# -*- coding: utf-8 -*- ########### SVN repository information ################### # $Date: 2020-06-12 14:06:19 +0000 (Fri, 12 Jun 2020)$ # $Author: toby$ # $Revision: 4482$ # $URL: trunk/GSASIIplot.py$ # $Id: GSASIIplot.py 4482 2020-06-12 14:06:19Z toby$ ########### SVN repository information ################### ''' *GSASIIplot: plotting routines* =============================== This module performs all visualization using matplotlib and OpenGL graphics. The following plotting routines are defined: ============================ =========================================================================== plotting routine action ============================ =========================================================================== :func:PlotPatterns Powder pattern plotting :func:PublishRietveldPlot Create publication-quality Rietveld plots from :func:PlotPatterns plot :func:PlotImage Plots of 2D detector images :func:PlotPeakWidths Plot instrument broadening terms as function of 2-theta/TOF :func:PlotCovariance Show covariance terms in 2D :func:PlotStructure Crystal structure plotting with balls, sticks, lines, ellipsoids, polyhedra and magnetic moments :func:PlotBeadModel Plots representation of protein shape from small angle scattering :func:Plot1DSngl 1D stick plots of structure factors :func:PlotSngl Structure factor plotting :func:Plot3DSngl 3D Structure factor plotting :func:PlotDeltSig Normal probability plot (powder or single crystal) :func:PlotISFG PDF analysis: displays I(Q), S(Q), F(Q) and G(r) :func:PlotCalib CW or TOF peak calibration :func:PlotXY Simple plot of xy data :func:PlotXYZ Simple contour plot of xyz data :func:PlotXYZvect Quiver Plot for 3D cartesian vectors :func:Plot3Dxyz Surface Plot for 3D vectors :func:PlotAAProb Protein "quality" plot :func:PlotStrain Plot of strain data, used for diagnostic purposes :func:PlotSASDSizeDist Small angle scattering size distribution plot :func:PlotPowderLines Plot powder pattern as a stick plot (vertical lines) :func:PlotSizeStrainPO Plot 3D mustrain/size/preferred orientation figure :func:PlotTexture Pole figure, inverse pole figure plotting :func:ModulationPlot Plots modulation information :func:PlotTorsion Plots MC torsion angles :func:PlotRama Ramachandran of energetically allowed regions for dihedral angles in protein :func:PlotSelectedSequence Plot one or more sets of values selected from the sequential refinement table :func:PlotIntegration Rectified plot of 2D image after image integration with 2-theta and azimuth as coordinates :func:PlotTRImage test plot routine :func:PlotRigidBody show rigid body structures as balls & sticks :func:PlotLayers show layer structures as balls & sticks :func:PlotFPAconvolutors plots the convolutors from Fundamental Parameters ============================ =========================================================================== These plotting routines place their graphics in the GSAS-II Plot Window, which contains a :class:G2PlotNoteBook tabbed panel allowing multiple plots to be viewed. Methods :meth:G2PlotNoteBook.addMpl (2-D matplotlib), :meth:G2PlotNoteBook.add3D (3-D matplotlib), and :meth:G2PlotNoteBook.addOgl (OpenGL) are used to create tabbed plot objects to hold plots of the following classes: :class:G2PlotMpl (2-D matplotlib), :class:G2Plot3D (3-D matplotlib), and :class:G2PlotOgl (OpenGL). Note that two :class:G2PlotNoteBook methods are potentially used to determine how plot updates after a refinement are handled: ============================================ ======================================================== class method description ============================================ ======================================================== :meth:G2PlotNoteBook.RegisterRedrawRoutine This specifies a function to redraw the plot after the data tree has been reloaded. Be sure this updates data objects with new values from the tree, when needed. :meth:G2PlotNoteBook.SetNoDelete Use this to indicate that a plot does not need to be updated after a refinement and should not be closed. ============================================ ======================================================== These two methods define the following attributes (variables) in the plot tab classes: ====================== =============== ============================================================ variable default use ====================== =============== ============================================================ replotFunction None Defines a routine to be called to update the plot after a refinement (unless None). Use :meth:G2PlotNoteBook.RegisterRedrawRoutine to define this (and replotArgs & replotKwArgs). Plotting functions that take significant time to complete should probably not use this.) replotArgs [] Defines the positional arguments to be supplied to the replotFunction function or method. replotKwArgs {} Defines the keyword arguments to be supplied to the replotFunction function or method. plotRequiresRedraw True If set to True, after a refinement, the plot will be closed (in :func:GSASIIdataGUI.GSASII.CleanupOldPlots) if it was not updated after the refinement. Set this to False using :meth:G2PlotNoteBook.SetNoDelete for plots that should not be deleted or do not change based on refinement results. plotInvalid False Used to track if a plot has been updated. Set to False in :meth:G2PlotNoteBook.FindPlotTab when a plot is drawn. After a refinement is completed, method :func:GSASIIdataGUI.GSASII.ResetPlots sets plotInvalid to False for all plots before any routines are called. ====================== =============== ============================================================ Note that the plot toolbar is customized with :class:GSASIItoolbar ''' from __future__ import division, print_function import platform import time import copy import math import sys import os.path import numpy as np import numpy.ma as ma import numpy.linalg as nl # Don't depend on wx/matplotlib/scipy for scriptable; or for Sphinx docs try: import wx import wx.aui import wx.glcanvas import matplotlib as mpl if not mpl.get_backend(): #could be assigned by spyder debugger mpl.use('wxAgg') import matplotlib.collections as mplC import mpl_toolkits.mplot3d.axes3d as mp3d from scipy.ndimage.interpolation import map_coordinates except ImportError: pass import GSASIIpath Clip_on = GSASIIpath.GetConfigValue('Clip_on',True) GSASIIpath.SetVersionNumber("$Revision: 4482$") import GSASIIdataGUI as G2gd import GSASIIimage as G2img import GSASIIpwd as G2pwd import GSASIIIO as G2IO import GSASIIpwdGUI as G2pdG import GSASIIimgGUI as G2imG import GSASIIphsGUI as G2phG import GSASIIlattice as G2lat import GSASIIspc as G2spc import GSASIImath as G2mth import GSASIIctrlGUI as G2G import GSASIIobj as G2obj try: import pytexture as ptx except ImportError: print('binary load error: pytexture not found') #from OpenGL.GL import * import OpenGL.GL as GL import OpenGL.GLU as GLU import gltext import matplotlib.colors as mpcls try: from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas except ImportError: from matplotlib.backends.backend_wx import FigureCanvas as Canvas try: from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as Toolbar except ImportError: from matplotlib.backends.backend_wxagg import Toolbar as Toolbar # name changes in wx4.0.1 try: from matplotlib.backends.backend_agg import FigureCanvasAgg as hcCanvas except ImportError: from matplotlib.backends.backend_agg import FigureCanvas as hcCanvas # standard name except RuntimeError: # happens during doc builds pass # useful degree trig functions sind = lambda x: math.sin(x*math.pi/180.) cosd = lambda x: math.cos(x*math.pi/180.) tand = lambda x: math.tan(x*math.pi/180.) asind = lambda x: 180.*math.asin(x)/math.pi acosd = lambda x: 180.*math.acos(x)/math.pi atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi atand = lambda x: 180.*math.atan(x)/math.pi # numpy versions npsind = lambda x: np.sin(x*np.pi/180.) npcosd = lambda x: np.cos(x*np.pi/180.) nptand = lambda x: np.tan(x*np.pi/180.) npacosd = lambda x: 180.*np.arccos(x)/np.pi npasind = lambda x: 180.*np.arcsin(x)/np.pi npatand = lambda x: 180.*np.arctan(x)/np.pi npatan2d = lambda x,y: 180.*np.arctan2(x,y)/np.pi try: # fails on doc build sq8ln2 = np.sqrt(8.0*np.log(2.0)) except TypeError: pass if '2' in platform.python_version_tuple()[0]: GkDelta = unichr(0x0394) Gkrho = unichr(0x03C1) super2 = unichr(0xb2) Angstr = unichr(0x00c5) Pwrm1 = unichr(0x207b)+unichr(0x0b9) else: GkDelta = chr(0x0394) Gkrho = chr(0x03C1) super2 = chr(0xb2) Angstr = chr(0x00c5) Pwrm1 = chr(0x207b)+chr(0x0b9) # misc global vars nxs = np.newaxis plotDebug = False timeDebug = GSASIIpath.GetConfigValue('Show_timing',False) obsInCaption = True # include the observed, calc,... items in the plot caption (PlotPatterns) #matplotlib 2.0.x dumbed down Paired to 16 colors - # this restores the pre 2.0 Paired color map found in matplotlib._cm.py _Old_Paired_data = {'blue': [(0.0, 0.89019608497619629, 0.89019608497619629), (0.090909090909090912, 0.70588237047195435, 0.70588237047195435), (0.18181818181818182, 0.54117649793624878, 0.54117649793624878), (0.27272727272727271, 0.17254902422428131, 0.17254902422428131), (0.36363636363636365, 0.60000002384185791, 0.60000002384185791), (0.45454545454545453, 0.10980392247438431, 0.10980392247438431), (0.54545454545454541, 0.43529412150382996, 0.43529412150382996), (0.63636363636363635, 0.0, 0.0), (0.72727272727272729, 0.83921569585800171, 0.83921569585800171), (0.81818181818181823, 0.60392159223556519, 0.60392159223556519), (0.90909090909090906, 0.60000002384185791, 0.60000002384185791), (1.0, 0.15686275064945221, 0.15686275064945221)], 'green': [(0.0, 0.80784314870834351, 0.80784314870834351), (0.090909090909090912, 0.47058823704719543, 0.47058823704719543), (0.18181818181818182, 0.87450981140136719, 0.87450981140136719), (0.27272727272727271, 0.62745100259780884, 0.62745100259780884), (0.36363636363636365, 0.60392159223556519, 0.60392159223556519), (0.45454545454545453, 0.10196078568696976, 0.10196078568696976), (0.54545454545454541, 0.74901962280273438, 0.74901962280273438), (0.63636363636363635, 0.49803921580314636, 0.49803921580314636), (0.72727272727272729, 0.69803923368453979, 0.69803923368453979), (0.81818181818181823, 0.23921568691730499, 0.23921568691730499), (0.90909090909090906, 1.0, 1.0), (1.0, 0.3490196168422699, 0.3490196168422699)], 'red': [(0.0, 0.65098041296005249, 0.65098041296005249), (0.090909090909090912, 0.12156862765550613, 0.12156862765550613), (0.18181818181818182, 0.69803923368453979, 0.69803923368453979), (0.27272727272727271, 0.20000000298023224, 0.20000000298023224), (0.36363636363636365, 0.9843137264251709, 0.9843137264251709), (0.45454545454545453, 0.89019608497619629, 0.89019608497619629), (0.54545454545454541, 0.99215686321258545, 0.99215686321258545), (0.63636363636363635, 1.0, 1.0), (0.72727272727272729, 0.7921568751335144, 0.7921568751335144), (0.81818181818181823, 0.41568627953529358, 0.41568627953529358), (0.90909090909090906, 1.0, 1.0), (1.0, 0.69411766529083252, 0.69411766529083252)]} #This can be done on request for other colors mpl.cm.register_cmap('Paired',data=_Old_Paired_data,lut=256) try: mpl.cm.register_cmap('Paired_r',data=mpl.cm._reverse_cmap_spec(_Old_Paired_data),lut=256) except: if GSASIIpath.GetConfigValue('debug'): print('MPL register_cmap for Paired_r failed') # options for publication-quality Rietveld plots plotOpt = {} plotOpt['labelSize'] = '11' plotOpt['dpi'] = 600 plotOpt['width'] = 8. plotOpt['height'] = 6. plotOpt['legend'] = {} plotOpt['colors'] = {} plotOpt['format'] = None plotOpt['initNeeded'] = True plotOpt['lineList'] = ('obs','calc','bkg','zero','diff') plotOpt['phaseList'] = [] plotOpt['phaseLabels'] = {} plotOpt['fmtChoices'] = {} plotOpt['lineWid'] = '1' def Write2csv(fil,dataItems,header=False): '''Write a line to a CSV file :param object fil: file object :param list dataItems: items to write as row in file :param bool header: True if all items should be written with quotes (default is False) ''' line = '' for item in dataItems: if line: line += ',' item = str(item) if header or ' ' in item: line += '"'+item+'"' else: line += item fil.write(line+'\n') class _tabPlotWin(wx.Panel): 'Creates a basic tabbed plot window for GSAS-II graphics' def __init__(self,parent,id=-1,dpi=None,**kwargs): self.replotFunction = None self.replotArgs = [] self.replotKwArgs = {} self.plotInvalid = False # valid self.plotRequiresRedraw = True # delete plot if not updated wx.Panel.__init__(self,parent,id=id,**kwargs) class G2PlotMpl(_tabPlotWin): 'Creates a Matplotlib 2-D plot in the GSAS-II graphics window' def __init__(self,parent,id=-1,dpi=None,publish=None,**kwargs): _tabPlotWin.__init__(self,parent,id=id,**kwargs) mpl.rcParams['legend.fontsize'] = 10 mpl.rcParams['axes.grid'] = False self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,6)) self.canvas = Canvas(self,-1,self.figure) self.toolbar = GSASIItoolbar(self.canvas,publish=publish) self.toolbar.Realize() self.plotStyle = {'qPlot':False,'dPlot':False,'sqrtPlot':False,'sqPlot':False,'logPlot':False} sizer=wx.BoxSizer(wx.VERTICAL) sizer.Add(self.canvas,1,wx.EXPAND) sizer.Add(self.toolbar,0,wx.LEFT|wx.EXPAND) self.SetSizer(sizer) def SetToolTipString(self,text): if 'phoenix' in wx.version(): return self.canvas.SetToolTip(text) else: return self.canvas.SetToolTipString(text) class G2PlotOgl(_tabPlotWin): 'Creates an OpenGL plot in the GSAS-II graphics window' def __init__(self,parent,id=-1,dpi=None,**kwargs): self.figure = _tabPlotWin.__init__(self,parent,id=id,**kwargs) if 'win' in sys.platform: #Windows (& Mac) already double buffered self.canvas = wx.glcanvas.GLCanvas(self,-1,**kwargs) else: #fix from Jim Hester for X systems attribs = (wx.glcanvas.WX_GL_DOUBLEBUFFER,wx.glcanvas.WX_GL_DEPTH_SIZE,24) self.canvas = wx.glcanvas.GLCanvas(self,-1,attribList=attribs,**kwargs) GL.glEnable(GL.GL_NORMALIZE) #GSASIIpath.IPyBreak() # create GL context i,j= wx.__version__.split('.')[0:2] if int(i)+int(j)/10. > 2.8: self.context = wx.glcanvas.GLContext(self.canvas) self.canvas.SetCurrent(self.context) else: self.context = None self.camera = {} sizer=wx.BoxSizer(wx.VERTICAL) sizer.Add(self.canvas,1,wx.EXPAND) self.SetSizer(sizer) class G2Plot3D(_tabPlotWin): 'Creates a 3D Matplotlib plot in the GSAS-II graphics window' def __init__(self,parent,id=-1,dpi=None,**kwargs): _tabPlotWin.__init__(self,parent,id=id,**kwargs) self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6)) self.canvas = Canvas(self,-1,self.figure) self.toolbar = Toolbar(self.canvas) self.toolbar = GSASIItoolbar(self.canvas) self.toolbar.Realize() sizer=wx.BoxSizer(wx.VERTICAL) sizer.Add(self.canvas,1,wx.EXPAND) sizer.Add(self.toolbar,0,wx.LEFT|wx.EXPAND) self.SetSizer(sizer) def SetToolTipString(self,text): if 'phoenix' in wx.version(): self.canvas.SetToolTip(wx.ToolTip(text)) else: self.canvas.SetToolTipString(text) class G2PlotNoteBook(wx.Panel): 'create a tabbed panel to hold a GSAS-II graphics window' def __init__(self,parent,id=-1,G2frame=None): wx.Panel.__init__(self,parent,id=id) #so one can't delete a plot page from tab!! self.nb = wx.aui.AuiNotebook(self, \ style=wx.aui.AUI_NB_DEFAULT_STYLE ^ wx.aui.AUI_NB_CLOSE_ON_ACTIVE_TAB) sizer = wx.BoxSizer() sizer.Add(self.nb,1,wx.EXPAND) self.SetSizer(sizer) self.status = parent.CreateStatusBar() self.status.SetFieldsCount(2) self.status.SetStatusWidths([150,-1]) self.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, self.OnPageChanged) self.nb.Bind(wx.EVT_KEY_UP,self.OnNotebookKey) self.G2frame = G2frame self.MPLwarn = False self.plotList = [] # contains the tab label for each plot self.panelList = [] # contains the panel object for each plot #self.skipPageChange = False # set to True when no plot update is needed self.allowZoomReset = True # this indicates plot should be updated not initialized # (BHT: should this be in tabbed panel rather than here?) self.lastRaisedPlotTab = None def OnNotebookKey(self,event): '''Called when a keystroke event gets picked up by the notebook window rather the child. This is not expected, but somehow it does sometimes on the Mac and perhaps Linux. Assume that the page associated with the currently displayed tab has a child, .canvas; give that child the focus and pass it the event. ''' try: Page = self.nb.GetPage(self.nb.GetSelection()) except ValueError: # occurs with no plot tabs return try: Page.canvas.SetFocus() wx.PostEvent(Page.canvas,event) except AttributeError: pass def SetNoDelete(self,name): '''Indicate that a plot does not need to be redrawn ''' if name not in self.plotList: print('Error, in SetNoDelete plot not found: '+name) return page = self.panelList[self.plotList.index(name)] page.plotRequiresRedraw = False # plot should not be deleted even if not redrawn def RegisterRedrawRoutine(self,name,routine=None,args=(),kwargs={}): '''Save information to determine how to redraw a plot :param str name: label on tab of plot :param Object routine: a function to be called :param args: a list of positional parameters for the function :param kwargs: a dict with keyword parameters for the function ''' if name not in self.plotList: print('Error, plot not found: '+name) return page = self.panelList[self.plotList.index(name)] page.replotFunction = routine page.replotArgs = args page.replotKWargs = kwargs def GetTabIndex(self,label): '''Look up a tab label and return the index in the notebook (this appears to be independent to the order it is dragged to -- at least in Windows) as well as the associated wx.Panel An exception is raised if the label is not found ''' for i in range(self.nb.GetPageCount()): if label == self.nb.GetPageText(i): return i,self.nb.GetPage(i) else: raise ValueError('Plot not found') # def RaiseLastPage(self,lastRaisedPlotTab,treeItemPlot): # '''Raises either the Last tab clicked on or what is drawn by the selected tree item # This is called after a refinement is completed by :meth:GSASIIdataGUI.GSASII.ResetPlots # ''' # plotNum = None # if lastRaisedPlotTab in self.plotList: # plotNum = self.plotList.index(lastRaisedPlotTab) # elif treeItemPlot in self.plotList: # plotNum = self.plotList.index(treeItemPlot) # if plotNum is not None: # wx.CallAfter(self.SetSelectionNoRefresh,plotNum) def FindPlotTab(self,label,Type,newImage=True,publish=None): '''Open a plot tab for initial plotting, or raise the tab if it already exists Set a flag (Page.plotInvalid) that it has been redrawn Record the name of the this plot in self.lastRaisedPlotTab ''' limits = None Plot = None try: new = False plotNum,Page = self.GetTabIndex(label) if Type == 'mpl' or Type == '3d': Axes = Page.figure.get_axes() Plot = Page.figure.gca() #get previous plot limits = [Plot.get_xlim(),Plot.get_ylim()] # save previous limits if len(Axes)>1 and Plot.get_aspect() == 'auto': # aspect will be equal for image plotting if Axes[1].get_aspect() != 'auto': #not colorbars! limits[1] = Axes[0].get_ylim() else: limits[1] = Axes[1].get_ylim() if newImage: Page.figure.clf() Plot = Page.figure.gca() #get a fresh plot after clf() self.SetSelectionNoRefresh(plotNum) # raises plot tab except (ValueError,AttributeError): new = True if Type == 'mpl': Plot = self.addMpl(label,publish=publish).gca() elif Type == 'ogl': Plot = self.addOgl(label) elif Type == '3d': Plot = mp3d.Axes3D(self.add3D(label)) plotNum = self.plotList.index(label) Page = self.nb.GetPage(plotNum) Page.plotInvalid = False # plot has just been drawn self.lastRaisedPlotTab = label self.RaisePageNoRefresh(Page) # Save the help name from the DataItem that has created the plot in Tabbed page object # so we can use it in self.OnHelp(). # Are there any cases where plot tabs are created that are not tied to Data Tree entries? # One example is GSASII.SumDialog, where a test plot is created. Are there others? try: Page.helpKey = self.G2frame.dataWindow.helpKey except AttributeError: Page.helpKey = 'Data tree' return new,plotNum,Page,Plot,limits def _addPage(self,name,page): '''Add the newly created page to the notebook and associated lists. :param name: the label placed on the tab, which should be unique :param page: the wx.Frame for the matplotlib, openGL, etc. window ''' #self.skipPageChange = True if name in self.plotList: print('Warning: duplicate plot name! Name='+name) self.nb.AddPage(page,name) self.plotList.append(name) # used to lookup plot in self.panelList # Note that order in lists make not agree with actual tab order; use self.nb.GetPageText(i) # where (self=G2plotNB) for latter self.panelList.append(page) # panel object for plot self.lastRaisedPlotTab = name #page.plotInvalid = False # plot has just been drawn #page.plotRequiresRedraw = True # set to False if plot should be retained even if not refreshed #page.replotFunction = None # used to specify a routine to redraw the routine #page.replotArgs = [] #page.replotKWargs = {} #self.skipPageChange = False def addMpl(self,name="",publish=None): 'Add a tabbed page with a matplotlib plot' page = G2PlotMpl(self.nb,publish=publish) self._addPage(name,page) return page.figure def add3D(self,name=""): 'Add a tabbed page with a 3D plot' page = G2Plot3D(self.nb) self._addPage(name,page) mplv = mpl.