmat = G2lat.cell2Gmat(cell) |
|---|
| 4254 | A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) |
|---|
| 4255 | B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) |
|---|
| 4256 | SGData = generalData['SGData'] |
|---|
| 4257 | if generalData['Type'] in ['modulated','magnetic']: |
|---|
| 4258 | SSGData = generalData['SSGData'] |
|---|
| 4259 | Mydir = generalData['Mydir'] |
|---|
| 4260 | Super = generalData.get('Super',0) |
|---|
| 4261 | atomData = data['Atoms'] |
|---|
| 4262 | mapPeaks = [] |
|---|
| 4263 | drawingData = data['Drawing'] |
|---|
| 4264 | if not drawingData: |
|---|
| 4265 | return #nothing setup, nothing to draw |
|---|
| 4266 | if 'Map Peaks' in data: |
|---|
| 4267 | mapPeaks = np.array(data['Map Peaks']) |
|---|
| 4268 | peakMax = 100. |
|---|
| 4269 | if len(mapPeaks): |
|---|
| 4270 | peakMax = np.max(mapPeaks.T[0]) |
|---|
| 4271 | resRBData = data['RBModels'].get('Residue',[]) |
|---|
| 4272 | vecRBData = data['RBModels'].get('Vector',[]) |
|---|
| 4273 | rbAtmDict = {} |
|---|
| 4274 | for rbObj in resRBData+vecRBData: |
|---|
| 4275 | exclList = ['X' for i in range(len(rbObj['Ids']))] |
|---|
| 4276 | rbAtmDict.update(dict(zip(rbObj['Ids'],exclList))) |
|---|
| 4277 | testRBObj = data.get('testRBObj',{}) |
|---|
| 4278 | rbObj = testRBObj.get('rbObj',{}) |
|---|
| 4279 | MCSA = data.get('MCSA',{}) |
|---|
| 4280 | mcsaModels = MCSA.get('Models',[]) |
|---|
| 4281 | if len(mcsaModels) > 1: |
|---|
| 4282 | XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA) |
|---|
| 4283 | mcsaXYZ = [] |
|---|
| 4284 | mcsaTypes = [] |
|---|
| 4285 | neqv = 0 |
|---|
| 4286 | for xyz,atyp in zip(XYZs,Types): |
|---|
| 4287 | equiv = G2spc.GenAtom(xyz,SGData,All=True,Move=False) |
|---|
| 4288 | neqv = max(neqv,len(equiv)) |
|---|
| 4289 | for item in equiv: |
|---|
| 4290 | mcsaXYZ.append(item[0]) |
|---|
| 4291 | mcsaTypes.append(atyp) |
|---|
| 4292 | mcsaXYZ = np.array(mcsaXYZ) |
|---|
| 4293 | mcsaTypes = np.array(mcsaTypes) |
|---|
| 4294 | nuniq = mcsaXYZ.shape[0]/neqv |
|---|
| 4295 | mcsaXYZ = np.reshape(mcsaXYZ,(nuniq,neqv,3)) |
|---|
| 4296 | mcsaTypes = np.reshape(mcsaTypes,(nuniq,neqv)) |
|---|
| 4297 | cent = np.fix(np.sum(mcsaXYZ+2.,axis=0)/nuniq)-2 |
|---|
| 4298 | cent[0] = [0 |
|---|