__version__.split('.') if mplv[0] == '3' and (mplv[1] == '1' or mplv[1] == '2') and not self.MPLwarn: # patch for bad MPL 3D self.MPLwarn = True G2G.G2MessageBox(self,'3D plots with Matplotlib 3.1.x and 3.2.x are distorted, we suggest regressing to MPL 3.0.3 until 3.3.x or later is available.. You have '+mpl.__version__, 'Avoid Matplotlib 3.1 & 3.2') return page.figure def addOgl(self,name=""): 'Add a tabbed page with an openGL plot' page = G2PlotOgl(self.nb) self._addPage(name,page) self.RaisePageNoRefresh(page) # need to give window focus before GL use return page.figure def Delete(self,name): 'delete a tabbed page' try: item = self.plotList.index(name) del self.plotList[item] del self.panelList[item] self.nb.DeletePage(item) except ValueError: #no plot of this name - do nothing return def clear(self): 'clear all pages from plot window' for i in range(self.nb.GetPageCount()-1,-1,-1): self.nb.DeletePage(i) self.plotList = [] self.panelList = [] self.status.DestroyChildren() #get rid of special stuff on status bar def Rename(self,oldName,newName): 'rename a tab' try: item = self.plotList.index(oldName) self.plotList[item] = newName self.nb.SetPageText(item,newName) except ValueError: #no plot of this name - do nothing return def RaisePageNoRefresh(self,Page): 'Raises a plot tab without triggering a refresh via OnPageChanged' if plotDebug: print ('Raise'+str(self).split('0x')[1]) #self.skipPageChange = True Page.SetFocus() #self.skipPageChange = False def SetSelectionNoRefresh(self,plotNum): 'Raises a plot tab without triggering a refresh via OnPageChanged' if plotDebug: print ('Select'+str(self).split('0x')[1]) #self.skipPageChange = True self.nb.SetSelection(plotNum) # raises plot tab Page = self.G2frame.G2plotNB.nb.GetPage(plotNum) Page.SetFocus() #self.skipPageChange = False def OnPageChanged(self,event): '''respond to someone pressing a tab on the plot window. Called when a plot tab is clicked. on some platforms (Mac for sure) this is also called when a plot is created or selected with .SetSelection() or .SetFocus(). (removed) The self.skipPageChange is used variable is set to suppress repeated replotting. ''' tabLabel = event.GetEventObject().GetPageText(event.GetSelection()) self.lastRaisedPlotTab = tabLabel if plotDebug: # print ('PageChanged, self='+str(self).split('0x')[1]+tabLabel+str(self.skipPageChange)) print ('PageChanged, self='+str(self).split('0x')[1]+tabLabel) print ('event type='+event.GetEventType()) self.status.DestroyChildren() #get rid of special stuff on status bar self.status.SetStatusText('') # clear old status message self.status.SetStatusWidths([150,-1]) def InvokeTreeItem(self,pid): '''This is called to select an item from the tree using the self.allowZoomReset flag to prevent a reset to the zoom of the plot (where implemented) ''' self.allowZoomReset = False if pid: self.G2frame.GPXtree.SelectItem(pid) self.allowZoomReset = True if plotDebug: print ('invoke'+str(self).split('0x')[1]+str(pid)) class GSASIItoolbar(Toolbar): 'Override the matplotlib toolbar so we can add more icons' def __init__(self,plotCanvas,publish=None): '''Adds additional icons to toolbar''' self.arrows = {} # try to remove a button from the bar POS_CONFIG_SPLTS_BTN = 6 # position of button to remove try: self.toolitems = self.toolitems[:POS_CONFIG_SPLTS_BTN]+self.toolitems[POS_CONFIG_SPLTS_BTN+1:] deleted = True except: deleted = False Toolbar.__init__(self,plotCanvas) # G2path = os.path.split(os.path.abspath(__file__))[0] self.updateActions = None # defines a call to be made as part of plot updates self.plotCanvas = plotCanvas # 2nd try to remove a button from the bar if not deleted: self.DeleteToolByPos(POS_CONFIG_SPLTS_BTN) #doesn't work in some wxpython versions self.parent = self.GetParent() self.AddToolBarTool('Key press','Select key press','key.ico',self.OnKey) self.AddToolBarTool('Help on','Show help on this plot','help.ico',self.OnHelp) # add arrow keys to control zooming for direc in ('left','right','up','down', 'Expand X','Shrink X','Expand Y','Shrink Y'): if ' ' in direc: sprfx = '' prfx = 'Zoom: ' else: sprfx = 'Shift ' prfx = 'Shift plot ' fil = ''.join([i[0].lower() for i in direc.split()]+['arrow.ico']) self.arrows[direc] = self.AddToolBarTool(sprfx+direc,prfx+direc,fil,self.OnArrow) # G2path = os.path.split(os.path.abspath(__file__))[0] if publish: self.AddToolBarTool('Publish plot','Create publishable version of plot','publish.ico',publish) def AddToolBarTool(self,label,title,filename,callback): G2path = os.path.split(os.path.abspath(__file__))[0] bmpFilename = os.path.normpath(os.path.join(G2path, filename)) if not os.path.exists(bmpFilename): print('Could not find bitmap file "%s"; skipping' % bmpFilename) bmp = wx.EmptyBitmap(32,32) else: bmp = wx.Bitmap(bmpFilename) if 'phoenix' in wx.version(): button = self.AddTool(wx.ID_ANY, label, bmp, title) else: button = self.AddSimpleTool(wx.ID_ANY, bmp, label, title) wx.EVT_TOOL.Bind(self, button.GetId(), button.GetId(), callback) return button.GetId() def _update_view(self): '''Overrides the post-buttonbar update action to invoke a redraw; needed for plot magnification ''' if self.updateActions: wx.CallAfter(*self.updateActions) Toolbar._update_view(self) def OnArrow(self,event): 'reposition limits to scan or zoom by button press' ax = self.plotCanvas.figure.get_axes()[0] xmin,xmax,ymin,ymax = ax.axis() #print xmin,xmax,ymin,ymax if event.Id == self.arrows['right']: delta = (xmax-xmin)/10. xmin -= delta xmax -= delta elif event.Id == self.arrows['left']: delta = (xmax-xmin)/10. xmin += delta xmax += delta elif event.Id == self.arrows['up']: delta = (ymax-ymin)/10. ymin -= delta ymax -= delta elif event.Id == self.arrows['down']: delta = (ymax-ymin)/10. ymin += delta ymax += delta elif event.Id == self.arrows['Expand X']: delta = (xmax-xmin)/10. xmin += delta xmax -= delta elif event.Id == self.arrows['Expand Y']: delta = (ymax-ymin)/10. ymin += delta ymax -= delta elif event.Id == self.arrows['Shrink X']: delta = (xmax-xmin)/10. xmin -= delta xmax += delta elif event.Id == self.arrows['Shrink Y']: delta = (ymax-ymin)/10. ymin -= delta ymax += delta else: # should not happen! if GSASIIpath.GetConfigValue('debug'): GSASIIpath.IPyBreak() self.parent.toolbar.push_current() #NB: self.parent.toolbar = self ax.axis((xmin,xmax,ymin,ymax)) #print xmin,xmax,ymin,ymax self.plotCanvas.figure.canvas.draw() self.parent.toolbar.draw() # self.parent.toolbar.push_current() if self.updateActions: wx.CallAfter(*self.updateActions) def OnHelp(self,event): 'Respond to press of help button on plot toolbar' bookmark = self.Parent.helpKey # get help category used to create plot #if GSASIIpath.GetConfigValue('debug'): print 'plot help: key=',bookmark G2G.ShowHelp(bookmark,self.TopLevelParent) def OnKey(self,event): '''Provide user with list of keystrokes defined for plot as well as an alternate way to access the same functionality ''' parent = self.GetParent() if parent.Choice: # remove the 1st entry in list if key press if 'key press' in parent.Choice[0].lower(): choices = list(parent.Choice[1:]) else: choices = list(parent.Choice) dlg = wx.SingleChoiceDialog(parent,'Select a keyboard command', 'Key press list',choices) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() event.key = choices[sel][0] if event.key != ' ': parent.keyPress(event) else: dlg.Destroy() G2G.G2MessageBox(self.TopLevelParent, 'Use this command only from the keyboard', 'Key not in menu') return dlg.Destroy() # these routines are not currently in use, but there are probably good # places in the graphics to disable the zoom/pan to release the mouse bind # # use as Page.canvas.toolbar.reset_zoompan() # def get_zoompan(self): """Return "ZOOM" if Zoom is active, , "PAN" if Pan is active, or None if neither """ return self._active def reset_zoompan(self): '''Turns off Zoom or Pan mode, if on. Ignored if neither is set ''' if self._active == 'ZOOM': self._active = None if self._idPress is not None: self._idPress = self.canvas.mpl_disconnect(self._idPress) self.mode = '' if self._idRelease is not None: self._idRelease = self.canvas.mpl_disconnect(self._idRelease) self.mode = '' self.canvas.widgetlock.release(self) if hasattr(self,'_NTB2_ZOOM'): self.ToggleTool(self._NTB2_ZOOM, False) elif hasattr(self,'wx_ids'): self.ToggleTool(self.wx_ids['Zoom'], False) else: print('Unable to reset Zoom button, please report this with matplotlib version') elif self._active == 'PAN': self._active = None if self._idPress is not None: self._idPress = self.canvas.mpl_disconnect(self._idPress) self.mode = '' if self._idRelease is not None: self._idRelease = self.canvas.mpl_disconnect(self._idRelease) self.mode = '' self.canvas.widgetlock.release(self) if hasattr(self,'_NTB2_PAN'): self.ToggleTool(self._NTB2_PAN, False) elif hasattr(self,'wx_ids'): self.ToggleTool(self.wx_ids['Pan'], False) else: print('Unable to reset Pan button, please report this with matplotlib version') def SetCursor(page): mode = page.toolbar._active if mode == 'PAN': if 'phoenix' in wx.version(): page.canvas.Cursor = wx.Cursor(wx.CURSOR_SIZING) else: page.canvas.SetCursor(wx.StockCursor(wx.CURSOR_SIZING)) elif mode == 'ZOOM': if 'phoenix' in wx.version(): page.canvas.Cursor = wx.Cursor(wx.CURSOR_MAGNIFIER) else: page.canvas.SetCursor(wx.StockCursor(wx.CURSOR_MAGNIFIER)) else: if 'phoenix' in wx.version(): page.canvas.Cursor = wx.Cursor(wx.CURSOR_CROSS) else: page.canvas.SetCursor(wx.StockCursor(wx.CURSOR_CROSS)) ################################################################################ ##### PlotSngl ################################################################################ def PlotSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=''): '''Structure factor plotting package - displays zone of reflections as rings proportional to F, F**2, etc. as requested ''' from matplotlib.patches import Circle global HKL,HKLF,HKLref HKLref = hklRef def OnSCKeyPress(event): i = zones.index(Data['Zone']) newPlot = False pwdrChoice = {'f':'Fo','s':'Fosq','u':'Unit Fc'} hklfChoice = {'1':'|DFsq|>sig','3':'|DFsq|>3sig','w':'|DFsq|/sig','f':'Fo','s':'Fosq','i':'Unit Fc'} if event.key == 'h': Data['Zone'] = '100' newPlot = True elif event.key == 'k': Data['Zone'] = '010' newPlot = True elif event.key == 'l': Data['Zone'] = '001' newPlot = True elif event.key == 'i': Data['Scale'] *= 1.1 elif event.key == 'd': Data['Scale'] /= 1.1 elif event.key in ['+','=']: Data['Layer'] = min(Data['Layer']+1,HKLmax[i]) elif event.key == '-': Data['Layer'] = max(Data['Layer']-1,HKLmin[i]) elif event.key == '0': Data['Layer'] = 0 Data['Scale'] = 1.0 elif event.key in hklfChoice and 'HKLF' in Name: Data['Type'] = hklfChoice[event.key] newPlot = True elif event.key in pwdrChoice and 'PWDR' in Name: Data['Type'] = pwdrChoice[event.key] newPlot = True PlotSngl(G2frame,newPlot,Data,HKLref,Title) def OnSCMotion(event): xpos = event.xdata if xpos: xpos = round(xpos) #avoid out of frame mouse position ypos = round(event.ydata) zpos = Data['Layer'] if '100' in Data['Zone']: HKLtxt = '(%d,%d,%d)'%(zpos,xpos,ypos) elif '010' in Data['Zone']: HKLtxt = '(%d,%d,%d)'%(xpos,zpos,ypos) elif '001' in Data['Zone']: HKLtxt = '(%d,%d,%d)'%(xpos,ypos,zpos) Page.SetToolTipString(HKLtxt) G2frame.G2plotNB.status.SetStatusText('HKL = '+HKLtxt,0) def OnSCPress(event): zpos = Data['Layer'] xpos = event.xdata if xpos: pos = int(round(event.xdata)),int(round(event.ydata)) if '100' in Data['Zone']: hkl = np.array([zpos,pos[0],pos[1]]) elif '010' in Data['Zone']: hkl = np.array([pos[0],zpos,pos[1]]) elif '001' in Data['Zone']: hkl = np.array([pos[0],pos[1],zpos]) h,k,l = hkl hklf = HKLF[np.where(np.all(HKL-hkl == [0,0,0],axis=1))] if len(hklf): Fosq,sig,Fcsq = hklf[0] HKLtxt = '( %.2f %.3f %.2f %.2f)'%(Fosq,sig,Fcsq,(Fosq-Fcsq)/(scale*sig)) G2frame.G2plotNB.status.SetStatusText('Fosq, sig, Fcsq, delFsq/sig = '+HKLtxt,1) def OnPick(event): pick = event.artist HKLtext = pick.get_gid() Page.SetToolTipString(HKLtext) G2frame.G2plotNB.status.SetStatusText('H = '+HKLtext,0) Name = G2frame.GPXtree.GetItemText(G2frame.PatternId) if not Title: Title = Name new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Structure Factors','mpl') if not new: if not newPlot: xylim = copy.copy(lim) else: Page.canvas.mpl_connect('button_press_event', OnSCPress) Page.canvas.mpl_connect('motion_notify_event', OnSCMotion) Page.canvas.mpl_connect('pick_event', OnPick) Page.canvas.mpl_connect('key_press_event', OnSCKeyPress) Page.keyPress = OnSCKeyPress Page.Choice = (' key press','i: increase scale','d: decrease scale', 'h: select 100 zone','k: select 010 zone','l: select 001 zone', 'f: select Fo','s: select Fosq','u: select unit Fc', '+: increase index','-: decrease index','0: zero layer',) if 'HKLF' in Name: Page.Choice += ('w: select |DFsq|/sig','1: select |DFsq|>sig','3: select |DFsq|>3sig',) try: Plot.set_aspect(aspect='equal') except: #broken in mpl 3.1.1; worked in mpl 3.0.3 pass Type = Data['Type'] scale = Data['Scale'] HKLmax = Data['HKLmax'] HKLmin = Data['HKLmin'] FosqMax = Data['FoMax'] Super = Data['Super'] SuperVec = [] if Super: SuperVec = np.array(Data['SuperVec'][0]) FoMax = math.sqrt(FosqMax) xlabel = ['k, h=','h, k=','h, l='] ylabel = ['l','l','k'] zones = ['100','010','001'] pzone = [[1,2],[0,2],[0,1]] izone = zones.index(Data['Zone']) Plot.set_title(Data['Type']+' for '+Title) HKL = [] HKLF = [] sumFo = 0. sumDF = 0. # GSASIIpath.IPyBreak() for refl in HKLref: H = refl[:3] if 'HKLF' in Name: Fosq,sig,Fcsq = refl[5+Super:8+Super] else: Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super] if Super: HKL.append(H+SuperVec*refl[3]) else: HKL.append(H) HKLF.append([Fosq,sig,Fcsq]) if H[izone] == Data['Layer']: A = 0 B = 0 if Type == 'Fosq': A = scale*Fosq/FosqMax sumFo += A B = scale*Fcsq/FosqMax C = abs(A-B) sumDF += C elif Type == 'Fo': A = scale*math.sqrt(max(0,Fosq))/FoMax sumFo += A B = scale*math.sqrt(max(0,Fcsq))/FoMax C = abs(A-B) sumDF += C elif Type == 'Unit Fc': A = scale/2 B = scale/2 C = 0.0 if Fcsq and Fosq > 0: A *= min(1.0,Fosq/Fcsq) C = abs(A-B) elif Type == '|DFsq|/sig': if sig > 0.: A = scale*(Fosq-Fcsq)/(3*sig) B = 0 elif Type == '|DFsq|>sig': if sig > 0.: A = scale*(Fosq-Fcsq)/(3*sig) if abs(A) < 1.0: A = 0 B = 0 elif Type == '|DFsq|>3sig': if sig > 0.: A = scale*(Fosq-Fcsq)/(3*sig) if abs(A) < 3.0: A = 0 B = 0 if Super: h = H+SuperVec*refl[3] if refl[3]: hid = '(%d,%d,%d,%d)'%(refl[0],refl[1],refl[2],refl[3]) else: hid = '(%d,%d,%d)'%(refl[0],refl[1],refl[2]) else: h = H hid = '(%d,%d,%d)'%(refl[0],refl[1],refl[2]) xy = (h[pzone[izone][0]],h[pzone[izone][1]]) if Type in ['|DFsq|/sig','|DFsq|>sig','|DFsq|>3sig']: if A > 0.0: Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w',picker=1.,gid=hid)) else: Plot.add_artist(Circle(xy,radius=-A,ec='r',fc='w',picker=1.,gid=hid)) else: if A > 0.0 and A > B: Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w')) if B: Plot.add_artist(Circle(xy,radius=B,ec='b',fc='w',picker=1.,gid=hid)) if A < B: Plot.add_artist(Circle(xy,radius=A,ec='g',fc='w')) radius = C if radius > 0: if A > B: if refl[3+Super] < 0: Plot.add_artist(Circle(xy,radius=radius,ec=(0.,1,.0,.1),fc='g')) else: Plot.add_artist(Circle(xy,radius=radius,fc='g',ec='g')) else: if refl[3+Super] < 0: Plot.add_artist(Circle(xy,radius=radius,fc=(1.,0.,0.,.1),ec='r')) else: Plot.add_artist(Circle(xy,radius=radius,ec='r',fc='r')) # print 'plot time: %.3f'%(time.time()-time0) HKL = np.array(HKL) HKLF = np.array(HKLF) Plot.set_xlabel(xlabel[izone]+str(Data['Layer']),fontsize=12) Plot.set_ylabel(ylabel[izone],fontsize=12) if sumFo and sumDF: G2frame.G2plotNB.status.SetStatusText(xlabel[izone].split(',')[1]+str(Data['Layer'])+ \ ' layer R = %6.2f%s'%(100.*sumDF/sumFo,'%'),1) else: G2frame.G2plotNB.status.SetStatusText('Use K-box to set plot controls',1) if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) # xylim = [] Page.toolbar.push_current() Page.toolbar.draw() else: Plot.set_xlim((HKLmin[pzone[izone][0]],HKLmax[pzone[izone][0]])) Plot.set_ylim((HKLmin[pzone[izone][1]],HKLmax[pzone[izone][1]])) Page.canvas.draw() ################################################################################ ##### Plot1DSngl ################################################################################ def Plot1DSngl(G2frame,newPlot=False,hklRef=None,Super=0,Title=False): '''1D Structure factor plotting package - displays reflections as sticks proportional to F, F**2, etc. as requested ''' global xylim,X Name = G2frame.GPXtree.GetItemText(G2frame.PatternId) def OnKeyPress(event): if event.key == 'q': Page.qaxis = not Page.qaxis elif event.key == 'f': Page.faxis = not Page.faxis Draw() def OnMotion(event): global X xpos = event.xdata limx = Plot.get_xlim() if xpos: #avoid out of frame mouse position Xpos = xpos if Page.qaxis: dT = np.fabs(2.*np.pi/limx[0]-2.*np.pi/limx[1])/100. Xpos = 2.*np.pi/xpos found = hklRef[np.where(np.fabs(hklRef.T[4+Super]-Xpos) < dT/2.)] else: dT = np.fabs(limx[1]-limx[0])/100. found = hklRef[np.where(np.fabs(hklRef.T[4+Super]-xpos) < dT/2.)] s = '' if len(found): if Super: #SS reflections fmt = "{:.0f},{:.0f},{:.0f},{:.0f}" n = 4 else: fmt = "{:.0f},{:.0f},{:.0f}" n = 3 for i,hkl in enumerate(found): if i >= 3: s += '\n...' break if s: s += '\n' s += fmt.format(*hkl[:n]) ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('d =%9.3f F^2 =%9.3f'%(Xpos,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select '+Title+Name+' pattern first',1) Page.SetToolTipString(s) def Draw(): global xylim Plot.clear() Plot.set_title(Title) Plot.set_xlabel(r'd, '+Angstr,fontsize=14) Plot.set_ylabel(r'F'+super2,fontsize=14) colors=['b','r','g','c','m','k'] Page.keyPress = OnKeyPress if Page.qaxis: Plot.set_xlabel(r'q, '+Angstr+Pwrm1,fontsize=14) X = 2.*np.pi/hklRef.T[4+Super] else: X = hklRef.T[4+Super] if Page.faxis: Plot.set_ylabel(r'F',fontsize=14) Y = np.nan_to_num(np.sqrt(hklRef.T[8+Super])) Z = np.sqrt(hklRef.T[9+Super]) else: Y = hklRef.T[8+Super] Z = hklRef.T[9+Super] Ymax = np.max(Y) XY = np.vstack((X,X,np.zeros_like(X),Y)).reshape((2,2,-1)).T XZ = np.vstack((X,X,np.zeros_like(X),Z)).reshape((2,2,-1)).T XD = np.vstack((X,X,np.zeros_like(X)-Ymax/10.,Y-Z-Ymax/10.)).reshape((2,2,-1)).T lines = mplC.LineCollection(XY,color=colors[0]) Plot.add_collection(lines) lines = mplC.LineCollection(XZ,color=colors[1]) Plot.add_collection(lines) lines = mplC.LineCollection(XD,color=colors[2]) Plot.add_collection(lines) xylim = np.array([[np.min(X),np.max(X)],[np.min(Y-Z-Ymax/10.),np.max(np.concatenate((Y,Z)))]]) dxylim = np.array([xylim[0][1]-xylim[0][0],xylim[1][1]-xylim[1][0]])/20. xylim[0,0] -= dxylim[0] xylim[0,1] += dxylim[0] xylim[1,0] -= dxylim[1] xylim[1,1] += dxylim[1] Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) if not newPlot: print('not newPlot') Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) xylim = [] Page.toolbar.push_current() Page.toolbar.draw() Page.canvas.draw() else: Page.canvas.draw() new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(Title+Name,'mpl') Page.Offset = [0,0] if not new: if not newPlot: xylim = copy.copy(lim) else: newPlot = True Page.qaxis = False Page.faxis = False Page.canvas.mpl_connect('key_press_event', OnKeyPress) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Offset = [0,0] Page.Choice = (' key press','g: toggle grid','f: toggle Fhkl/F^2hkl plot','q: toggle q/d plot') Draw() ################################################################################ ##### Plot3DSngl ################################################################################ def Plot3DSngl(G2frame,newPlot=False,Data=None,hklRef=None,Title=False): '''3D Structure factor plotting package - displays reflections as rings proportional to F, F**2, etc. as requested as 3D array ''' global ifBox ifBox = False def OnKeyBox(event): mode = cb.GetValue() if mode in ['jpeg','bmp','tiff',]: try: import Image as Im except ImportError: try: from PIL import Image as Im except ImportError: print ("PIL/pillow Image module not present. Cannot save images without this") raise Exception("PIL/pillow Image module not found") try: Fname = os.path.join(Mydir,generalData['Name']+'.'+mode) except NameError: #for when generalData doesn't exist! Fname = (os.path.join(Mydir,'unknown'+'.'+mode)).replace('*','+') print (Fname+' saved') size = Page.canvas.GetSize() GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1) Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB,GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) try: im.frombytes(Pix) except AttributeError: im.fromstring(Pix) im = im.transpose(Im.FLIP_TOP_BOTTOM) im.save(Fname,mode) cb.SetValue(' save as/key:') G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1) else: event.key = cb.GetValue()[0] cb.SetValue(' save as/key:') wx.CallAfter(OnKey,event) Page.canvas.SetFocus() # redirect the Focus from the button back to the plot def OnKey(event): #on key UP!! global ifBox Choice = {'F':'Fo','S':'Fosq','U':'Unit','D':'dFsq','W':'dFsq/sig'} viewChoice = {'L':np.array([[0,0,1],[1,0,0],[0,1,0]]),'K':np.array([[0,1,0],[0,0,1],[1,0,0]]),'H':np.array([[1,0,0],[0,0,1],[0,1,0]])} try: keyCode = event.GetKeyCode() if keyCode > 255: keyCode = 0 key = chr(keyCode) except AttributeError: #if from OnKeyBox above key = str(event.key).upper() if key in ['C','H','K','L']: if key == 'C': Data['Zone'] = False key = 'L' Data['viewKey'] = key drawingData['viewPoint'][0] = np.array(drawingData['default']) drawingData['viewDir'] = viewChoice[key][0] drawingData['viewUp'] = viewChoice[key][1] drawingData['oldxy'] = [] if Data['Zone']: if key == 'L': Q = [-1,0,0,0] else: V0 = viewChoice[key][0] V1 = viewChoice[key][1] V0 = np.inner(Amat,V0) V1 = np.inner(Amat,V1) V0 /= nl.norm(V0) V1 /= nl.norm(V1) A = np.arccos(np.sum(V1*V0)) Q = G2mth.AV2Q(-A,viewChoice[key][2]) G2frame.G2plotNB.status.SetStatusText('zone = %s'%(str(list(viewChoice[key][0]))),1) else: V0 = viewChoice[key][0] V = np.inner(Bmat,V0) V /= np.sqrt(np.sum(V**2)) V *= np.array([0,0,1]) A = np.arccos(np.sum(V*V0)) Q = G2mth.AV2Q(-A,viewChoice[key][2]) drawingData['Quaternion'] = Q elif key in 'O': drawingData['viewPoint'][0] = [0,0,0] elif key in 'Z': Data['Zone'] = not Data['Zone'] elif key in 'B': ifBox = not ifBox elif key in ['+','=']: Data['Scale'] *= 1.25 elif key == '-': Data['Scale'] /= 1.25 elif key == 'P': vec = viewChoice[Data['viewKey']][0] drawingData['viewPoint'][0] -= vec elif key == 'N': vec = viewChoice[Data['viewKey']][0] drawingData['viewPoint'][0] += vec elif key == '0': drawingData['viewPoint'][0] = np.array([0,0,0]) Data['Scale'] = 1.0 elif key == 'I': Data['Iscale'] = not Data['Iscale'] elif key in Choice: Data['Type'] = Choice[key] Draw('key') Name = G2frame.GPXtree.GetItemText(G2frame.PatternId) if Title and Title in G2frame.GetPhaseData(): #NB: save image as e.g. jpeg will fail if False; MyDir is unknown generalData = G2frame.GetPhaseData()[Title]['General'] cell = generalData['Cell'][1:7] Mydir = generalData['Mydir'] else: Title = 'Unknown' cell = [10,10,10,90,90,90] Mydir = G2frame.dirname drawingData = Data['Drawing'] Super = Data['Super'] SuperVec = [] if Super: SuperVec = np.array(Data['SuperVec'][0]) Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse Gmat,gmat = G2lat.cell2Gmat(cell) B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Bmat,[0,0,1])) Wt = np.array([255,255,255]) Rd = np.array([255,0,0]) Gr = np.array([0,255,0]) Bl = np.array([0,0,255]) 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]]) uEdges = np.array([ [uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]], [uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]], [uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]]) uColors = [Rd,Gr,Bl, Wt,Wt,Wt, Wt,Wt,Wt, Wt,Wt,Wt] def FillHKLRC(): sumFo2 = 0. sumDF2 = 0. sumFo = 0. sumDF = 0. R = np.zeros(len(hklRef)) C = [] HKL = [] for i,refl in enumerate(hklRef): H = refl[:3] if 'HKLF' in Name: Fosq,sig,Fcsq = refl[5+Super:8+Super] if refl[3+Super] < 0: Fosq,sig,Fcsq = [0,1,0] else: Fosq,sig,Fcsq = refl[8+Super],1.0,refl[9+Super] sumFo2 += Fosq sumDF2 += abs(Fosq-Fcsq) if Fosq > 0.: sumFo += np.sqrt(Fosq) sumDF += abs(np.sqrt(Fosq)-np.sqrt(Fcsq)) if Super: HKL.append(H+SuperVec*refl[3]) else: HKL.append(H) if Data['Type'] == 'Unit': R[i] = 0.1 C.append(Gr) elif Data['Type'] == 'Fosq': if Fosq > 0: R[i] = Fosq C.append(Gr) else: R[i] = -Fosq C.append(Rd) elif Data['Type'] == 'Fo': if Fosq > 0: R[i] = np.sqrt(Fosq) C.append(Gr) else: R[i] = np.sqrt(-Fosq) C.append(Rd) elif Data['Type'] == 'dFsq/sig': dFsig = (Fosq-Fcsq)/sig if dFsig > 0: R[i] = dFsig C.append(Gr) else: R[i] = -dFsig C.append(Rd) elif Data['Type'] == 'dFsq': dF = Fosq-Fcsq if dF > 0: R[i] = dF C.append(Gr) else: R[i] = -dF C.append(Rd) R /= np.max(R) R *= Data['Scale'] R = np.where(R<1.e-5,1.e-5,R) if Data['Iscale']: R = np.where(R<=1.,R,1.) C = np.array(C) C = (C.T*R).T R = np.ones_like(R)*0.05 RF = 100. RF2 = 100. if sumFo and sumDF: RF = 100.*sumDF/sumFo RF2 = 100.*sumDF2/sumFo2 return HKL,zip(list(R),C),RF,RF2 def GetTruePosition(xy): View = GL.glGetIntegerv(GL.GL_VIEWPORT) Proj = GL.glGetDoublev(GL.GL_PROJECTION_MATRIX) Model = GL.glGetDoublev(GL.GL_MODELVIEW_MATRIX) Zmax = 1. xy = [int(xy[0]),int(View[3]-xy[1])] for i,ref in enumerate(hklRef): h,k,l = ref[:3] try: X,Y,Z = GLU.gluProject(h,k,l,Model,Proj,View) XY = [int(X),int(Y)] if np.allclose(xy,XY,atol=10) and Z < Zmax: Zmax = Z return [int(h),int(k),int(l)] except ValueError: return [int(h),int(k),int(l)] def SetTranslation(newxy): #first get translation vector in screen coords. oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy drawingData['oldxy'] = list(newxy) V = np.array([-dxy[0],dxy[1],0.]) #then transform to rotated crystal coordinates & apply to view point Q = drawingData['Quaternion'] V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V)) Tx,Ty,Tz = drawingData['viewPoint'][0] Tx += V[0]*0.1 Ty += V[1]*0.1 Tz += V[2]*0.1 drawingData['viewPoint'][0] = np.array([Tx,Ty,Tz]) def SetRotation(newxy): 'Perform a rotation in x-y space due to a left-mouse drag' #first get rotation vector in screen coords. & angle increment oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! drawingData['oldxy'] = list(newxy) V = np.array([dxy[1],dxy[0],0.]) A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) if not A: return # nothing changed, nothing to do # next transform vector back to xtal coordinates via inverse quaternion # & make new quaternion Q = drawingData['Quaternion'] V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V)) DQ = G2mth.AVdeg2Q(A,V) Q = G2mth.prodQQ(Q,DQ) drawingData['Quaternion'] = Q # finally get new view vector - last row of rotation matrix VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2]) VD /= np.sqrt(np.sum(VD**2)) drawingData['viewDir'] = VD def SetRotationZ(newxy): #first get rotation vector (= view vector) in screen coords. & angle increment View = GL.glGetIntegerv(GL.GL_VIEWPORT) cent = [View[2]/2,View[3]/2] oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! drawingData['oldxy'] = list(newxy) V = drawingData['viewDir'] A = [0,0] A[0] = dxy[1]*.25 A[1] = dxy[0]*.25 if newxy[0] > cent[0]: A[0] *= -1 if newxy[1] < cent[1]: A[1] *= -1 # next transform vector back to xtal coordinates & make new quaternion Q = drawingData['Quaternion'] V = np.inner(Amat,V) Qx = G2mth.AVdeg2Q(A[0],V) Qy = G2mth.AVdeg2Q(A[1],V) Q = G2mth.prodQQ(Q,Qx) Q = G2mth.prodQQ(Q,Qy) drawingData['Quaternion'] = Q def OnMouseDown(event): xy = event.GetPosition() drawingData['oldxy'] = list(xy) def OnMouseMove(event): if event.ShiftDown(): #don't want any inadvertant moves when picking return newxy = event.GetPosition() if event.Dragging(): if event.LeftIsDown(): SetRotation(newxy) elif event.RightIsDown(): SetTranslation(newxy) Tx,Ty,Tz = drawingData['viewPoint'][0] elif event.MiddleIsDown(): SetRotationZ(newxy) Draw('move') else: hkl = GetTruePosition(newxy) if hkl: h,k,l = hkl Page.SetToolTipString('%d,%d,%d'%(h,k,l)) G2frame.G2plotNB.status.SetStatusText('hkl = %d,%d,%d'%(h,k,l),1) def OnMouseWheel(event): if event.ShiftDown(): return drawingData['cameraPos'] += event.GetWheelRotation()/120. drawingData['cameraPos'] = max(0.1,min(20.00,drawingData['cameraPos'])) Draw('wheel') def SetBackground(): R,G,B,A = Page.camera['backColor'] GL.glClearColor(R,G,B,A) GL.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT) def SetLights(): GL.glEnable(GL.GL_DEPTH_TEST) # GL.glShadeModel(GL.GL_SMOOTH) GL.glEnable(GL.GL_LIGHTING) GL.glEnable(GL.GL_LIGHT0) GL.glLightModeli(GL.GL_LIGHT_MODEL_TWO_SIDE,0) GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[1,1,1,1]) GL.glLightfv(GL.GL_LIGHT0,GL.GL_DIFFUSE,[1,1,1,1]) def RenderBox(x,y,z): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(1) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glColor4ubv([0,0,0,0]) GL.glBegin(GL.GL_LINES) for line,color in zip(uEdges,uColors): GL.glColor3ubv(color) GL.glVertex3fv(line[0]) GL.glVertex3fv(line[1]) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderUnitVectors(x,y,z,labxyz=['','','']): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(1) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glBegin(GL.GL_LINES) for line,color in list(zip(uEdges,uColors))[:3]: GL.glColor3ubv(color) GL.glVertex3fv([0,0,0]) # GL.glVertex3fv(-line[1]) GL.glVertex3fv(line[1]) GL.glEnd() GL.glRotate(180,1,0,0) #fix to flip about x-axis for ix,txt in enumerate(labxyz): if txt: pos = uEdges[ix][1] GL.glTranslate(pos[0],-1.5*pos[1],-pos[2]) text = gltext.TextElement(text=txt,font=Font) text.draw_text(scale=0.05) GL.glTranslate(-pos[0],1.5*pos[1],pos[2]) GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderDots(XYZ,RC): GL.glEnable(GL.GL_COLOR_MATERIAL) XYZ = np.array(XYZ) GL.glPushMatrix() for xyz,rc in zip(XYZ,RC): x,y,z = xyz r,c = rc GL.glColor3ubv(c) GL.glPointSize(r*50) GL.glBegin(GL.GL_POINTS) GL.glVertex3fv(xyz) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def Draw(caller=''): #useful debug? # if caller: # print caller # end of useful debug VS = np.array(Page.canvas.GetSize()) aspect = float(VS[0])/float(VS[1]) cPos = drawingData['cameraPos'] Zclip = drawingData['Zclip']*cPos/20. if Data['Zone']: Zclip = 0.01 Q = drawingData['Quaternion'] Tx,Ty,Tz = drawingData['viewPoint'][0][:3] G,g = G2lat.cell2Gmat(cell) GS = G GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1]) GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2]) GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2]) HKL,RC,RF,RF2 = FillHKLRC() G2frame.G2plotNB.status.SetStatusText \ ('Plot type = %s for %s; RF = %6.2f%%, RF%s = %6.2f%%'%(Data['Type'],Name,RF,super2,RF2),1) SetBackground() GL.glInitNames() GL.glPushName(0) GL.glMatrixMode(GL.GL_PROJECTION) GL.glLoadIdentity() GL.glViewport(0,0,VS[0],VS[1]) GLU.gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip) GLU.gluLookAt(0,0,cPos,0,0,0,0,1,0) SetLights() GL.glMatrixMode(GL.GL_MODELVIEW) GL.glLoadIdentity() matRot = G2mth.Q2Mat(Q) matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) GL.glMultMatrixf(matRot.T) GL.glMultMatrixf(B4mat) GL.glTranslate(-Tx,-Ty,-Tz) x,y,z = drawingData['viewPoint'][0] if ifBox: RenderBox(x,y,z) else: RenderUnitVectors(x,y,z) RenderUnitVectors(0,0,0,labxyz=['h','k','l']) RenderDots(HKL,RC) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Page.canvas.SwapBuffers() # Plot3DSngl execution starts here (N.B. initialization above) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('3D Structure Factors','ogl') if new: Page.views = False Font = Page.GetFont() Page.Choice = None choice = [' save as/key:','jpeg','tiff','bmp','h: view down h','k: view down k','l: view down l', 'z: zero zone toggle','c: reset to default','o: set view point = 0,0,0','b: toggle box ','+: increase scale','-: decrease scale', 'f: Fobs','s: Fobs**2','u: unit','d: Fo-Fc','w: DF/sig','i: toggle intensity scaling'] cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice) cb.Bind(wx.EVT_COMBOBOX, OnKeyBox) cb.SetValue(' save as/key:') Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel) Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_KEY_UP, OnKey) Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove) # Page.canvas.Bind(wx.EVT_SIZE, OnSize) Page.camera['position'] = drawingData['cameraPos'] Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0]) Page.camera['backColor'] = np.array(list(drawingData['backColor'])+[0,])/255. Page.controls = Data try: Page.canvas.SetCurrent() except: pass Draw('main') # if firstCall: Draw('main') # draw twice the first time that graphics are displayed ################################################################################ ##### PlotPatterns ################################################################################ def ReplotPattern(G2frame,newPlot,plotType,PatternName=None,PickName=None): '''This does the same as PlotPatterns except that it expects the information to be plotted (pattern name, item picked in tree + eventually the reflection list) to be passed as names rather than references to wx tree items, defined as class entries ''' if PatternName: pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, PatternName) if pId: G2frame.PatternId = pId else: if GSASIIpath.GetConfigValue('debug'): print('PatternName not found',PatternName) return if PickName == PatternName: G2frame.PickId = G2frame.PatternId elif PickName: pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.PatternId, PickName) if pId: G2frame.PickId = pId else: if GSASIIpath.GetConfigValue('debug'): print('PickName not found',PickName) return elif GSASIIpath.GetConfigValue('debug'): print('Possible PickId problem PickId=',G2frame.PickId) # for now I am not sure how to regenerate G2frame.HKL G2frame.HKL = [] # TODO PlotPatterns(G2frame,newPlot,plotType) def PlotPatterns(G2frame,newPlot=False,plotType='PWDR',data=None, extraKeys=[],refineMode=False): '''Powder pattern plotting package - displays single or multiple powder patterns as intensity vs 2-theta, q or TOF. Can display multiple patterns as "waterfall plots" or contour plots. Log I plotting available. Note that plotting information will be found in: G2frame.PatternId (contains the tree item for the current histogram) G2frame.PickId (contains the actual selected tree item (can be child of histogram) G2frame.HKL (used for tool tip display of hkl for selected phase reflection list) ''' def PublishPlot(event): msg = "" if 'PWDR' not in plottype: msg += " * only PWDR histograms can be used" if G2frame.Contour or not G2frame.SinglePlot: if msg: msg += '\n' msg += " * only when a single histogram is plotted" if Page.plotStyle['logPlot']: if msg: msg += '\n' msg += " * only when the intensity scale is linear/sqrt (not log)" if G2frame.Weight: if msg: msg += '\n' msg += " * only when weight plot is set to no weight plot" if msg: msg = 'Publication export is only available under limited plot settings\n'+msg G2G.G2MessageBox(G2frame,msg,'Wrong plot settings') print(msg) else: PublishRietveldPlot(G2frame,Pattern,Plot,Page) def OnPlotKeyPress(event): try: #one way to check if key stroke will work on plot Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1) return newPlot = False if event.key == 'w': # and not Page.plotStyle['qPlot'] and not Page.plotStyle['dPlot']: #can't do weight plots when x-axis is different G2frame.Weight = not G2frame.Weight if not G2frame.Weight and 'PWDR' in plottype: G2frame.SinglePlot = True elif 'PWDR' in plottype: # Turning on Weight plot clears previous limits G2frame.FixedLimits['dylims'] = ['',''] newPlot = True elif event.key == 'e' and plottype in ['SASD','REFD']: G2frame.ErrorBars = not G2frame.ErrorBars elif event.key == '.': Page.plotStyle['WgtDiagnostic'] = not Page.plotStyle.get('WgtDiagnostic',False) newPlot = True elif event.key == 'b' and plottype not in ['SASD','REFD'] and not Page.plotStyle['logPlot'] and not Page.plotStyle['sqrtPlot']: G2frame.SubBack = not G2frame.SubBack elif event.key == 'n': if G2frame.Contour: pass else: Page.plotStyle['logPlot'] = not Page.plotStyle['logPlot'] if Page.plotStyle['logPlot']: Page.plotStyle['sqrtPlot'] = False else: Page.plotStyle['Offset'][0] = 0 newPlot = True elif event.key == 's' and 'PWDR' in plottype: Page.plotStyle['sqrtPlot'] = not Page.plotStyle['sqrtPlot'] if Page.plotStyle['sqrtPlot']: Page.plotStyle['logPlot'] = False G2frame.SubBack = False Ymax = max(Pattern[1][1]) if Page.plotStyle['sqrtPlot']: Page.plotStyle['delOffset'] = .02*np.sqrt(Ymax) Page.plotStyle['refOffset'] = -0.1*np.sqrt(Ymax) Page.plotStyle['refDelt'] = .1*np.sqrt(Ymax) else: Page.plotStyle['delOffset'] = .02*Ymax Page.plotStyle['refOffset'] = -0.1*Ymax Page.plotStyle['refDelt'] = .1*Ymax newPlot = True elif event.key == 'S' and 'PWDR' in plottype: choice = [m for m in mpl.cm.datad.keys()] # if not m.endswith("_r") choice.sort() dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.ContourColor = choice[sel] else: G2frame.ContourColor = GSASIIpath.GetConfigValue('Contour_color','Paired') dlg.Destroy() newPlot = True elif event.key == 'u' and (G2frame.Contour or not G2frame.SinglePlot): if G2frame.Contour: G2frame.Cmax = min(1.0,G2frame.Cmax*1.2) elif Page.plotStyle['Offset'][0] < 100.: Page.plotStyle['Offset'][0] += 1. elif event.key == 'd' and (G2frame.Contour or not G2frame.SinglePlot): if G2frame.Contour: G2frame.Cmax = max(0.0,G2frame.Cmax*0.8) elif Page.plotStyle['Offset'][0] > -100.: Page.plotStyle['Offset'][0] -= 1. elif event.key == 'U': if G2frame.Contour: G2frame.Cmin += (G2frame.Cmax - G2frame.Cmin)/5. elif Page.plotStyle['Offset'][0] < 100.: Page.plotStyle['Offset'][0] += 10. elif event.key == 'D': if G2frame.Contour: G2frame.Cmin -= (G2frame.Cmax - G2frame.Cmin)/5. elif Page.plotStyle['Offset'][0] > -100.: Page.plotStyle['Offset'][0] -= 10. elif event.key == 'g': mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid'] elif event.key == 'l' and not G2frame.SinglePlot: Page.plotStyle['Offset'][1] -= 1. elif event.key == 'r' and not G2frame.SinglePlot: Page.plotStyle['Offset'][1] += 1. elif event.key == 'o': if G2frame.SinglePlot and not G2frame.Contour: global obsInCaption # include the observed, calc,... items in the plot caption (PlotPatterns) obsInCaption = not obsInCaption elif not G2frame.SinglePlot: G2frame.Cmax = 1.0 G2frame.Cmin = 0.0 Page.plotStyle['Offset'] = [0,0] elif event.key == 'c' and 'PWDR' in plottype: newPlot = True if not G2frame.Contour: G2frame.SinglePlot = False Page.plotStyle['Offset'] = [0.,0.] G2frame.FixedLimits['cylims'] = ['',''] # reset manual limits else: G2frame.SinglePlot = True G2frame.Contour = not G2frame.Contour if G2frame.Contour: Page.plotStyle['qPlot'] = False Page.plotStyle['dPlot'] = False elif event.key == 'a' and 'PWDR' in plottype and G2frame.SinglePlot and not ( Page.plotStyle['logPlot'] or Page.plotStyle['sqrtPlot'] or G2frame.Contour): # add a magnification region try: xpos = event.xdata if xpos is None: return #avoid out of frame mouse position if 'Magnification' not in Pattern[0]: Pattern[0]['Magnification'] = [] try: if Page.plotStyle['qPlot']: xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos) elif Page.plotStyle['dPlot']: xpos = G2lat.Dsp2pos(Parms,xpos) except ValueError: return except AttributeError: # invoked when this is called from dialog rather than key press xpos = (Pattern[1][0][-1]+Pattern[1][0][0])/2 # set to middle of pattern if not Pattern[0]['Magnification']: Pattern[0]['Magnification'] = [[None,1.]] Pattern[0]['Magnification'] += [[xpos,2.]] wx.CallAfter(G2gd.UpdatePWHKPlot,G2frame,plottype,G2frame.PatternId) return elif event.key == 'q': newPlot = True if 'PWDR' in plottype: Page.plotStyle['qPlot'] = not Page.plotStyle['qPlot'] if Page.plotStyle['qPlot']: G2frame.Contour = False Page.plotStyle['dPlot'] = False elif plottype in ['SASD','REFD']: Page.plotStyle['sqPlot'] = not Page.plotStyle['sqPlot'] elif event.key == 't' and 'PWDR' in plottype: if G2frame.Contour: G2frame.TforYaxis = not G2frame.TforYaxis else: Page.plotStyle['dPlot'] = not Page.plotStyle['dPlot'] if Page.plotStyle['dPlot']: G2frame.Contour = False Page.plotStyle['qPlot'] = False newPlot = True elif event.key == 'm': if not G2frame.Contour: G2frame.SinglePlot = not G2frame.SinglePlot G2frame.Contour = False newPlot = True elif event.key == 'f' and not G2frame.SinglePlot: choices = G2gd.GetGPXtreeDataNames(G2frame,plotType) dlg = G2G.G2MultiChoiceDialog(G2frame,'Select dataset to plot', 'Multidata plot selection',choices) if dlg.ShowModal() == wx.ID_OK: G2frame.selections = [] select = dlg.GetSelections() if select: for Id in select: G2frame.selections.append(choices[Id]) else: G2frame.selections = None dlg.Destroy() newPlot = True elif event.key in ['+','=']: G2frame.plusPlot = not G2frame.plusPlot elif event.key == 'i' and G2frame.Contour: #for smoothing contour plot choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning', 'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel', 'mitchell','sinc','lanczos'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.Interpolate = choice[sel] else: G2frame.Interpolate = 'nearest' dlg.Destroy() elif event.key in [KeyItem[0] for KeyItem in extraKeys]: for KeyItem in extraKeys: if event.key == KeyItem[0]: KeyItem[1]() break else: #print('no binding for key',event.key) return wx.CallAfter(PlotPatterns,G2frame,newPlot=newPlot,plotType=plottype,extraKeys=extraKeys) def OnMotion(event): 'Update the status line with infor based on the mouse position' SetCursor(Page) if event.button and G2frame.Contour and G2frame.TforYaxis: ytics = imgAx.get_yticks() ytics = np.where(ytics 6: #SS reflections fmt = "{:.0f},{:.0f},{:.0f},{:.0f}" n = 4 else: fmt = "{:.0f},{:.0f},{:.0f}" n = 3 for i,hkl in enumerate(found): if i >= 3: s += '\n...' break if s: s += '\n' s += fmt.format(*hkl[:n]) elif G2frame.itemPicked: # not sure when this will happen s = '%9.5f'%(xpos) Page.SetToolTipString(s) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select '+plottype+' pattern first',1) def OnPress(event): #ugh - this removes a matplotlib error for mouse clicks in log plots np.seterr(invalid='ignore') def onMoveDiffCurve(event): '''Respond to a menu command to move the difference curve. ''' if not DifLine[0]: print('No difference curve!') return G2frame.itemPicked = DifLine[0] G2frame.G2plotNB.Parent.Raise() OnPick(None) def onMoveTopTick(event): '''Respond to a menu command to move the tick locations. ''' if len(Page.phaseList) == 0: print("there are tick marks (no phases)") return G2frame.itemPicked = Page.tickDict[Page.phaseList[0]] G2frame.G2plotNB.Parent.Raise() OnPick(None) def onMoveTickSpace(event): '''Respond to a menu command to move the tick spacing. ''' if len(Page.phaseList) == 0: print("there are tick marks (no phases)") return G2frame.itemPicked = Page.tickDict[Page.phaseList[-1]] G2frame.G2plotNB.Parent.Raise() OnPick(None) def onMovePeak(event): selectedPeaks = list(set([row for row,col in G2frame.phaseDisplay.GetSelectedCells()] + G2frame.phaseDisplay.GetSelectedRows())) if len(selectedPeaks) != 1: G2G.G2MessageBox(G2frame,'You must select one peak in the table first. # selected ='+ str(len(selectedPeaks)),'Select one peak') return G2frame.itemPicked = G2frame.Lines[selectedPeaks[0]+2] # 1st 2 lines are limits G2frame.G2plotNB.Parent.Raise() OnPick(None) def OnPick(event): '''Respond to an item being picked. This usually means that the item will be dragged with the mouse. ''' def OnDragMarker(event): '''Respond to dragging of a plot Marker ''' if event.xdata is None or event.ydata is None: return # ignore if cursor out of window if G2frame.itemPicked is None: return # not sure why this happens, if it does Page.canvas.restore_region(savedplot) G2frame.itemPicked.set_data([event.xdata], [event.ydata]) Page.figure.gca().draw_artist(G2frame.itemPicked) Page.canvas.blit(Page.figure.gca().bbox) def OnDragLine(event): '''Respond to dragging of a plot line ''' if event.xdata is None: return # ignore if cursor out of window if G2frame.itemPicked is None: return # not sure why this happens Page.canvas.restore_region(savedplot) coords = G2frame.itemPicked.get_data() coords[0][0] = coords[0][1] = event.xdata coords = G2frame.itemPicked.set_data(coords) Page.figure.gca().draw_artist(G2frame.itemPicked) Page.canvas.blit(Page.figure.gca().bbox) def OnDragTickmarks(event): '''Respond to dragging of the reflection tick marks ''' if event.ydata is None: return # ignore if cursor out of window if Page.tickDict is None: return # not sure why this happens, if it does Page.canvas.restore_region(savedplot) if Page.pickTicknum: refDelt = -(event.ydata-Page.plotStyle['refOffset'])/Page.pickTicknum refOffset = Page.plotStyle['refOffset'] else: #1st row of refl ticks refOffset = event.ydata refDelt = Page.plotStyle['refDelt'] for pId,phase in enumerate(Page.phaseList): pos = refOffset - pId*refDelt coords = Page.tickDict[phase].get_data() coords[1][:] = pos Page.tickDict[phase].set_data(coords) Page.figure.gca().draw_artist(Page.tickDict[phase]) Page.canvas.blit(Page.figure.gca().bbox) def OnDragDiffCurve(event): '''Respond to dragging of the difference curve ''' if event.ydata is None: return # ignore if cursor out of window if G2frame.itemPicked is None: return # not sure why this happens Page.canvas.restore_region(savedplot) coords = G2frame.itemPicked.get_data() coords[1][:] += Page.diffOffset + event.ydata Page.diffOffset = -event.ydata G2frame.itemPicked.set_data(coords) Page.figure.gca().draw_artist(G2frame.itemPicked) Page.canvas.blit(Page.figure.gca().bbox) global Page try: Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) except TypeError: return if event is None: # called from a menu command rather than by click on mpl artist mouse = 1 pick = G2frame.itemPicked ind = np.array([0]) else: if G2frame.itemPicked is not None: return pick = event.artist mouse = event.mouseevent xpos = pick.get_xdata() ypos = pick.get_ydata() ind = event.ind xy = list(list(zip(np.take(xpos,ind),np.take(ypos,ind)))[0]) # convert from plot units if Page.plotStyle['qPlot']: #qplot - convert back to 2-theta xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0]) elif Page.plotStyle['dPlot']: #dplot - convert back to 2-theta xy[0] = G2lat.Dsp2pos(Parms,xy[0]) # if Page.plotStyle['sqrtPlot']: # xy[1] = xy[1]**2 PatternId = G2frame.PatternId PickId = G2frame.PickId if PickId and G2frame.GPXtree.GetItemText(PickId) == 'Peak List': if ind.all() != [0] and ObsLine[0].get_label() in str(pick): #picked a data point, add a new peak data = G2frame.GPXtree.GetItemPyData(G2frame.PickId) XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1]) data['peaks'].append(XY) data['sigDict'] = {} #now invalid G2pdG.UpdatePeakGrid(G2frame,data) PlotPatterns(G2frame,plotType=plottype,extraKeys=extraKeys) else: #picked a peak list line # prepare to animate move of line G2frame.itemPicked = pick pick.set_linestyle(':') # set line as dotted Page = G2frame.G2plotNB.nb.GetPage(plotNum) Page.figure.gca() Page.canvas.draw() # refresh without dotted line & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragLine) pick.set_linestyle('--') # back to dashed elif PickId and G2frame.GPXtree.GetItemText(PickId) in ['Limits','Unit Cells List']: if ind.all() != [0]: #picked a data point LimitId = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits') data = G2frame.GPXtree.GetItemPyData(LimitId) if Page.plotStyle['qPlot']: #qplot - convert back to 2-theta xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0]) elif Page.plotStyle['dPlot']: #dplot - convert back to 2-theta xy[0] = G2lat.Dsp2pos(Parms,xy[0]) if G2frame.ifGetExclude: excl = [0,0] excl[0] = max(data[1][0],min(xy[0],data[1][1])) excl[1] = excl[0]+0.1 data.append(excl) G2frame.ifGetExclude = False else: if mouse.button==1: data[1][0] = min(xy[0],data[1][1]) if mouse.button==3: data[1][1] = max(xy[0],data[1][0]) G2frame.GPXtree.SetItemPyData(LimitId,data) G2pdG.UpdateLimitsGrid(G2frame,data,plottype) wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) else: #picked a limit line # prepare to animate move of line G2frame.itemPicked = pick pick.set_linestyle(':') # set line as dotted Page = G2frame.G2plotNB.nb.GetPage(plotNum) Page.figure.gca() Page.canvas.draw() # refresh without dotted line & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragLine) pick.set_linestyle('--') # back to dashed elif PickId and G2frame.GPXtree.GetItemText(PickId) == 'Models': if ind.all() != [0]: #picked a data point LimitId = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits') data = G2frame.GPXtree.GetItemPyData(LimitId) if mouse.button==1: data[1][0] = min(xy[0],data[1][1]) if mouse.button==3: data[1][1] = max(xy[0],data[1][0]) G2frame.GPXtree.SetItemPyData(LimitId,data) wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) else: #picked a limit line G2frame.itemPicked = pick elif PickId and (G2frame.GPXtree.GetItemText(PickId) == 'Reflection Lists' or 'PWDR' in G2frame.GPXtree.GetItemText(PickId) ): G2frame.itemPicked = pick Page = G2frame.G2plotNB.nb.GetPage(plotNum) Page.figure.gca() if DifLine[0] is G2frame.itemPicked: # pick of difference curve Page.canvas.draw() # save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) Page.diffOffset = Page.plotStyle['delOffset'] G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragDiffCurve) elif G2frame.itemPicked in G2frame.MagLines: # drag of magnification marker pick.set_dashes((1,4)) # set line as dotted sparse Page.canvas.draw() # refresh without dotted line & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragLine) pick.set_dashes((1,1)) # back to dotted else: # pick of plot tick mark (is anything else possible?) pick = str(G2frame.itemPicked).split('(',1)[1][:-1] if pick not in Page.phaseList: # picked something other than a tickmark return Page.pickTicknum = Page.phaseList.index(pick) resetlist = [] for pId,phase in enumerate(Page.phaseList): # set the tickmarks to a lighter color col = Page.tickDict[phase].get_color() rgb = mpcls.ColorConverter().to_rgb(col) rgb_light = [(2 + i)/3. for i in rgb] resetlist.append((Page.tickDict[phase],rgb)) Page.tickDict[phase].set_color(rgb_light) Page.tickDict[phase].set_zorder(99) # put on top Page.canvas.draw() # refresh with dimmed tickmarks savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) for f,v in resetlist: # reset colors back f.set_zorder(0) f.set_color(v) # reset colors back to original values G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragTickmarks) elif PickId and G2frame.GPXtree.GetItemText(PickId) == 'Background': # selected a fixed background point. Can move it or delete it. backPts = G2frame.dataWindow.wxID_BackPts for mode in backPts: # what menu is selected? if G2frame.dataWindow.BackMenu.FindItemById(backPts[mode]).IsChecked(): break # mode will be 'Add' or 'Move' or 'Del' if pick.get_marker() == 'D': # find the closest point backDict = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background'))[1] d2 = [(x-xy[0])**2+(y-xy[1])**2 for x,y in backDict['FixedPoints']] G2frame.fixPtMarker = d2.index(min(d2)) if mode == 'Move': # animate move of FixedBkg marker G2frame.itemPicked = pick pick.set_marker('|') # change the point appearance Page = G2frame.G2plotNB.nb.GetPage(plotNum) Page.figure.gca() Page.canvas.draw() # refresh with changed point & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragMarker) pick.set_marker('D') # put it back elif mode == 'Del': del backDict['FixedPoints'][G2frame.fixPtMarker] wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) return def OnRelease(event): '''This is called when the mouse button is released when a plot object is dragged due to an item pick, or when invoked via a menu item (such as in onMoveDiffCurve), or for background points, which may be added/moved/deleted here. New peaks are also added here. ''' plotNum = G2frame.G2plotNB.plotList.index('Powder Patterns') Page = G2frame.G2plotNB.nb.GetPage(plotNum) if G2frame.cid is not None: # if there is a drag connection, delete it Page.canvas.mpl_disconnect(G2frame.cid) G2frame.cid = None if event.xdata is None or event.ydata is None: # ignore drag if cursor is outside of plot if GSASIIpath.GetConfigValue('debug'): print('Ignoring drag, invalid pos:',event.xdata,event.ydata) wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) return if not G2frame.PickId: if GSASIIpath.GetConfigValue('debug'): print('Ignoring drag, G2frame.PickId is not set') return PickId = G2frame.PickId # points to item in tree if G2frame.GPXtree.GetItemText(PickId) == 'Background' and event.xdata: if Page.toolbar._active: # prevent ops. if a toolbar zoom button pressed # after any mouse release event (could be a zoom), redraw magnification lines if magLineList: wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) return # Background page, deal with fixed background points if G2frame.SubBack or G2frame.Weight or G2frame.Contour or not G2frame.SinglePlot: return backDict = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background'))[1] if 'FixedPoints' not in backDict: backDict['FixedPoints'] = [] try: Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) except TypeError: return # unit conversions xy = [event.xdata,event.ydata] try: if Page.plotStyle['qPlot']: #qplot - convert back to 2-theta xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0]) elif Page.plotStyle['dPlot']: #dplot - convert back to 2-theta xy[0] = G2lat.Dsp2pos(Parms,xy[0]) except: return if Page.plotStyle['sqrtPlot']: xy[1] = xy[1]**2 backPts = G2frame.dataWindow.wxID_BackPts for mode in backPts: # what menu is selected? if G2frame.dataWindow.BackMenu.FindItemById(backPts[mode]).IsChecked(): break if mode == 'Add': backDict['FixedPoints'].append(xy) Plot = Page.figure.gca() Plot.plot(event.xdata,event.ydata,'rD',clip_on=Clip_on,picker=3.) Page.canvas.draw() return elif G2frame.itemPicked is not None: # end of drag in move backDict['FixedPoints'][G2frame.fixPtMarker] = xy G2frame.itemPicked = None wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) return if G2frame.itemPicked is None: # after any mouse release event (could be a zoom) where nothing is selected, # redraw magnification lines if magLineList: wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) return if DifLine[0] is G2frame.itemPicked: # respond to dragging of the difference curve data = G2frame.GPXtree.GetItemPyData(PickId) ypos = event.ydata Page.plotStyle['delOffset'] = -ypos G2frame.itemPicked = None wx.CallAfter(PlotPatterns,G2frame,plotType=plottype,extraKeys=extraKeys) return elif G2frame.itemPicked in G2frame.MagLines: # drag of magnification marker xpos = event.xdata try: if Page.plotStyle['qPlot']: #qplot - convert back to 2-theta xpos = G2lat.Dsp2pos(Parms,2*np.pi/xpos) elif Page.plotStyle['dPlot']: #dplot - convert back to 2-theta xpos = G2lat.Dsp2pos(Parms,xpos) except: return magIndex = G2frame.MagLines.index(G2frame.itemPicked) data = G2frame.GPXtree.GetItemPyData(PickId) data[0]['Magnification'][magIndex][0] = xpos wx.CallAfter(G2gd.UpdatePWHKPlot,G2frame,plottype,G2frame.PatternId) return Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) xpos = event.xdata if G2frame.GPXtree.GetItemText(PickId) in ['Peak List','Limits','Unit Cells List'] and xpos: lines = [] for line in G2frame.Lines: lines.append(line.get_xdata()[0]) try: lineNo = lines.index(G2frame.itemPicked.get_xdata()[0]) except ValueError: lineNo = -1 nxcl = len(exclLines) if lineNo in [0,1] or lineNo in exclLines: LimitId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits') limits = G2frame.GPXtree.GetItemPyData(LimitId) Id = lineNo//2+1 id2 = lineNo%2 if Page.plotStyle['qPlot'] and 'PWDR' in plottype: limits[Id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos) elif Page.plotStyle['dPlot'] and 'PWDR' in plottype: limits[Id][id2] = G2lat.Dsp2pos(Parms,xpos) else: limits[Id][id2] = xpos if Id > 1 and limits[Id][0] > limits[Id][1]: limits[Id].reverse() limits[1][0] = min(max(limits[0][0],limits[1][0]),limits[1][1]) limits[1][1] = max(min(limits[0][1],limits[1][1]),limits[1][0]) if G2frame.GPXtree.GetItemText(G2frame.PickId) == 'Limits': G2pdG.UpdateLimitsGrid(G2frame,limits,plottype) elif lineNo > 1+nxcl: PeakId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List') peaks = G2frame.GPXtree.GetItemPyData(PeakId) if event.button == 3: del peaks['peaks'][lineNo-2-nxcl] else: if Page.plotStyle['qPlot']: peaks['peaks'][lineNo-2-nxcl][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos) elif Page.plotStyle['dPlot']: peaks['peaks'][lineNo-2-nxcl][0] = G2lat.Dsp2pos(Parms,xpos) else: peaks['peaks'][lineNo-2-nxcl][0] = xpos peaks['sigDict'] = {} #no longer valid G2pdG.UpdatePeakGrid(G2frame,peaks) elif G2frame.GPXtree.GetItemText(PickId) in ['Models',] and xpos: lines = [] for line in G2frame.Lines: lines.append(line.get_xdata()[0]) try: lineNo = lines.index(G2frame.itemPicked.get_xdata()[0]) except ValueError: lineNo = -1 if lineNo in [0,1]: LimitId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits') data = G2frame.GPXtree.GetItemPyData(LimitId) data[1][lineNo] = xpos data[1][0] = min(max(data[0][0],data[1][0]),data[1][1]) data[1][1] = max(min(data[0][1],data[1][1]),data[1][0]) elif (G2frame.GPXtree.GetItemText(PickId) == 'Reflection Lists' or 'PWDR' in G2frame.GPXtree.GetItemText(PickId)) and xpos: Id = G2gd.GetGPXtreeItemId(G2frame,PatternId,'Reflection Lists') if Id: pick = str(G2frame.itemPicked).split('(',1)[1][:-1] if 'line' not in pick: #avoid data points, etc. data = G2frame.GPXtree.GetItemPyData(G2frame.PatternId) if pick in Page.phaseList: num = Page.phaseList.index(pick) if num: Page.plotStyle['refDelt'] = -(event.ydata-Page.plotStyle['refOffset'])/num else: #1st row of refl ticks Page.plotStyle['refOffset'] = event.ydata elif GSASIIpath.GetConfigValue('debug'): # should not happen! print('How did we get here?') GSASIIpath.IPyBreak() PlotPatterns(G2frame,plotType=plottype,extraKeys=extraKeys) G2frame.itemPicked = None def onSetPlotLim(event): '''Specify plot limits manually ''' def onChecked(event): try: i = cbox.index(event.EventObject) showChecked(i) except: pass def showChecked(i): checked = cbox[i].GetValue() if not checked: # fake out validation to avoid ugly yellow dbox[i].invalid = False dbox[i]._IndicateValidity() else: # reset validation dbox[i].SetValue(dbox[i].GetValue()) dbox[i].Enable(checked) def applyLims(event): Page.toolbar.push_current() CurLims = {} CurLims['xlims'] = list(Plot.get_xlim()) if G2frame.Weight: CurLims['ylims'] = list(Page.figure.axes[1].get_ylim()) CurLims['dylims'] = list(Page.figure.axes[2].get_ylim()) elif G2frame.Contour: CurLims['ylims'] = list(Plot.get_ylim()) CurLims['cylims'] = list(Page.Img.get_clim()) else: CurLims['ylims'] = list(Plot.get_ylim()) CurLims['dylims'] = [0,0] for var in 'xlims','ylims','dylims','cylims': for i in range(2): if not G2frame.UseLimits[var][i]: continue try: CurLims[var][i] = float(G2frame.FixedLimits[var][i]) CurLims[var][i] = float(G2frame.FixedLimits[var][i]) except: pass Plot.set_xlim(CurLims['xlims']) if G2frame.Weight: Page.figure.axes[1].set_ylim(CurLims['ylims']) Page.figure.axes[2].set_ylim(CurLims['dylims']) elif G2frame.Contour: Plot.set_ylim(CurLims['ylims']) Page.Img.set_clim(CurLims['cylims']) else: Plot.set_ylim(CurLims['ylims']) Page.toolbar.push_current() Plot.figure.canvas.draw() # onSetPlotLim starts here dlg = wx.Dialog(G2frame.plotFrame, style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER) vbox = wx.BoxSizer(wx.VERTICAL) vbox.Add(wx.StaticText(dlg,wx.ID_ANY, 'Set Plot limits' ),0,wx.ALL) gsizer = wx.FlexGridSizer(cols=5,hgap=2,vgap=2) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,' '),0,wx.ALL) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'use'),0,wx.ALL) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,' min'),0,wx.ALL) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'use'),0,wx.ALL) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,' max'),0,wx.ALL) cbox = [] dbox = [] lblkeys = [(' x-axis ','xlims'),(' y-axis ','ylims')] if G2frame.Weight: lblkeys += [('(obs-calc)/sig ','dylims')] elif G2frame.Contour: lblkeys += [('contour','cylims')] for lbl,key in lblkeys: gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,lbl),0,wx.ALL) for i in range(2): cbox.append(G2G.G2CheckBox(dlg,'',G2frame.UseLimits[key],i, OnChange=onChecked)) dbox.append(G2G.ValidatedTxtCtrl(dlg,G2frame.FixedLimits[key],i, typeHint=float)) gsizer.Add(cbox[-1]) gsizer.Add(dbox[-1]) showChecked(-1) vbox.Add(gsizer) vbox.Add((10,10),1,wx.ALL|wx.EXPAND,1) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add((-1,-1),1,wx.ALL|wx.EXPAND,1) #btn = wx.Button(dlg, wx.ID_CLOSE) #btn.Bind(wx.EVT_BUTTON,lambda event:dlg.EndModal(wx.ID_CANCEL)) #hbox.Add(btn) btn = wx.Button(dlg, wx.ID_ANY, label='Apply') btn.Bind(wx.EVT_BUTTON,applyLims) hbox.Add(btn) OKbtn = wx.Button(dlg, wx.ID_OK) OKbtn.Bind(wx.EVT_BUTTON,lambda event:dlg.EndModal(wx.ID_OK)) hbox.Add(OKbtn) hbox.Add((-1,-1),1,wx.ALL|wx.EXPAND,1) vbox.Add(hbox,1,wx.ALL|wx.EXPAND,1) dlg.SetSizer(vbox) vbox.Fit(dlg) dlg.ShowModal() dlg.Destroy() applyLims(None) # apply limits #GSASIIpath.IPyBreak() def onPlotFormat(event): '''Change the appearance of the current plot''' changePlotSettings(G2frame,Plot) def refPlotUpdate(Histograms,cycle=None,restore=False): '''called to update an existing plot during a Rietveld fit ''' if restore: (G2frame.SinglePlot,G2frame.Contour,G2frame.Weight, G2frame.plusPlot,G2frame.SubBack,Page.plotStyle['logPlot']) = savedSettings return if plottingItem not in Histograms: histoList = [i for i in Histograms.keys() if i.startswith('PWDR ')] if len(histoList) == 0: print('Skipping plot, no PWDR item found!') return plotItem = histoList[0] else: plotItem = plottingItem if Page.plotStyle['dPlot'] or Page.plotStyle['qPlot']: print("Skipping plot, can't do this for d-plots or q-plots!") return xye = np.array(ma.getdata(Histograms[plotItem]['Data'])) # strips mask xye0 = Histograms[plotItem]['Data'][0] # if Page.plotStyle['qPlot']: # X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye0) # Ibeg = np.searchsorted(X,2.*np.pi/G2lat.Pos2dsp(Parms,limits[1][0])) # Ifin = np.searchsorted(X,2.*np.pi/G2lat.Pos2dsp(Parms,limits[1][1])) # elif Page.plotStyle['dPlot']: # X = G2lat.Pos2dsp(Parms,xye0) # Ibeg = np.searchsorted(X,G2lat.Pos2dsp(Parms,limits[1][1])) # Ifin = np.searchsorted(X,G2lat.Pos2dsp(Parms,limits[1][0])) # else: X = copy.deepcopy(xye0) Ibeg = np.searchsorted(X,limits[1][0]) Ifin = np.searchsorted(X,limits[1][1]) if Page.plotStyle['sqrtPlot']: olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1])) Z = np.where(xye[3]>=0.,np.sqrt(xye[3]),-np.sqrt(-xye[3])) W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4])) #D = np.where(xye[5],(Y-Z),0.)-Page.plotStyle['delOffset'] np.seterr(invalid=olderr['invalid']) else: Y = copy.copy(xye[1]) Z = copy.copy(xye[3]) W = copy.copy(xye[4]) #D = xye[5]-Page.plotStyle['delOffset'] #powder background DZ = (xye[1]-xye[3])*np.sqrt(xye[2]) DifLine[0].set_xdata(X[Ibeg:Ifin]) DifLine[0].set_ydata(DZ[Ibeg:Ifin]) lims = [min(DZ[Ibeg:Ifin]),max(DZ[Ibeg:Ifin])] if all(np.isfinite(lims)): Plot1.set_ylim(lims) CalcLine[0].set_xdata(X) ObsLine[0].set_xdata(X) BackLine[0].set_xdata(X) CalcLine[0].set_ydata(Z) ObsLine[0].set_ydata(Y) BackLine[0].set_ydata(W) if cycle: Title = '{} cycle #{}'.format(plotItem,cycle) else: Title = plotItem if Page.plotStyle['sqrtPlot']: Plot.set_title(r'$\sqrt{I}$ for '+Title) else: Plot.set_title(Title) Page.canvas.draw() def incCptn(string): '''Adds a underscore to "hide" a MPL object from the legend if obsInCaption is False ''' if obsInCaption: return string else: return '_'+string #===================================================================================== # beginning PlotPatterns execution global exclLines,Page global DifLine # BHT: probably does not need to be global global Ymax global Pattern,mcolors,Plot,Page,imgAx,Temps plottype = plotType if not G2frame.PatternId: return if 'PKS' in plottype: PlotPowderLines(G2frame) return if data is None: data = G2frame.GPXtree.GetItemPyData(G2frame.PatternId) if G2frame.PickId and plottype not in ['SASD','REFD'] and 'PWDR' in G2frame.GPXtree.GetItemText(G2frame.PickId): publish = PublishPlot else: publish = None new,plotNum,Page,Plot,limits = G2frame.G2plotNB.FindPlotTab('Powder Patterns','mpl',publish=publish) #patch if 'Offset' not in Page.plotStyle and plotType in ['PWDR','SASD','REFD']: #plot offset data Ymax = max(data[1][1]) Page.plotStyle.update({'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-0.1*Ymax, 'refDelt':0.1*Ymax,}) #end patch try: G2frame.FixedLimits except: G2frame.FixedLimits = {i:['',''] for i in ('xlims','ylims','dylims','cylims')} try: G2frame.UseLimits except: G2frame.UseLimits = {i:[False,False] for i in ('xlims','ylims','dylims','cylims')} #===================================================================================== # code to setup for plotting Rietveld results. Turns off multiplot, # sqrtplot, turn on + and weight plot, but sqrtPlot qPlot and dPlot are not changed. # Magnification regions are ignored. # the last-plotted histogram (from G2frame.PatternId) is used for this plotting # (except in seq. fitting) # Returns a pointer to refPlotUpdate, which is used to update the plot when this # returns if refineMode: plottingItem = G2frame.GPXtree.GetItemText(G2frame.PatternId) # save settings to be restored after refinement with repPlotUpdate({},restore=True) savedSettings = (G2frame.SinglePlot,G2frame.Contour,G2frame.Weight, G2frame.plusPlot,G2frame.SubBack,Page.plotStyle['logPlot']) G2frame.SinglePlot = True G2frame.Contour = False G2frame.Weight = True G2frame.plusPlot = True G2frame.SubBack = False Page.plotStyle['logPlot'] = False #===================================================================================== if not new: G2frame.xylim = copy.copy(limits) else: if plottype in ['SASD','REFD']: Page.plotStyle['logPlot'] = True G2frame.ErrorBars = True newPlot = True G2frame.Cmin = 0.0 G2frame.Cmax = 1.0 Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.canvas.mpl_connect('pick_event', OnPick) Page.canvas.mpl_connect('button_release_event', OnRelease) Page.canvas.mpl_connect('button_press_event',OnPress) Page.bindings = [] # redo OnPlotKeyPress binding each time the Plot is updated # since needs values that may have been changed after 1st call for b in Page.bindings: Page.canvas.mpl_disconnect(b) Page.bindings = [] Page.bindings.append(Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress)) if not G2frame.PickId: print('No plot, G2frame.PickId,G2frame.PatternId=',G2frame.PickId,G2frame.PatternId) return elif 'PWDR' in G2frame.GPXtree.GetItemText(G2frame.PickId): Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() refColors=['b','r','c','g','m','k'] Page.phaseColors = {p:refColors[i%len(refColors)] for i,p in enumerate(Phases)} Phases = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Reflection Lists')) Page.phaseList = sorted(Phases.keys()) # define an order for phases (once!) G2frame.Bind(wx.EVT_MENU, onMoveDiffCurve, id=G2frame.dataWindow.moveDiffCurve.GetId()) G2frame.Bind(wx.EVT_MENU, onMoveTopTick, id=G2frame.dataWindow.moveTickLoc.GetId()) G2frame.Bind(wx.EVT_MENU, onMoveTickSpace, id=G2frame.dataWindow.moveTickSpc.GetId()) G2frame.Bind(wx.EVT_MENU, onSetPlotLim, id=G2frame.dataWindow.setPlotLim.GetId()) G2frame.Bind(wx.EVT_MENU, onPlotFormat, id=G2frame.dataWindow.setPlotFmt.GetId()) G2frame.dataWindow.moveDiffCurve.Enable(False) G2frame.dataWindow.moveTickLoc.Enable(False) G2frame.dataWindow.moveTickSpc.Enable(False) elif G2frame.GPXtree.GetItemText(G2frame.PickId) == 'Peak List': G2frame.Bind(wx.EVT_MENU, onMovePeak, id=G2frame.dataWindow.movePeak.GetId()) # save information needed to reload from tree and redraw if not refineMode: kwargs={'PatternName':G2frame.GPXtree.GetItemText(G2frame.PatternId)} if G2frame.PickId: kwargs['PickName'] = G2frame.GPXtree.GetItemText(G2frame.PickId) G2frame.G2plotNB.RegisterRedrawRoutine(G2frame.G2plotNB.lastRaisedPlotTab,ReplotPattern, (G2frame,newPlot,plotType),kwargs) # now start plotting G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar Page.tickDict = {} DifLine = [''] if G2frame.Contour: Page.Choice = (' key press','b: toggle subtract background', 'd: lower contour max','u: raise contour max', 'D: lower contour min','U: raise contour min', 'o: reset contour limits','g: toggle grid', 'i: interpolation method','S: color scheme','c: contour off','t: temperature for y-axis','s: toggle sqrt plot') else: if 'PWDR' in plottype: Page.Choice = [' key press', 'a: add magnification region','b: toggle subtract background', 'c: contour on','g: toggle grid','m: toggle multidata plot', 'n: toggle log(I)',] if obsInCaption: Page.Choice += ['o: remove obs, calc,... from legend',] else: Page.Choice += ['o: add obs, calc,... to legend',] Page.Choice += ['q: toggle q plot','s: toggle sqrt plot', 't: toggle d-spacing plot','w: toggle (Io-Ic)/sig plot', '+: no selection'] if Page.plotStyle['sqrtPlot'] or Page.plotStyle['logPlot']: del Page.Choice[1] del Page.Choice[1] elif not G2frame.SinglePlot: del Page.Choice[1] if not G2frame.SinglePlot: Page.Choice = Page.Choice+ \ ['u/U: offset up/10x','d/D: offset down/10x','l: offset left','r: offset right', 'o: reset offset','f: select data',] elif plottype in ['SASD','REFD']: Page.Choice = [' key press', 'b: toggle subtract background file','g: toggle grid', 'm: toggle multidata plot','n: toggle semilog/loglog', 'q: toggle S(q) plot','w: toggle (Io-Ic)/sig plot','+: toggle selection',] if not G2frame.SinglePlot: Page.Choice = Page.Choice+ \ ['u: offset up','d: offset down','l: offset left', 'r: offset right','o: reset offset',] for KeyItem in extraKeys: Page.Choice = Page.Choice + [KeyItem[0] + ': '+KeyItem[2],] magLineList = [] # null value indicates no magnification Page.toolbar.updateActions = None # no update actions G2frame.cid = None Page.keyPress = OnPlotKeyPress PickId = G2frame.PickId PatternId = G2frame.PatternId try: colors = GSASIIpath.GetConfigValue('Plot_Colors').split() for color in colors: if color not in ['k','r','g','b','m','c']: print('**** bad color code: '+str(color)+' - redo Preferences/Plot Colors ****') raise Exception except: colors = ['b','g','r','c','m','k'] Lines = [] exclLines = [] time0 = time.time() if G2frame.SinglePlot and PatternId: Pattern = G2frame.GPXtree.GetItemPyData(PatternId) Pattern.append(G2frame.GPXtree.GetItemText(PatternId)) PlotList = [Pattern,] PId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background') Pattern[0]['BackFile'] = ['',-1.0,False] if PId: Pattern[0]['BackFile'] = G2frame.GPXtree.GetItemPyData(PId)[1].get('background PWDR',['',-1.0,False]) Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, G2frame.PatternId, 'Instrument Parameters')) Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters')) ParmList = [Parms,] SampleList = [Sample,] Title = data[0].get('histTitle') if not Title: Title = Pattern[-1] else: #G2frame.selection Title = os.path.split(G2frame.GSASprojectfile)[1] if G2frame.selections is None: choices = G2gd.GetGPXtreeDataNames(G2frame,plotType) else: choices = G2frame.selections PlotList = [] ParmList = [] SampleList = [] Temps = [] # loop through tree looking for matching histograms to plot Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while Id: name = G2frame.GPXtree.GetItemText(Id) pid = Id Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if name not in choices: continue Pattern = G2frame.GPXtree.GetItemPyData(pid) if len(Pattern) < 3: # put name on end if needed Pattern.append(G2frame.GPXtree.GetItemText(pid)) if 'Offset' not in Page.plotStyle: #plot offset data Ymax = max(Pattern[1][1]) Page.plotStyle.update({'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-0.1*Ymax,'refDelt':0.1*Ymax,}) PId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background') Pattern[0]['BackFile'] = ['',-1.0,False] if PId: Pattern[0]['BackFile'] = G2frame.GPXtree.GetItemPyData(PId)[1].get('background PWDR',['',-1.0,False]) PlotList.append(Pattern) ParmList.append(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pid,'Instrument Parameters'))[0]) SampleList.append(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pid, 'Sample Parameters'))) Temps.append('%.1fK'%SampleList[-1]['Temperature']) if not G2frame.Contour: PlotList.reverse() ParmList.reverse() SampleList.reverse() if timeDebug: print('plot build time: %.3f for %dx%d patterns'%(time.time()-time0,len(PlotList[0][1][1]),len(PlotList))) lenX = 0 Ymax = None for ip,Pattern in enumerate(PlotList): xye = Pattern[1] #bxye = G2pdG.GetFileBackground(G2frame,xye,Pattern) if xye[1] is None: continue if Ymax is None: Ymax = max(xye[1]) Ymax = max(Ymax,max(xye[1])) if Ymax is None: return # nothing to plot offsetX = Page.plotStyle['Offset'][1] offsetY = Page.plotStyle['Offset'][0] if Page.plotStyle['logPlot']: Title = 'log('+Title+')' elif Page.plotStyle['sqrtPlot']: Title = r'$\sqrt{I}$ for '+Title Ymax = np.sqrt(Ymax) elif Page.plotStyle.get('WgtDiagnostic',False): Title = 'Scaling diagnostic for '+Title if G2frame.SubBack: Title += ' - background' if Page.plotStyle['qPlot'] or plottype in ['SASD','REFD'] and not G2frame.Contour: xLabel = r'$Q, \AA^{-1}$' elif Page.plotStyle['dPlot'] and 'PWDR' in plottype and not G2frame.Contour: xLabel = r'$d, \AA$' else: if 'C' in ParmList[0]['Type'][0]: xLabel = r'$\mathsf{2\theta}$' else: if G2frame.Contour: xLabel = r'Channel no.' else: xLabel = r'$TOF, \mathsf{\mu}$s' if G2frame.Weight: Plot.set_visible(False) #hide old plot frame, will get replaced below GS_kw = {'height_ratios':[4, 1],} # try: Plot,Plot1 = Page.figure.subplots(2,1,sharex=True,gridspec_kw=GS_kw) # except AttributeError: # figure.Figure.subplots added in MPL 2.2 # Plot,Plot1 = MPLsubplots(Page.figure, 2, 1, sharex=True, gridspec_kw=GS_kw) Plot1.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16) Plot1.set_xlabel(xLabel,fontsize=16) Page.figure.subplots_adjust(left=16/100.,bottom=16/150., right=.98,top=1.-16/200.,hspace=0) else: Plot.set_xlabel(xLabel,fontsize=16) if 'C' in ParmList[0]['Type'][0]: if 'PWDR' in plottype: if Page.plotStyle['sqrtPlot']: Plot.set_ylabel(r'$\sqrt{Intensity}$',fontsize=16) elif Page.plotStyle.get('WgtDiagnostic',False): Plot.set_ylabel('Intensity * Weight') else: Plot.set_ylabel(r'$Intensity$',fontsize=16) elif plottype == 'SASD': if Page.plotStyle['sqPlot']: Plot.set_ylabel(r'$S(Q)=I*Q^{4}$',fontsize=16) else: Plot.set_ylabel(r'$Intensity,\ cm^{-1}$',fontsize=16) elif plottype == 'REFD': if Page.plotStyle['sqPlot']: Plot.set_ylabel(r'$S(Q)=R*Q^{4}$',fontsize=16) else: Plot.set_ylabel(r'$Reflectivity$',fontsize=16) else: #neutron TOF if Page.plotStyle['sqrtPlot']: Plot.set_ylabel(r'$\sqrt{Normalized\ intensity}$',fontsize=16) else: Plot.set_ylabel(r'$Normalized\ intensity$',fontsize=16) mpl.rcParams['image.cmap'] = G2frame.ContourColor mcolors = mpl.cm.ScalarMappable() #wants only default as defined in previous line!! mcolors.set_array([]) # needed for MPL <=3.0.x if G2frame.Contour: ContourZ = [] ContourY = [] Nseq = 0 Nmax = len(PlotList)-1 time0 = time.time() for N,Pattern in enumerate(PlotList): Parms = ParmList[N] Sample = SampleList[N] ifpicked = False LimitId = 0 NoffY = offsetY*(Nmax-N) if Pattern[1] is None: continue # skip over uncomputed simulations xye = np.array(ma.getdata(Pattern[1])) # strips mask = X,Yo,W,Yc,Yb,Yd xye0 = Pattern[1][0] # keeps mask if PickId: ifpicked = Pattern[2] == G2frame.GPXtree.GetItemText(PatternId) LimitId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Limits') limits = G2frame.GPXtree.GetItemPyData(LimitId) # recompute mask from excluded regions, in case they have changed excls = limits[2:] for excl in excls: xye0 = ma.masked_inside(xye[0],excl[0],excl[1],copy=False) #excluded region mask if not G2frame.Contour: xye0 = ma.masked_outside(xye[0],limits[1][0],limits[1][1],copy=False) #now mask for limits if Page.plotStyle['qPlot'] and 'PWDR' in plottype: X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye0) elif Page.plotStyle['dPlot'] and 'PWDR' in plottype: X = G2lat.Pos2dsp(Parms,xye0) else: X = copy.deepcopy(xye0) if not lenX: lenX = len(X) # show plot magnification factors magMarkers = [] Plot.magLbls = [] multArray = np.ones_like(Pattern[1][0]) if 'PWDR' in plottype and G2frame.SinglePlot and not ( Page.plotStyle['logPlot'] or Page.plotStyle['sqrtPlot'] or G2frame.Contour): if not refineMode: magLineList = data[0].get('Magnification',[]) if ('C' in ParmList[0]['Type'][0] and Page.plotStyle['dPlot']) or \ ('T' in ParmList[0]['Type'][0] and Page.plotStyle['qPlot']): # reversed regions relative to data order tcorner = 1 tpos = 1.0 halign = 'right' else: tcorner = 0 tpos = 1.0 halign = 'left' ml0 = None for x,m in magLineList: ml = m if int(m) == m: ml = int(m) if x is None: magMarkers.append(None) multArray *= m ml0 = ml continue multArray[Pattern[1][0]>x] = m if Page.plotStyle['qPlot']: x = 2.*np.pi/G2lat.Pos2dsp(Parms,x) elif Page.plotStyle['dPlot']: x = G2lat.Pos2dsp(Parms,x) # is range in displayed range (defined after newplot)? if not newPlot: (xmin,xmax),ylim = G2frame.xylim if x < xmin: ml0 = ml continue if x > xmax: continue magMarkers.append(Plot.axvline(x,color='0.5',dashes=(1,1),picker=2.,label='_magline')) lbl = Plot.annotate("x{}".format(ml), xy=(x, tpos), xycoords=("data", "axes fraction"), verticalalignment='bottom',horizontalalignment=halign,label='_maglbl') Plot.magLbls.append(lbl) if ml0: lbl = Plot.annotate("x{}".format(ml0), xy=(tcorner, tpos), xycoords="axes fraction", verticalalignment='bottom',horizontalalignment=halign,label='_maglbl') Plot.magLbls.append(lbl) Page.toolbar.updateActions = (PlotPatterns,G2frame) multArray = ma.getdata(multArray) if 'PWDR' in plottype: YI = copy.copy(xye[1]) #yo if G2frame.SubBack: YI -= xye[4] #background if Page.plotStyle['sqrtPlot']: olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error Y = np.where(YI>=0.,np.sqrt(YI),-np.sqrt(-YI))+NoffY*Ymax/100.0 np.seterr(invalid=olderr['invalid']) elif Page.plotStyle.get('WgtDiagnostic',False): Y = xye[1]*xye[2] #Y-obs*wt elif 'PWDR' in plottype and G2frame.SinglePlot and not \ (Page.plotStyle['logPlot'] or Page.plotStyle['sqrtPlot'] or G2frame.Contour): Y = YI*multArray+NoffY*Ymax/100.0 else: Y = YI+NoffY*Ymax/100.0 elif plottype in ['SASD','REFD']: if plottype == 'SASD': B = xye[5] #Yo - Yc else: B = np.zeros_like(xye[5]) if Page.plotStyle['sqPlot']: Y = xye[1]*Sample['Scale'][0]*(1.05)**NoffY*X**4 else: Y = xye[1]*Sample['Scale'][0]*(1.05)**NoffY if LimitId and ifpicked: limits = np.array(G2frame.GPXtree.GetItemPyData(LimitId)) lims = limits[1] if Page.plotStyle['qPlot'] and 'PWDR' in plottype: lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims) elif Page.plotStyle['dPlot'] and 'PWDR' in plottype: lims = G2lat.Pos2dsp(Parms,lims) Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.)) Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.)) for i,item in enumerate(limits[2:]): Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.)) Lines.append(Plot.axvline(item[1],color='m',dashes=(5,5),picker=3.)) exclLines += [2*i+2,2*i+3] if G2frame.Contour: if lenX == len(X): ContourY.append(N) if G2frame.SubBack: ContourZ.append(Y) else: ContourZ.append(Y) if 'C' in ParmList[0]['Type'][0]: ContourX = X else: #'T'OF ContourX = range(lenX) Nseq += 1 if G2frame.TforYaxis: Plot.set_ylabel('Temperature',fontsize=14) else: Plot.set_ylabel('Data sequence',fontsize=14) else: if G2frame.plusPlot: pP = '+' else: pP = '' if plottype in ['SASD','REFD'] and Page.plotStyle['logPlot']: X *= (1.01)**(offsetX*N) else: xlim = Plot.get_xlim() DX = xlim[1]-xlim[0] X += 0.002*offsetX*DX*N if G2frame.GPXtree.GetItemText(PickId) == 'Limits': Xum = ma.getdata(X) # unmasked version of X, use for data limits (only) else: Xum = X[:] if ifpicked: ZI = copy.copy(xye[3]) #Yc if Page.plotStyle['sqrtPlot']: olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error Z = np.where(ZI>=0.,np.sqrt(ZI),-np.sqrt(-ZI)) np.seterr(invalid=olderr['invalid']) else: if 'PWDR' in plottype and G2frame.SinglePlot and not ( Page.plotStyle['logPlot'] or Page.plotStyle['sqrtPlot'] or G2frame.Contour): Z = ZI*multArray+NoffY*Ymax/100.0 #yc else: Z = ZI+NoffY*Ymax/100.0 #yc if 'PWDR' in plottype: if Page.plotStyle['sqrtPlot']: olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error W = np.where(xye[4]>=0.,np.sqrt(xye[4]),-np.sqrt(-xye[4])) #yb np.seterr(invalid=olderr['invalid']) D = np.where(xye[5],(Y-Z),0.)-Page.plotStyle['delOffset'] elif Page.plotStyle.get('WgtDiagnostic',False): Z = D = W = np.zeros_like(Y) elif G2frame.SinglePlot and not ( Page.plotStyle['logPlot'] or Page.plotStyle['sqrtPlot'] or G2frame.Contour): W = xye[4]*multArray+NoffY*Ymax/100.0 #yb D = multArray*xye[5]-Page.plotStyle['delOffset'] #Yo-Yc else: W = xye[4]+NoffY*Ymax/100.0 #yb D = xye[5]-Page.plotStyle['delOffset'] #Yo-Yc elif plottype in ['SASD','REFD']: if Page.plotStyle['sqPlot']: W = xye[4]*X**4 #Yb Z = xye[3]*X**4 #Yc B = B*X**4 #(yo-Yc)*x**4 else: W = xye[4] #Yb if G2frame.SubBack: YB = Y-B ZB = Z else: YB = Y ZB = Z+B Plot.set_yscale("log",nonposy='mask') if np.any(W>0.): lims = [np.min(np.trim_zeros(W))/2.,np.max(Y)*2.] else: lims = [np.min(np.trim_zeros(YB))/2.,np.max(Y)*2.] if all(np.isfinite(lims)): Plot.set_ylim(bottom=lims[0],top=lims[1]) # Matplotlib artist lists used for refPlotUpdate ObsLine = None CalcLine = None BackLine = None DifLine = [None] if G2frame.Weight: Plot1.set_yscale("linear") wtFactor = Pattern[0]['wtFactor'] if plottype in ['SASD','REFD']: DZ = (Y-B-Z)*np.sqrt(wtFactor*xye[2]) else: DZ = (xye[1]-xye[3])*np.sqrt(wtFactor*xye[2]) DifLine = Plot1.plot(X,DZ,colors[3],picker=1.,label=incCptn('diff')) #(Io-Ic)/sig(Io) Plot1.axhline(0.,color='k') if Page.plotStyle['logPlot']: if 'PWDR' in plottype: Plot.set_yscale("log",nonposy='mask') Plot.plot(X,Y,marker=pP,color=colors[0],picker=3.,clip_on=Clip_on,label=incCptn('obs')) if G2frame.SinglePlot or G2frame.plusPlot: Plot.plot(X,Z,colors[1],picker=False,label=incCptn('calc')) if G2frame.plusPlot: Plot.plot(X,W,colors[2],picker=False,label=incCptn('bkg')) #background elif plottype in ['SASD','REFD']: Plot.set_xscale("log",nonposx='mask') Plot.set_yscale("log",nonposy='mask') if G2frame.ErrorBars: if Page.plotStyle['sqPlot']: Plot.errorbar(X,YB,yerr=X**4*Sample['Scale'][0]*np.sqrt(1./(Pattern[0]['wtFactor']*xye[2])), ecolor=colors[0],picker=3.,clip_on=Clip_on) else: Plot.errorbar(X,YB,yerr=Sample['Scale'][0]*np.sqrt(1./(Pattern[0]['wtFactor']*xye[2])), ecolor=colors[0],picker=3.,clip_on=Clip_on,label=incCptn('obs')) else: Plot.plot(X,YB,marker=pP,color=colors[0],picker=3.,clip_on=Clip_on,label=incCptn('obs')) Plot.plot(X,W,colors[1],picker=False,label=incCptn('bkg')) #const. background Plot.plot(X,ZB,colors[2],picker=False,label=incCptn('calc')) else: # not logPlot if G2frame.SubBack: if 'PWDR' in plottype: ObsLine = Plot.plot(Xum,Y,color=colors[0],marker=pP,picker=False,clip_on=Clip_on,label=incCptn('obs-bkg')) #Io-Ib if np.any(Z): #only if there is a calc pattern CalcLine = Plot.plot(X,Z-W,colors[1],picker=False,label=incCptn('calc-bkg')) #Ic-Ib else: Plot.plot(X,YB,color=colors[0],marker=pP,picker=3.,clip_on=Clip_on,label=incCptn('obs')) Plot.plot(X,ZB,colors[2],picker=False,label=incCptn('calc')) else: if 'PWDR' in plottype: ObsLine = Plot.plot(Xum,Y,color=colors[0],marker=pP,picker=3.,clip_on=Clip_on,label=incCptn('obs')) #Io CalcLine = Plot.plot(X,Z,colors[1],picker=False,label=incCptn('calc')) #Ic else: Plot.plot(X,YB,color=colors[0],marler=pP,picker=3.,clip_on=Clip_on,label=incCptn('obs')) Plot.plot(X,ZB,colors[2],picker=False,label=incCptn('calc')) if 'PWDR' in plottype and (G2frame.SinglePlot and G2frame.plusPlot): BackLine = Plot.plot(X,W,colors[2],picker=False,label=incCptn('bkg')) #Ib if not G2frame.Weight and np.any(Z): DifLine = Plot.plot(X,D,colors[3],picker=1.,label=incCptn('diff')) #Io-Ic Plot.axhline(0.,color='k',label='_zero') Page.SetToolTipString('') if PickId: if G2frame.GPXtree.GetItemText(PickId) == 'Peak List': tip = 'On data point: Pick peak - L or R MB. On line: L-move, R-delete' Page.SetToolTipString(tip) data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List')) selectedPeaks = list(set( [row for row,col in G2frame.reflGrid.GetSelectedCells()] + G2frame.reflGrid.GetSelectedRows())) G2frame.dataWindow.movePeak.Enable(len(selectedPeaks) == 1) # allow peak move from table when one peak is selected for i,item in enumerate(data['peaks']): if i in selectedPeaks: Ni = N+1 else: Ni = N if Page.plotStyle['qPlot']: Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color='b',picker=2.)) elif Page.plotStyle['dPlot']: Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color='b',picker=2.)) else: Lines.append(Plot.axvline(item[0],color='b',picker=2.)) if Ni == N+1: Lines[-1].set_lw(Lines[-1].get_lw()+1) if G2frame.GPXtree.GetItemText(PickId) == 'Limits': tip = 'On data point: Lower limit - L MB; Upper limit - R MB. On limit: MB down to move' Page.SetToolTipString(tip) data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits')) else: #not picked icolor = 256*N//len(PlotList) if Page.plotStyle['logPlot']: if 'PWDR' in plottype: Plot.semilogy(X,Y,color=mcolors.cmap(icolor),picker=False,nonposy='mask') elif plottype in ['SASD','REFD']: Plot.semilogy(X,Y,color=mcolors.cmap(icolor),picker=False,nonposy='mask') else: if 'PWDR' in plottype: Plot.plot(X,Y,color=mcolors.cmap(icolor),picker=False) elif plottype in ['SASD','REFD']: Plot.loglog(X,Y,mcolors.cmap(icolor),picker=False,nonposy='mask') Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.) if Page.plotStyle['logPlot'] and 'PWDR' in plottype: Plot.set_ylim(bottom=np.min(np.trim_zeros(Y))/2.,top=np.max(Y)*2.) if timeDebug: print('plot fill time: %.3f'%(time.time()-time0)) if not magLineList: Plot.set_title(Title) if PickId and not G2frame.Contour: Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters')) orange = [255/256.,128/256.,0.] if G2frame.GPXtree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']: peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Index Peak List')) if not len(peaks): return # are there any peaks? for peak in peaks[0]: if peak[2]: if Page.plotStyle['qPlot']: Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b') if Page.plotStyle['dPlot']: Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b') else: Plot.axvline(peak[0],color='b') for hkl in G2frame.HKL: clr = orange if len(hkl) > 6 and hkl[3]: clr = 'g' if Page.plotStyle['qPlot']: Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(3,3),lw=1.5) if Page.plotStyle['dPlot']: Plot.axvline(G2lat.Pos2dsp(Parms,hkl[-2]),color=clr,dashes=(3,3),lw=1.5) else: Plot.axvline(hkl[-2],color=clr,dashes=(3,3),lw=1.5) elif Page.plotStyle.get('WgtDiagnostic',False): pass # skip reflection markers elif (G2frame.GPXtree.GetItemText(PickId) in ['Reflection Lists'] or 'PWDR' in G2frame.GPXtree.GetItemText(PickId) or refineMode): Phases = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Reflection Lists')) l = GSASIIpath.GetConfigValue('Tick_length',8.0) w = GSASIIpath.GetConfigValue('Tick_width',1.) refColors=['b','r','c','g','m','k'] Page.phaseList = sorted(Phases.keys()) # define an order for phases (once!) Page.phaseColors = {p:refColors[i%len(refColors)] for i,p in enumerate(Phases)} for pId,phase in enumerate(Page.phaseList): if 'list' in str(type(Phases[phase])): continue if phase not in Page.phaseColors: continue peaks = Phases[phase].get('RefList',[]) if not len(peaks): continue if Phases[phase].get('Super',False): peak = np.array([[peak[5],peak[6]] for peak in peaks]) else: peak = np.array([[peak[4],peak[5]] for peak in peaks]) pos = Page.plotStyle['refOffset']-pId*Page.plotStyle['refDelt']*np.ones_like(peak) plsym = Page.phaseColors[phase]+'|' # yellow should never happen! if Page.plotStyle['qPlot']: Page.tickDict[phase],j = Plot.plot(2*np.pi/peak.T[0],pos,plsym,mew=w,ms=l,picker=3.,label=phase) elif Page.plotStyle['dPlot']: Page.tickDict[phase],j = Plot.plot(peak.T[0],pos,plsym,mew=w,ms=l,picker=3.,label=phase) else: Page.tickDict[phase],j = Plot.plot(peak.T[1],pos,plsym,mew=w,ms=l,picker=3.,label=phase) handles,legends = Plot.get_legend_handles_labels() #got double entries in the phase legends for some reason if handles: labels = dict(zip(legends,handles)) #this removes duplicate phase entries handles = [labels[item] for item in labels] legends = list(labels.keys()) if len(Phases) and obsInCaption: Plot.legend(handles,legends,title='Phases & Data',loc='best') else: Plot.legend(handles,legends,title='Data',loc='best') if G2frame.Contour: time0 = time.time() acolor = mpl.cm.get_cmap(G2frame.ContourColor) Page.Img = Plot.imshow(ContourZ,cmap=acolor, vmin=Ymax*G2frame.Cmin,vmax=Ymax*G2frame.Cmax, interpolation=G2frame.Interpolate, extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower') if G2frame.TforYaxis: imgAx = Page.Img.axes ytics = imgAx.get_yticks() ylabs = [Temps[int(i)] for i in ytics[:-1]] imgAx.set_yticklabels(ylabs) Page.figure.colorbar(Page.Img) if timeDebug: print('Contour display time: %.3f'%(time.time()-time0)) else: G2frame.Lines = Lines G2frame.MagLines = magMarkers if PickId and G2frame.GPXtree.GetItemText(PickId) == 'Background': # plot fixed background points backDict = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background'))[1] try: Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters')) except TypeError: Parms = None for x,y in backDict.get('FixedPoints',[]): # "normal" intensity modes only! if G2frame.SubBack or G2frame.Weight or G2frame.Contour or not G2frame.SinglePlot: break if y < 0 and (Page.plotStyle['sqrtPlot'] or Page.plotStyle['logPlot']): y = Page.figure.gca().get_ylim()[0] # put out of range point at bottom of plot elif Page.plotStyle['sqrtPlot']: y = math.sqrt(y) if Page.plotStyle['qPlot']: #Q - convert from 2-theta if Parms: x = 2*np.pi/G2lat.Pos2dsp(Parms,x) else: break elif Page.plotStyle['dPlot']: #d - convert from 2-theta if Parms: x = G2lat.Dsp2pos(Parms,x) else: break Plot.plot(x,y,'rD',clip_on=Clip_on,picker=3.) if not newPlot: # this restores previous plot limits (but I'm not sure why there are two .push_current calls) Page.toolbar.push_current() if G2frame.Contour: # for contour plots expand y-axis to include all histograms G2frame.xylim = (G2frame.xylim[0], (0.,len(PlotList)-1.)) Plot.set_xlim(G2frame.xylim[0]) Plot.set_ylim(G2frame.xylim[1]) Page.toolbar.push_current() Page.toolbar.draw() else: G2frame.xylim = Plot.get_xlim(),Plot.get_ylim() Page.canvas.draw() olderr = np.seterr(invalid='ignore') #ugh - this removes a matplotlib error for mouse clicks in log plots # and sqrt(-ve) in np.where usage if 'PWDR' in G2frame.GPXtree.GetItemText(G2frame.PickId): if len(Page.tickDict.keys()) == 1: G2frame.dataWindow.moveTickLoc.Enable(True) elif len(Page.tickDict.keys()) > 1: G2frame.dataWindow.moveTickLoc.Enable(True) G2frame.dataWindow.moveTickSpc.Enable(True) if DifLine[0]: G2frame.dataWindow.moveDiffCurve.Enable(True) if refineMode: return refPlotUpdate def PublishRietveldPlot(G2frame,Pattern,Plot,Page): '''Show a customizable "Rietveld" plot and export as a publication-quality file. Will only work when a single pattern is displayed. :param wx.Frame G2Frame: the main GSAS-II window :param list Pattern: list of np.array items with obs, calc (etc.) diffraction pattern :param mpl.axes Plot: axes of the graph in plot window :param wx.Panel Page: tabbed panel containing the plot ''' def Initialize(): '''Set up initial values in plotOpt ''' plotOpt['initNeeded'] = False # create a temporary hard-copy figure to get output options figure = mpl.figure.Figure(dpi=200,figsize=(6,8)) canvas = hcCanvas(figure) fmtDict = canvas.get_supported_filetypes() figure.clear() plotOpt['fmtChoices'] = [fmtDict[j]+', '+j for j in sorted(fmtDict)] plotOpt['fmtChoices'].append('Data file with plot elements, csv') plotOpt['fmtChoices'].append('Grace input file, agr') plotOpt['fmtChoices'].append('Igor Pro input file, itx') if plotOpt['format'] is None: if 'pdf' in fmtDict: plotOpt['format'] = fmtDict['pdf'] + ', pdf' else: plotOpt['format'] = plotOpt['fmtChoices'][0] plotOpt['lineWid'] = '1' plotOpt['tickSiz'] = '6' plotOpt['tickWid'] = '1' plotOpt['markerWid'] = '1' plotOpt['markerSiz'] = '8' plotOpt['markerSym'] = '+' #if mpl.__version__.split('.')[0] == '1': # G2G.G2MessageBox(G2frame.plotFrame, # ('You are using an older version of Matplotlib ({}). '.format(mpl.__version__) + # '\nPlot quality will be improved by updating (use conda update matplotlib)'), # 'Old matplotlib') def GetColors(): '''Set up initial values in plotOpt for colors and legend ''' if hasattr(mpcls,'to_rgba'): MPL2rgba = mpcls.to_rgba else: MPL2rgba = mpcls.ColorConverter().to_rgba plotOpt['phaseList'] = [] for i,l in enumerate(Plot.lines): lbl = l.get_label() if 'mag' in lbl: pass elif lbl[1:] in plotOpt['lineList']: # item not in legend if lbl[1:] in plotOpt['colors']: continue plotOpt['colors'][lbl[1:]] = MPL2rgba(l.get_color()) plotOpt['legend'][lbl[1:]] = False elif lbl in plotOpt['lineList']: if lbl in plotOpt['colors']: continue plotOpt['colors'][lbl] = MPL2rgba(l.get_color()) plotOpt['legend'][lbl] = True elif l in Page.tickDict.values(): plotOpt['phaseList'] .append(lbl) if lbl in plotOpt['colors']: continue plotOpt['colors'][lbl] = MPL2rgba(l.get_color()) plotOpt['legend'][lbl] = True def RefreshPlot(*args,**kwargs): '''Update the plot on the dialog ''' figure.clear() CopyRietveldPlot(G2frame,Pattern,Plot,Page,figure) figure.canvas.draw() # blocks of code used in grace .agr files linedef = '''@{0} legend "{1}" @{0} line color {2} @{0} errorbar color {2} @{0} symbol color {2} @{0} symbol {3} @{0} symbol fill color {2} @{0} linewidth {4} @{0} symbol linewidth {6} @{0} line type {7} @{0} symbol size {5} @{0} symbol char 46 @{0} symbol fill pattern 1 @{0} hidden false @{0} errorbar off\n''' linedef1 = '''@{0} legend "{1}" @{0} line color {2} @{0} errorbar color {2} @{0} symbol color {2} @{0} symbol fill color {2} @{0} symbol 11 @{0} linewidth 0 @{0} linestyle 0 @{0} symbol size {3} @{0} symbol linewidth {4} @{0} symbol char 124 @{0} symbol fill pattern 1 @{0} hidden false\n''' linedef2 = '''@{0} legend "{1}" @{0} line color {2} @{0} errorbar color {2} @{0} symbol color {2} @{0} symbol fill color {2} @{0} symbol 0 @{0} linewidth 0 @{0} linestyle 0 @{0} symbol size 1 @{0} symbol linewidth 0 @{0} symbol char 124 @{0} symbol fill pattern 1 @{0} hidden false @{0} errorbar on @{0} errorbar size 0 @{0} errorbar riser linewidth {3}\n''' linedef3 = '''@{0} legend "{1}" @{0} line color {2} @{0} errorbar color {2} @{0} symbol color {2} @{0} symbol {3} @{0} symbol fill color {2} @{0} linewidth {4} @{0} symbol linewidth {6} @{0} line type {7} @{0} symbol size {5} @{0} symbol char 46 @{0} symbol fill pattern 1 @{0} hidden false @{0} errorbar off\n''' def CopyRietveld2Grace(Pattern,Plot,Page,plotOpt,filename): '''Copy the contents of the Rietveld graph from the plot window to a Grace input file (tested with QtGrace). Uses values from Pattern to also generate a delta/sigma plot below. ''' def ClosestColorNumber(color): '''Convert a RGB value to the closest default Grace color ''' import matplotlib.colors as mpcls colorlist = ('white','black','red','green','blue','yellow','brown', 'gray','purple','cyan','magenta','orange') # ordered by grace's # if not hasattr(mpcls,'to_rgba'): mpcls = mpcls.ColorConverter() return (np.sum(([np.array(mpcls.to_rgb(c)) for c in colorlist] - np.array(color[:3]))**2,axis=1)).argmin() grace_symbols = {"":0, "o":1 ,"s":2, "D":3, "^":4, "3":5, 'v':6, "4": 7, "+":8, "P":8, "x":9, "X":9, "*":10, ".":11} fp = open(filename,'w') fp.write("# Grace project file\n#\n@version 50010\n") # size of plots on page xmar = (.15,1.2) ymar = (.15,.9) top2bottom = 4. # 4 to 1 spacing for top to bottom boxes # scaling for top box fp.write('@g{0} hidden false\n@with g{0}\n@legend {1}\n'.format(0,"on")) fp.write('@legend {}, {}\n'.format(xmar[1]-.2,ymar[1]-.05)) fp.write('@world xmin {}\n@world xmax {}\n'.format(Plot.get_xlim()[0],Plot.get_xlim()[1])) fp.write('@world ymin {}\n@world ymax {}\n'.format(Plot.get_ylim()[0],Plot.get_ylim()[1])) fp.write('@view xmin {}\n@view xmax {}\n'.format(xmar[0],xmar[1])) fp.write('@view ymin {}\n@view ymax {}\n'.format((1./top2bottom)*(ymar[1]-ymar[0])+ymar[0],ymar[1])) xticks = Plot.get_xaxis().get_majorticklocs() fp.write('@{}axis tick major {}\n'.format('x',xticks[1]-xticks[0])) yticks = Plot.get_yaxis().get_majorticklocs() fp.write('@{}axis tick major {}\n'.format('y',yticks[1]-yticks[0])) fp.write('@{}axis ticklabel char size {}\n'.format('x',0)) # turns off axis labels if 'sqrt' in Plot.yaxis.get_label().get_text(): ylbl = 'sqrt(Intensity)' # perhaps there is a way to get the symbol in xmgrace but I did not find it else: ylbl = 'Intensity' fp.write('@{0}axis label "{1}"\n@{0}axis label char size {2}\n'.format( 'y',ylbl,float(plotOpt['labelSize'])/8.)) fp.write('@{0}axis label place spec\n@{0}axis label place {1}, {2}\n'.format('y',0.0,0.1)) # ====================================================================== # plot magnification lines and labels (first, so "under" data) for i,l in enumerate(Plot.lines): lbl = l.get_label() if 'mag' not in lbl: continue #ax0.axvline(l.get_data()[0][0],color='0.5',dashes=(1,1)) # vertical line s = '@with line\n@ line on\n@ line loctype world\n@ line g0\n' fp.write(s) s = '@ line {0}, {1}, {0}, {2}\n' fp.write(s.format( l.get_data()[0][0],Plot.get_ylim()[0],Plot.get_ylim()[1])) s = '@ line linewidth 2\n@ line linestyle 2\n@ line color 1\n@ line arrow 0\n@line def\n' fp.write(s) for l in Plot.texts: if 'mag' not in l.get_label(): continue if l.xycoords[0] == 'data': xpos = l.get_position()[0] elif l.get_position()[0] == 0: xpos = Plot.get_xlim()[0] else: xpos = Plot.get_xlim()[1]*.95 s = '@with string\n@ string on\n@ string loctype world\n' fp.write(s) s = '@ string g{0}\n@ string {1}, {2}\n@ string color 1\n' fp.write(s.format(0,xpos,Plot.get_ylim()[1])) s = '@ string rot 0\n@ string font 0\n@ string just 4\n' fp.write(s) s = '@ string char size {1}\n@ string def "{0}"\n' fp.write(s.format(l.get_text(),float(plotOpt['labelSize'])/8.)) datnum = -1 # ====================================================================== # plot data for l in Plot.lines: if l.get_label() in ('obs','calc','bkg','zero','diff'): lbl = l.get_label() elif l.get_label()[1:] in ('obs','calc','bkg','zero','diff'): lbl = l.get_label()[1:] else: continue c = plotOpt['colors'].get(lbl,l.get_color()) gc = ClosestColorNumber(c) if sum(c) == 4.0: # white on white, skip continue marker = l.get_marker() lineWid = l.get_lw() siz = l.get_markersize() mkwid = l.get_mew() glinetyp = 1 if lbl == 'obs': obsartist = l gsiz = float(plotOpt['markerSiz'])/8. marker = plotOpt['markerSym'] gmw = float(plotOpt['markerWid']) gsym = grace_symbols.get(marker,5) glinetyp = 0 else: gsym = 0 gsiz = 0 gmw = 0 lineWid = float(plotOpt['lineWid']) if plotOpt['legend'].get(lbl): glbl = lbl else: glbl = "" datnum += 1 fp.write("@type xy\n") if lbl == 'zero': fp.write("{} {}\n".format(Plot.get_xlim()[0],0)) fp.write("{} {}\n".format(Plot.get_xlim()[1],0)) elif not ma.any(l.get_xdata().mask): for x,y in zip(l.get_xdata(),l.get_ydata()): fp.write("{} {}\n".format(x,y)) else: for x,y,m in zip(l.get_xdata(),l.get_ydata(),l.get_xdata().mask): if not m: fp.write("{} {}\n".format(x,y)) fp.write("&\n") fp.write(linedef.format("s"+str(datnum),glbl,gc,gsym,lineWid,gsiz,gmw,glinetyp)) #====================================================================== # reflection markers. Create a single hidden entry for the legend # and use error bars for the vertical lines for l in Plot.lines: glbl = lbl = l.get_label() if l not in Page.tickDict.values(): continue c = plotOpt['colors'].get(lbl,l.get_color()) gc = ClosestColorNumber(c) siz = float(plotOpt['tickSiz'])*(Plot.get_ylim()[1] - Plot.get_ylim()[0])/(100*6) # 1% for siz=6 mkwid = float(plotOpt['tickWid']) if sum(c) == 4.0: continue # white: ignore if plotOpt['legend'].get(lbl): # invisible data point for datnum += 1 fp.write("@type xy\n") fp.write("-1 -1\n".format(x,y)) fp.write("&\n") fp.write(linedef1.format( "s"+str(datnum),glbl,gc,float(plotOpt['tickSiz'])/8.,mkwid)) # plot values with error bars datnum += 1 fp.write("@type xydy\n") for x,y in zip(l.get_xdata(),l.get_ydata()): fp.write("{} {} {}\n".format(x,y,siz)) fp.write("&\n") fp.write(linedef2.format("s"+str(datnum),'',gc,mkwid)) #====================================================================== # Start (obs-cal)/sigma plot rsig = np.sqrt(Pattern[1][2]) rsig[rsig>1] = 1 fp.write("@type xy\n") l = obsartist ysig = Pattern[1][5]*rsig # scaling for bottom box fp.write('@g{0} hidden false\n@with g{0}\n@legend {1}\n'.format(1,"off")) fp.write('@world xmin {}\n@world xmax {}\n'.format(Plot.get_xlim()[0],Plot.get_xlim()[1])) fp.write('@world ymin {}\n@world ymax {}\n'.format(ysig.min(),ysig.max())) fp.write('@view xmin {}\n@view xmax {}\n'.format(xmar[0],xmar[1])) fp.write('@view ymin {}\n@view ymax {}\n'.format( ymar[0],(1./top2bottom)*(ymar[1]-ymar[0])+ymar[0])) if 'theta' in Plot.get_xlabel(): xlbl = r'2\f{Symbol}q' elif 'TOF' in Plot.get_xlabel(): xlbl = r'TOF, \f{Symbol}m\f{}s' else: xlbl = Plot.get_xlabel().replace('$','') fp.write('@{0}axis label "{1}"\n@{0}axis label char size {2}\n'.format( 'x',xlbl,float(plotOpt['labelSize'])/8.)) fp.write('@{0}axis label "{1}"\n@{0}axis label char size {2}\n'.format( 'y',r'\f{Symbol}D/s',float(plotOpt['labelSize'])/8.)) xticks = Plot.get_xaxis().get_majorticklocs() # come up with a "nice" tick interval for (o-c)/sig, since I am not sure # if this can be defaulted ytick = (ysig.max()-ysig.min())/5. l10 = np.log10(ytick) if l10 < 0: yti = int(10**(1 + l10 - int(l10))) # r = -0.5 else: yti = int(10**(l10 - int(l10))) # r = 0.5 if yti == 3: yti = 2 elif yti > 5: yti = 5 ytick = yti * 10**int(np.log10(ytick/yti)+.5) fp.write('@{}axis tick major {}\n'.format('x',xticks[1]-xticks[0])) fp.write('@{}axis tick major {}\n'.format('y',ytick)) rsig = np.sqrt(Pattern[1][2]) rsig[rsig>1] = 1 fp.write("@type xy\n") l = obsartist if ma.any(l.get_xdata().mask): for x,y,m in zip(l.get_xdata(),Pattern[1][5]*rsig,l.get_xdata().mask): if not m: fp.write("{} {}\n".format(x,y)) else: for x,y in zip(l.get_xdata(),Pattern[1][5]*rsig): fp.write("{} {}\n".format(x,y)) fp.write("&\n") fp.write(linedef3.format("s1",'',1,0,1.0,0,0,1)) fp.close() print('file',filename,'written') def CopyRietveld2Igor(Pattern,Plot,Page,plotOpt,filename,G2frame): '''Copy the contents of the Rietveld graph from the plot window to a Igor Pro input file (tested with v7.05). Uses values from Pattern to also generate a delta/sigma plot below. Coded with lots of help from Jan Ilavsky. ''' import itertools # delay this until called, since not commonly needed InameDict = {'obs':'Intensity', 'calc':'FitIntensity', 'bkg':'Background','diff':'Difference', 'omcos':'NormResidual','zero':'Zero'} igor_symbols = {"o":19, "s":18, "D":29, "^":17, "3":46, 'v':23, "4":49, "+":1, "P":60, "x":0, "X":62, "*":2} def Write2cols(fil,dataItems): '''Write a line to a file in space-separated columns. Skips masked items. :param object fil: file object :param list dataItems: items to write as row in file ''' line = '' for item in dataItems: if ma.is_masked(item): return if line: line += ' ' item = str(item) if ' ' in item: line += '"'+item+'"' else: line += item fil.write(line+'\n') proj = os.path.splitext(G2frame.GSASprojectfile)[0] if not proj: proj = 'GSASIIproject' proj = proj.replace(' ','') valueList = [] markerSettings = [] Icolor = {} legends = [] zerovals = None fontsize = 18*float(plotOpt['labelSize'])/12. for i,l in enumerate(Plot.lines): lbl = l.get_label() if plotOpt['legend'].get(lbl[1:]): legends.append((InameDict[lbl[1:]],lbl[1:])) if l.get_label()[1:] in ('obs','calc','bkg','zero','diff'): lbl = l.get_label()[1:] if plotOpt['legend'].get(lbl) and lbl in InameDict: legends.append((InameDict[lbl],lbl)) if lbl == 'obs': x = l.get_xdata() valueList.append(x) zerovals = (x.min(),x.max()) gsiz = 5*float(plotOpt['markerSiz'])/8. marker = plotOpt['markerSym'] gsym = igor_symbols.get(marker,12) gmw = float(plotOpt['markerWid']) markerSettings.append( 'mode({0})=3,marker({0})={1},msize({0})={2},mrkThick({0})={3}' .format('Intensity',gsym,gsiz,gmw)) elif lbl in ('calc','bkg','zero','diff'): markerSettings.append( 'mode({0})=0, lsize({0})={1}' .format(InameDict[lbl],plotOpt['lineWid'])) else: continue c = plotOpt['colors'].get(lbl,l.get_color()) #if sum(c) == 4.0: continue Icolor[InameDict[lbl]] = [j*65535 for j in c[0:3]] if lbl != 'zero': valueList.append(l.get_ydata()) valueList.append(Pattern[1][5]*np.sqrt(Pattern[1][2])) # invert lists into columns, use iterator for all values if hasattr(itertools,'zip_longest'): #Python 3+ invertIter = itertools.zip_longest(*valueList,fillvalue=' ') else: invertIter = itertools.izip_longest(*valueList,fillvalue=' ') fp = open(filename,'w') fp.write('''IGOR X setDataFolder root: X // *** Replace GSAS2Data with name of current project in GSAS. X // *** this name will get "order" number (0,1,2...) to be unique and data will be stored there. X // *** and the graph will also be named using this base name. X NewDataFolder/O/S$(UniqueName(CleanupName("{}",0),11, 0)) X string GSAXSProjectName = GetDataFolder(0) WAVES /D/O TwoTheta, Intensity, FitIntensity, Background, Difference, NormResidual BEGIN '''.format(proj)) for row in invertIter: Write2cols(fp,row) fp.write('''END X // *** static part of the code, NB reflection tickmarks later **** X SetScale d 0,0, "degree", TwoTheta X // *** this is where graph is created and data added X string G_Name=CleanupName(GSAXSProjectName,0) X Display/K=1/W=(50,40,850,640) Intensity vs twoTheta; DoWindow/C $(G_Name) X DoWindow/T$(G_Name), G_Name X AppendToGraph FitIntensity vs TwoTheta X AppendToGraph Background vs TwoTheta X AppendToGraph Difference vs TwoTheta X AppendToGraph/L=Res_left/B=Res_bot NormResidual vs TwoTheta X // *** Here we have modification of the four axes used in the graph X ModifyGraph mode=2,lsize=5, mirror=2 X SetAxis/A/E=2 Res_left X ModifyGraph freePos(Res_left)={0,kwFraction} X ModifyGraph freePos(Res_bot)={0.2,kwFraction} X ModifyGraph standoff(bottom)=0 X ModifyGraph axisEnab(left)={0.2,1} X ModifyGraph axisEnab(Res_left)={0,0.2} X ModifyGraph lblPosMode(Res_left)=1, mirror(Res_bot)=0 X ModifyGraph tickUnit(bottom)=1,manTick=0,manMinor(bottom)={0,50} X ModifyGraph tick(Res_bot)=1,noLabel(Res_bot)=2,standoff(Res_bot)=0 X ModifyGraph manMinor(Res_bot)={0,50},tick(Res_bot)=2 X ModifyGraph axThick=2 X ModifyGraph mirror(Res_bot)=0,nticks(Res_left)=3,highTrip(left)=1e+06,manTick(bottom)=0 X ModifyGraph btLen=5 ''') fp.write('X ModifyGraph gfSize={}\n'.format(int(fontsize+.5))) # line at zero if not zerovals: zerovals = (Plot.get_xlim()[0],Plot.get_xlim()[1]) fp.write('X // *** add line at y=zero\n') fp.write('WAVES /D/O ZeroX, Zero\nBEGIN\n') fp.write(' {0} 0.0\n {1} 0.0\n'.format(*zerovals)) fp.write('END\nX AppendToGraph Zero vs ZeroX\n') if 'sqrt' in Plot.yaxis.get_label().get_text(): ylabel = '\u221AIntensity' else: ylabel = 'Intensity' fp.write('''X // *** add axis labels and position them X Label left "{1}" X Label Res_left "{2}" X Label bottom "{0}" X ModifyGraph lblPosMode=0,lblPos(Res_left)=84 '''.format("2Î˜",ylabel,"âˆ†/Ïƒ")) fp.write('''X // *** set display limits. X SetAxis left {2}, {3} X SetAxis bottom {0}, {1} X SetAxis Res_bot {0}, {1} ''' .format(Plot.get_xlim()[0],Plot.get_xlim()[1], Plot.get_ylim()[0],Plot.get_ylim()[1])) fp.write('X // *** modify how data are displayed ****\n') # fp.write( # '''X // *** here starts mostly static part of the code, here we modify how data are displayed **** # X ModifyGraph mode(FitIntensity)=0,rgb(FitIntensity)=(1,39321,19939), lsize(FitIntensity)=1 # X ModifyGraph mode(Background)=0,lsize(Background)=2, rgb(Background)=(65535,0,0) # X ModifyGraph mode(Difference)=0,lsize(Difference)=2,rgb(Difference)=(0,65535,65535) # X // *** modifications for the bottom graph, here we modify how data are displayed **** # X ModifyGraph mode(NormResidual)=0,lsize(NormResidual)=1,rgb(NormResidual)=(0,0,0) # X // *** end of modifications for the main data in graph # ''') for m in markerSettings: fp.write('X ModifyGraph {}\n'.format(m)) for lbl in Icolor: fp.write('X ModifyGraph rgb({})=({:.0f},{:.0f},{:.0f})\n' .format(lbl,*Icolor[lbl])) fp.write('X ModifyGraph mode(NormResidual)=0,lsize(NormResidual)=1,rgb(NormResidual)=(0,0,0)\n') fp.write('X // *** End modify how data are displayed ****\n') # loop over reflections ticknum = 0 for i,l in enumerate(Plot.lines): lbl = l.get_label() if l in Page.tickDict.values(): c = plotOpt['colors'].get(lbl,l.get_color()) if sum(c) == 4.0: continue # white is invisible ticknum += 1 phasename = 'tick{}'.format(ticknum) if plotOpt['legend'].get(lbl): legends.append((phasename,plotOpt['phaseLabels'].get(lbl,lbl))) tickpos = l.get_ydata()[0] fp.write( '''X // reflection tickmark for phase {1} WAVES /D/O {0}X, {0} BEGIN '''.format(phasename,lbl)) for x in l.get_xdata(): fp.write('{} {}\n'.format(x,tickpos)) fp.write('''END X // *** controls for {1} reflection tickmarks X AppendToGraph {0} vs {0}X X ModifyGraph mode({0})=3,mrkThick({0})=2,gaps({0})=0 X ModifyGraph marker({0})=10,rgb({0})=({2},{3},{4}) '''.format(phasename,lbl,*[j*65535 for j in c[0:3]])) # plot magnification lines and labels j = 0 for i,l in enumerate(Plot.lines): lbl = l.get_label() if 'mag' not in lbl: continue j += 1 fp.write('WAVES /D/O mag{0}X, mag{0}\nBEGIN\n'.format(j)) fp.write(' {0} {1}\n {0} {2}\n'.format( l.get_data()[0][0],Plot.get_ylim()[0],Plot.get_ylim()[1])) fp.write('END\nX AppendToGraph mag{0} vs mag{0}X\n'.format(j)) fp.write('X ModifyGraph lstyle(mag{0})=3,rgb(mag{0})=(0,0,0)\n'.format(j)) for l in Plot.texts: if 'mag' not in l.get_label(): continue if l.xycoords[0] == 'data': xpos = l.get_position()[0] elif l.get_position()[0] == 0: xpos = Plot.get_xlim()[0] else: xpos = Plot.get_xlim()[1]*.95 fp.write('X SetDrawEnv xcoord=bottom, ycoord= abs,textyjust=2,fsize={}\n'.format(fontsize)) fp.write('X DrawText {0},2,"{1}"\n'.format(xpos,l.get_text())) # legend s = "" for nam,txt in legends: if s: s += r'\r' s += r'\\s({}) {}'.format(nam,txt) fp.write('X Legend/C/N=text0/J "{}"\n'.format(s)) fp.close() def CopyRietveld2csv(Pattern,Plot,Page,filename): '''Copy the contents of the Rietveld graph from the plot window to .csv file ''' import itertools # delay this since not commonly called or needed lblList = [] valueList = [] lblList.append('Axis-limits') valueList.append(list(Plot.get_xlim())+list(Plot.get_ylim())) tickpos = {} for i,l in enumerate(Plot.lines): if l.get_label() in ('obs','calc','bkg','zero','diff'): lbl = l.get_label() elif l.get_label()[1:] in ('obs','calc','bkg','zero','diff'): lbl = l.get_label()[1:] else: lbl = l.get_label() if 'mag' in lbl: pass elif lbl in ('obs','calc','bkg','zero','diff'): if lbl == 'obs': lblList.append('x') valueList.append(l.get_xdata()) c = plotOpt['colors'].get(lbl,l.get_color()) if sum(c) == 4.0: continue lblList.append(lbl) valueList.append(l.get_ydata()) elif l in Page.tickDict.values(): c = plotOpt['colors'].get(lbl,l.get_color()) if sum(c) == 4.0: continue tickpos[lbl] = l.get_ydata()[0] lblList.append(lbl) valueList.append(l.get_xdata()) if tickpos: lblList.append('tick-pos') valueList.append([]) for i in tickpos: valueList[-1].append(i) valueList[-1].append(tickpos[i]) # add (obs-calc)/sigma [=(obs-calc)*sqrt(weight)] lblList.append('diff/sigma') valueList.append(Pattern[1][5]*np.sqrt(Pattern[1][2])) if sum(Pattern[1][0].mask): # are there are excluded points? If so, add them too lblList.append('excluded') valueList.append(1*Pattern[1][0].mask) # magnifcation values for l in Plot.texts: lbl = l.get_label() if 'mag' not in lbl: continue if l.xycoords == 'axes fraction': lbl = 'initial-mag' lblList.append(lbl) valueList.append([l.get_text()]) else: lbl = 'mag' lblList.append(lbl) valueList.append([l.get_text(),l.get_position()[0]]) # invert lists into columns, use iterator for all values if hasattr(itertools,'zip_longest'): #Python 3+ invertIter = itertools.zip_longest(*valueList,fillvalue=' ') else: invertIter = itertools.izip_longest(*valueList,fillvalue=' ') fp = open(filename,'w') Write2csv(fp,lblList,header=True) for row in invertIter: Write2csv(fp,row) fp.close() def onSave(event): '''Write the current plot to a file ''' hcfigure = mpl.figure.Figure(dpi=plotOpt['dpi'],figsize=(plotOpt['width'],plotOpt['height'])) CopyRietveldPlot(G2frame,Pattern,Plot,Page,hcfigure) longFormatName,typ = plotOpt['format'].split(',') fil = G2G.askSaveFile(G2frame,'','.'+typ.strip(),longFormatName) if 'csv' in typ and fil: CopyRietveld2csv(Pattern,Plot,Page,fil) dlg.EndModal(wx.ID_OK) elif 'agr' in typ and fil: CopyRietveld2Grace(Pattern,Plot,Page,plotOpt,fil) dlg.EndModal(wx.ID_OK) elif 'itx' in typ and fil: CopyRietveld2Igor(Pattern,Plot,Page,plotOpt,fil,G2frame) dlg.EndModal(wx.ID_OK) elif fil: if hcfigure.canvas is None: if GSASIIpath.GetConfigValue('debug'): print('creating canvas') hcCanvas(hcfigure) hcfigure.savefig(fil,format=typ.strip()) dlg.EndModal(wx.ID_OK) def OnSelectColour(event): '''Respond to a change in color ''' # lbl = plotOpt['colorButtons'].get(list(event.GetEventObject())[:3]) if event.GetEventObject() not in plotOpt['colorButtons']: print('Unexpected button',str(event.GetEventObject())) return lbl = plotOpt['colorButtons'][event.GetEventObject()] c = event.GetValue() plotOpt['colors'][lbl] = (c.Red()/255.,c.Green()/255.,c.Blue()/255.,c.alpha/255.) RefreshPlot() # start of PublishRietveldPlot if plotOpt['initNeeded']: Initialize() GetColors() dlg = wx.Dialog(G2frame.plotFrame, style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER) vbox = wx.BoxSizer(wx.VERTICAL) # size choices symChoices = ('+','x','.','o','^','v','*','|') txtChoices = [str(i) for i in range (8,26)] sizChoices = [str(i) for i in range (2,21)] lwidChoices = ('0.5','0.7','1','1.5','2','2.5','3','4') sizebox = wx.BoxSizer(wx.HORIZONTAL) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,'Text size'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,txtChoices,None,None,plotOpt,'labelSize',RefreshPlot, size=(50,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add((1,1),1,wx.EXPAND,1) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,' Obs type'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,symChoices,None,None,plotOpt,'markerSym',RefreshPlot, size=(40,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,' size'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,sizChoices,None,None,plotOpt,'markerSiz',RefreshPlot, size=(50,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,' width'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,lwidChoices,None,None,plotOpt,'markerWid',RefreshPlot, size=(50,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add((1,1),1,wx.EXPAND,1) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,' Line widths'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,lwidChoices,None,None,plotOpt,'lineWid',RefreshPlot, size=(50,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add((1,1),1,wx.EXPAND,1) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,' Tick size'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,sizChoices,None,None,plotOpt,'tickSiz',RefreshPlot, size=(50,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add(wx.StaticText(dlg,wx.ID_ANY,' width'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,lwidChoices,None,None,plotOpt,'tickWid',RefreshPlot, size=(50,-1)) sizebox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) sizebox.Add((1,1),1,wx.EXPAND,1) helpinfo = '''---- Help on creating hard copy ---- Select options such as the size of text and colors for plot contents here. Tricks: * Use a color of pure white to remove an element from the plot (light gray is plotted) * LaTeX-like coding can be used for phase labels such as $\\rm FeO_2$ (for a subscript 2) or $\\gamma$-Ti for a Greek "gamma" Note that the dpi value is ignored for svg and pdf files, which are drawn with vector graphics (infinite resolution). Likewise, the agr and itx options create input files for programs Grace (QtGrace) and Igor Pro, that largely duplicate the displayed plot. Once read into Grace or Igor the graphs can then be customized. ''' hlp = G2G.HelpButton(dlg,helpinfo) sizebox.Add(hlp,0,wx.ALL) vbox.Add(sizebox,0,wx.ALL|wx.EXPAND) # table of colors and legend options cols = 1+len(plotOpt['lineList']) + len(plotOpt['phaseList'] ) gsizer = wx.FlexGridSizer(cols=cols,hgap=2,vgap=2) gsizer.Add((-1,-1)) for lbl in plotOpt['lineList']: gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,lbl),0,wx.ALL) for lbl in plotOpt['phaseList']: if lbl not in plotOpt['phaseLabels']: plotOpt['phaseLabels'][lbl] = lbl val = G2G.ValidatedTxtCtrl(dlg,plotOpt['phaseLabels'],lbl,size=(110,-1), style=wx.ALIGN_CENTER,OnLeave=RefreshPlot) gsizer.Add(val,0,wx.ALL) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'Include in legend'),0,wx.ALL) for lbl in list(plotOpt['lineList']) + list(plotOpt['phaseList'] ): if lbl not in plotOpt['legend']: plotOpt['legend'][lbl] = False ch = G2G.G2CheckBox(dlg,'',plotOpt['legend'],lbl,RefreshPlot) gsizer.Add(ch,0,wx.ALL|wx.ALIGN_CENTER) gsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'Color'),0,wx.ALL) plotOpt['colorButtons'] = {} for lbl in list(plotOpt['lineList']) + list(plotOpt['phaseList']): import wx.lib.colourselect as csel if lbl not in plotOpt['colors']: plotOpt['colors'][lbl] = (0.5, 0.5, 0.5, 1) color = wx.Colour(*[int(255*i) for i in plotOpt['colors'][lbl]]) b = csel.ColourSelect(dlg, -1, '', color) b.Bind(csel.EVT_COLOURSELECT, OnSelectColour) plotOpt['colorButtons'][b] = lbl gsizer.Add(b,0,wx.ALL|wx.ALIGN_CENTER) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add((1,1),1,wx.EXPAND,1) hbox.Add(gsizer,0,wx.ALL) hbox.Add((1,1),1,wx.EXPAND,1) vbox.Add(hbox,0,wx.ALL|wx.EXPAND) # hard copy options hbox = wx.BoxSizer(wx.HORIZONTAL) txt = wx.StaticText(dlg,wx.ID_ANY,'Hard copy ') hbox.Add(txt,0,wx.ALL|wx.ALIGN_CENTER_VERTICAL) txt = wx.StaticText(dlg,wx.ID_ANY,'Pixels/inch:') hbox.Add(txt,0,wx.ALL|wx.ALIGN_CENTER_VERTICAL) val = G2G.ValidatedTxtCtrl(dlg,plotOpt,'dpi',min=60,max=1600,size=(40,-1)) hbox.Add(val,0,wx.ALL) txt = wx.StaticText(dlg,wx.ID_ANY,' Width (in):') hbox.Add(txt,0,wx.ALL|wx.ALIGN_CENTER_VERTICAL) val = G2G.ValidatedTxtCtrl(dlg,plotOpt,'width',min=3.,max=20.,nDig=(5,1),size=(45,-1)) hbox.Add(val,0,wx.ALL) txt = wx.StaticText(dlg,wx.ID_ANY,' Height (in):') hbox.Add(txt,0,wx.ALL|wx.ALIGN_CENTER_VERTICAL) val = G2G.ValidatedTxtCtrl(dlg,plotOpt,'height',min=3.,max=20.,nDig=(5,1),size=(45,-1)) hbox.Add(val,0,wx.ALL) txt = wx.StaticText(dlg,wx.ID_ANY,'File format:') hbox.Add(txt,0,wx.ALL|wx.ALIGN_CENTER_VERTICAL) val = G2G.EnumSelector(dlg,plotOpt,'format',plotOpt['fmtChoices']) hbox.Add(val,0,wx.ALL) vbox.Add(hbox,0,wx.ALL|wx.ALIGN_CENTER) # screen preview figure = mpl.figure.Figure(figsize=(plotOpt['width'],plotOpt['height'])) canvas = Canvas(dlg,-1,figure) vbox.Add(canvas,1,wx.ALL|wx.EXPAND,1) # buttons at bottom btnsizer = wx.StdDialogButtonSizer() btn = wx.Button(dlg, wx.ID_CANCEL) btnsizer.AddButton(btn) btn = wx.Button(dlg, wx.ID_SAVE) #btn.SetDefault() btn.Bind(wx.EVT_BUTTON,onSave) btnsizer.AddButton(btn) btnsizer.Realize() vbox.Add((-1,5)) vbox.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) dlg.SetSizer(vbox) vbox.Fit(dlg) dlg.Layout() dlg.CenterOnParent() CopyRietveldPlot(G2frame,Pattern,Plot,Page,figure) # preview plot figure.canvas.draw() dlg.ShowModal() dlg.Destroy() return def CopyRietveldPlot(G2frame,Pattern,Plot,Page,figure): '''Copy the contents of the Rietveld graph from the plot window to another mpl figure which can be on screen or can be a file for hard copy. Uses values from Pattern to also generate a delta/sigma plot below the main figure, since the weights are not available from the plot. :param list Pattern: histogram object from data tree :param mpl.axes Plot: The axes object from the Rietveld plot :param wx.Panel Page: The tabbed panel for the Rietveld plot :param mpl.figure figure: The figure object from the Rietveld plot ''' gs = mpl.gridspec.GridSpec(2, 1, height_ratios=[4, 1]) ax0 = figure.add_subplot(gs[0]) ax1 = figure.add_subplot(gs[1]) figure.subplots_adjust(left=int(plotOpt['labelSize'])/100.,bottom=int(plotOpt['labelSize'])/150., right=.98,top=1.-int(plotOpt['labelSize'])/200.,hspace=0.0) ax0.tick_params('x',direction='in',labelbottom=False) ax0.tick_params(labelsize=plotOpt['labelSize']) ax1.tick_params(labelsize=plotOpt['labelSize']) if mpl.__version__.split('.')[0] == '1': # deal with older matplotlib, which puts too many ticks ax1.yaxis.set_major_locator(mpl.ticker.MaxNLocator(nbins=2)) ax1.yaxis.set_minor_locator(mpl.ticker.MaxNLocator(nbins=4)) ax1.set_xlabel(Plot.get_xlabel(),fontsize=plotOpt['labelSize']) ax0.set_ylabel(Plot.get_ylabel(),fontsize=plotOpt['labelSize']) ax1.set_ylabel(r'$\Delta/\sigma$',fontsize=plotOpt['labelSize']) ax0.set_xlim(Plot.get_xlim()) ax1.set_xlim(Plot.get_xlim()) ax0.set_ylim(Plot.get_ylim()) legLbl = [] legLine = [] obsartist = None for i,l in enumerate(Plot.lines): if l.get_label() in ('obs','calc','bkg','zero','diff'): lbl = l.get_label() elif l.get_label()[1:] in ('obs','calc','bkg','zero','diff'): lbl = l.get_label()[1:] else: lbl = l.get_label() if 'mag' in lbl: ax0.axvline(l.get_data()[0][0],color='0.5',dashes=(1,1)) elif lbl in ('obs','calc','bkg','zero','diff'): marker = l.get_marker() lineWid = l.get_lw() siz = l.get_markersize() mew = l.get_mew() if lbl == 'obs': obsartist = l siz = float(plotOpt['markerSiz']) marker = plotOpt['markerSym'] mew = float(plotOpt['markerWid']) else: lineWid = float(plotOpt['lineWid']) c = plotOpt['colors'].get(lbl,l.get_color()) if sum(c) == 4.0: continue if plotOpt['legend'].get(lbl): uselbl = lbl else: uselbl = '_'+lbl if lbl == 'zero': art = [ax0.axhline(0.,color=c, lw=lineWid,label=uselbl,ls=l.get_ls(), marker=marker,ms=siz,mew=mew)] else: art = ax0.plot(l.get_xdata(),l.get_ydata(),color=c, lw=lineWid,label=uselbl,ls=l.get_ls(), marker=marker,ms=siz,mew=mew, ) if plotOpt['legend'].get(lbl): legLbl.append(uselbl) legLine.append(art[0]) elif l in Page.tickDict.values(): c = plotOpt['colors'].get(lbl,l.get_color()) #siz = l.get_markersize() siz = float(plotOpt['tickSiz']) #mew = l.get_mew() mew = float(plotOpt['tickWid']) if sum(c) == 4.0: continue if not plotOpt['legend'].get(lbl): uselbl = '_'+lbl else: uselbl = plotOpt['phaseLabels'][lbl] art = ax0.plot(l.get_xdata(),l.get_ydata(),color=c, lw=l.get_lw(),ls=l.get_ls(),label=uselbl, marker=l.get_marker(),ms=siz,mew=mew, ) if plotOpt['legend'].get(lbl): legLbl.append(uselbl) legLine.append(art[0]) for l in Plot.texts: if 'mag' not in l.get_label(): continue ax0.annotate(l.get_text(), xy=(l.get_position()), xycoords=l.xycoords, verticalalignment='bottom', horizontalalignment=l.get_horizontalalignment(), fontsize=float(plotOpt['labelSize'])) rsig = np.sqrt(Pattern[1][2]) rsig[rsig>1] = 1 if obsartist: ax1.plot(obsartist.get_xdata(),Pattern[1][5]*rsig,color='k') if legLine: ax0.legend(legLine,legLbl,loc='best',prop={'size':plotOpt['labelSize']}) ################################################################################ ##### PlotDeltSig ################################################################################ def PlotDeltSig(G2frame,kind,PatternName=None): 'Produces normal probability plot for a powder or single crystal histogram' if PatternName: G2frame.PatternId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, PatternName) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Error analysis','mpl') if new: G2frame.Cmin = 0.0 G2frame.Cmax = 1.0 # save information needed to reload from tree and redraw G2frame.G2plotNB.RegisterRedrawRoutine(G2frame.G2plotNB.lastRaisedPlotTab, PlotDeltSig,(G2frame,kind,G2frame.GPXtree.GetItemText(G2frame.PatternId))) Page.Choice = None PatternId = G2frame.PatternId Pattern = G2frame.GPXtree.GetItemPyData(PatternId) Pattern.append(G2frame.GPXtree.GetItemText(PatternId)) wtFactor = Pattern[0]['wtFactor'] if kind == 'PWDR': limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1] xye = np.array(Pattern[1]) xmin = np.searchsorted(xye[0],limits[0]) xmax = np.searchsorted(xye[0],limits[1]) DS = xye[5][xmin:xmax]*np.sqrt(wtFactor*xye[2][xmin:xmax]) elif kind == 'HKLF': refl = Pattern[1]['RefList'] im = 0 if Pattern[1]['Super']: im = 1 DS = [] for ref in refl: if ref[6+im] > 0.: DS.append((ref[5+im]-ref[7+im])/ref[6+im]) G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar DS.sort() EDS = np.zeros_like(DS) DX = np.linspace(0.,1.,num=len(DS),endpoint=True) np.seterr(invalid='ignore') #avoid problem at DX==0 T = np.sqrt(np.log(1.0/DX**2)) top = 2.515517+0.802853*T+0.010328*T**2 bot = 1.0+1.432788*T+0.189269*T**2+0.001308*T**3 EDS = np.where(DX>0,-(T-top/bot),(T-top/bot)) low1 = np.searchsorted(EDS,-1.) hi1 = np.searchsorted(EDS,1.) slp,intcp = np.polyfit(EDS[low1:hi1],DS[low1:hi1],deg=1) frac = 100.*(hi1-low1)/len(DS) G2frame.G2plotNB.status.SetStatusText( \ 'Over range -1. to 1. :'+' slope = %.3f, intercept = %.3f for %.2f%% of the fitted data'%(slp,intcp,frac),1) Plot.set_title('Normal probability for '+Pattern[-1]) Plot.set_xlabel(r'expected $\mathsf{\Delta/\sigma}$',fontsize=14) Plot.set_ylabel(r'observed $\mathsf{\Delta/\sigma}$',fontsize=14) Plot.plot(EDS,DS,'r+',label='result') Plot.plot([-2,2],[-2,2],'k',dashes=(5,5),label='ideal') Plot.legend(loc='upper left') np.seterr(invalid='warn') Page.canvas.draw() ################################################################################ ##### PlotISFG ################################################################################ def PlotISFG(G2frame,data,newPlot=False,plotType='',peaks=None): ''' Plotting package for PDF analysis; displays I(Q), S(Q), F(Q) and G(r) as single or multiple plots with waterfall and contour plots as options ''' global Peaks Peaks = peaks G2frame.ShiftDown = False if not plotType: plotType = G2frame.G2plotNB.plotList[G2frame.G2plotNB.nb.GetSelection()] if plotType not in ['I(Q)','S(Q)','F(Q)','G(R)','g(r)','delt-G(R)']: return def OnPlotKeyUp(event): if event.key == 'shift': G2frame.ShiftDown = False return def OnPlotKeyPress(event): if event.key == 'shift': G2frame.ShiftDown = True return newPlot = False if G2frame.ShiftDown: event.key = event.key.upper() if event.key == 'u': if G2frame.Contour: G2frame.Cmax = min(1.0,G2frame.Cmax*1.2) elif Page.Offset[1] < 100.: Page.Offset[1] += 1. elif event.key == 'd': if G2frame.Contour: G2frame.Cmax = max(0.0,G2frame.Cmax*0.8) elif Page.Offset[1] > -100.: Page.Offset[1] -= 1. elif event.key == 'U': if G2frame.Contour: G2frame.Cmin += (G2frame.Cmax - G2frame.Cmin)/5. elif Page.Offset[1] < 100.: Page.Offset[1] += 10. elif event.key == 'D': if G2frame.Contour: G2frame.Cmin -= (G2frame.Cmax - G2frame.Cmin)/5. elif Page.Offset[1] > -100.: Page.Offset[1] -= 10. elif event.key == 'l': Page.Offset[0] -= 1. elif event.key == 'r': Page.Offset[0] += 1. elif event.key == 'o': if G2frame.Contour: G2frame.Interpolate = 'nearest' G2frame.Cmin = 0.0 G2frame.Cmax = 1.0 else: Page.Offset = [0,0] elif event.key == 'm': G2frame.SinglePlot = not G2frame.SinglePlot elif event.key == 'c': newPlot = True G2frame.Contour = not G2frame.Contour if G2frame.Contour: G2frame.SinglePlot = False else: Page.Offset = [0.,0.] G2frame.SinglePlot = not G2frame.SinglePlot elif not G2frame.Contour and event.key == 'w': G2frame.Waterfall = not G2frame.Waterfall elif event.key == 'f' and not G2frame.SinglePlot: choices = G2gd.GetGPXtreeDataNames(G2frame,'PDF ') dlg = G2G.G2MultiChoiceDialog(G2frame,'Select dataset to plot', 'Multidata plot selection',choices) if dlg.ShowModal() == wx.ID_OK: G2frame.PDFselections = [] select = dlg.GetSelections() if select: for Id in select: G2frame.PDFselections.append(choices[Id]) else: G2frame.PDFselections = None dlg.Destroy() elif event.key == 's': choice = [m for m in mpl.cm.datad.keys()] # if not m.endswith("_r") choice.sort() dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.ContourColor = choice[sel] else: G2frame.ContourColor = GSASIIpath.GetConfigValue('Contour_color','Paired') dlg.Destroy() elif event.key == 'i': #for smoothing contour plot choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning', 'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel', 'mitchell','sinc','lanczos'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.Interpolate = choice[sel] else: G2frame.Interpolate = 'nearest' dlg.Destroy() elif event.key == 't' and not G2frame.Contour: G2frame.Legend = not G2frame.Legend elif event.key == 'g': mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid'] PlotISFG(G2frame,data,newPlot=newPlot,plotType=plotType) def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: if G2frame.Contour: G2frame.G2plotNB.status.SetStatusText('R =%.3fA pattern ID =%5d'%(xpos,int(ypos)),1) else: G2frame.G2plotNB.status.SetStatusText('R =%.3fA %s =%.2f'%(xpos,plotType,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select '+plotType+' pattern first',1) def OnPick(event): def OnDragLine(event): '''Respond to dragging of a plot line ''' if event.xdata is None: return # ignore if cursor out of window Page.canvas.restore_region(savedplot) coords = G2frame.itemPicked.get_data() coords[0][0] = coords[0][1] = event.xdata coords = G2frame.itemPicked.set_data(coords) Page.figure.gca().draw_artist(G2frame.itemPicked) Page.canvas.blit(Page.figure.gca().bbox) if Peaks == None: return if G2frame.itemPicked is not None: return pick = event.artist mouse = event.mouseevent xpos = pick.get_xdata() ypos = pick.get_ydata() ind = event.ind xy = list(zip(np.take(xpos,ind),np.take(ypos,ind)))[0] if not ind[0]: # a limit line - allow it to drag # prepare to animate move of line G2frame.itemPicked = pick pick.set_linestyle(':') # set line as dotted Page = G2frame.G2plotNB.nb.GetPage(plotNum) Page.figure.gca() Page.canvas.draw() # refresh without dotted line & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragLine) pick.set_linestyle('--') # back to dashed else: # a profile point, e.g. a peak if mouse.button == 1: # El = data['ElList'].keys()[0] Peaks['Peaks'].append([xy[0],(xy[1]-Peaks['Background'][1][1]*xy[0])/4.7,.085,'','O','O',0.]) Peaks['Peaks'] = G2mth.sortArray(Peaks['Peaks'],0,reverse=False) PlotISFG(G2frame,data,peaks=Peaks,newPlot=False) G2pdG.UpdatePDFPeaks(G2frame,Peaks,data) def OnRelease(event): if Peaks == None: return if G2frame.itemPicked == None: return if G2frame.cid is not None: # if there is a drag connection, delete it Page.canvas.mpl_disconnect(G2frame.cid) G2frame.cid = None if event.xdata is None or event.ydata is None: # ignore drag if cursor is outside of plot Page.canvas.mpl_disconnect(G2frame.cid) G2frame.cid = None PlotISFG(G2frame,data,peaks=Peaks,newPlot=False) return lines = [] for line in G2frame.Lines: lines.append(line.get_xdata()[0]) try: lineNo = lines.index(G2frame.itemPicked.get_xdata()[0]) except ValueError: lineNo = -1 if lineNo in [0,1]: Peaks['Limits'][lineNo] = event.xdata if event.button == 3: del Peaks['Peaks'][lineNo-2] G2frame.itemPicked = None wx.CallAfter(G2pdG.UpdatePDFPeaks,G2frame,Peaks,data) wx.CallAfter(PlotISFG,G2frame,data,peaks=Peaks,newPlot=False) # PlotISFG continues here ############################################################ xylim = [] new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(plotType,'mpl') if not new: if not newPlot: xylim = copy.copy(lim) else: newPlot = True G2frame.Cmin = 0.0 G2frame.Cmax = 1.0 Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) Page.canvas.mpl_connect('key_release_event', OnPlotKeyUp) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.canvas.mpl_connect('pick_event', OnPick) Page.canvas.mpl_connect('button_release_event', OnRelease) Page.Offset = [0,0] G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar if Peaks == None: if G2frame.Contour: Page.Choice = (' key press','d: lower contour max','u: raise contour max', 'D: lower contour min','U: raise contour min','o: reset to default','g: toggle grid', 'i: interpolation method','s: color scheme','c: contour off','f: select data', ) else: Page.Choice = (' key press','l: offset left','r: offset right','d/D: offset down/10x','u/U: offset up/10x', 'o: reset offset','t: toggle legend','c: contour on','g: toggle grid','w: toggle waterfall colors (slow!)', 'm: toggle multiplot','s: color scheme','f: select data' ) Page.keyPress = OnPlotKeyPress else: G2frame.cid = None Page.Choice = () PatternId = G2frame.PatternId if not PatternId: return pId = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'PDF Controls') if not pId: return PDFdata = G2frame.GPXtree.GetItemPyData(pId) numbDen = 0. if 'ElList' in PDFdata: numbDen = G2pwd.GetNumDensity(PDFdata['ElList'],PDFdata['Form Vol']) if G2frame.SinglePlot: if 'G(R)' not in data: return PlotList = [data[plotType],] try: name = PlotList[0][2] except: name = '' else: PlotList = [] if G2frame.PDFselections is None: choices = G2gd.GetGPXtreeDataNames(G2frame,'PDF ') else: choices = G2frame.PDFselections for item in choices: Pid = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item) Id = G2gd.GetGPXtreeItemId(G2frame,Pid,'PDF Controls') Pattern = G2frame.GPXtree.GetItemPyData(Id) if Pattern: PlotList.append(Pattern[plotType]) name = plotType if plotType in ['G(R)','g(r)']: Plot.set_xlabel(r'r,$\AA$',fontsize=14) Plot.set_ylabel(r'%s, $\AA^{-2}$'%plotType,fontsize=14) if lim is not None: lim[0] = list([lim[0][0],data['Rmax']]) Plot.set_xlim(lim[0]) else: Plot.set_xlabel(r'$Q,\AA^{-1}$',fontsize=14) Plot.set_ylabel(r''+plotType,fontsize=14) Plot.set_title(name) colors=['b','g','r','c','m','k'] Ymax = 0.01 lenX = 0 for Pattern in PlotList: if not len(Pattern): return #no PDF's yet xye = Pattern[1] Ymax = max(Ymax,max(xye[1])) XYlist = [] if G2frame.Contour: ContourZ = [] ContourY = [] Nseq = 0 for N,Pattern in enumerate(PlotList): xye = Pattern[1] X = xye[0] if not lenX: lenX = len(X) if G2frame.Contour and len(PlotList)>1: Y = xye[1] if lenX == len(X): ContourY.append(N) ContourZ.append(Y) ContourX = X Nseq += 1 Plot.set_ylabel('Data sequence',fontsize=12) else: X = xye[0]+Page.Offset[0]*.005*N Y = xye[1]+Page.Offset[1]*.01*N XYlist.append(list(zip(X,Y))) # if G2frame.Legend: # Plot.plot(X,Y,colors[N%6],picker=False,label='Azm:'+Pattern[2].split('=')[1]) # else: # Plot.plot(X,Y,colors[N%6],picker=False) if G2frame.Contour and len(PlotList)>1: acolor = mpl.cm.get_cmap(G2frame.ContourColor) Img = Plot.imshow(ContourZ,cmap=acolor, vmin=Ymax*G2frame.Cmin,vmax=Ymax*G2frame.Cmax, interpolation=G2frame.Interpolate, extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower') Page.figure.colorbar(Img) else: XYlist = np.array(XYlist) Xmin = np.amin(XYlist.T[0]) Xmax = np.amax(XYlist.T[0]) dx = 0.02*(Xmax-Xmin) Ymin = np.amin(XYlist.T[1]) Ymax = np.amax(XYlist.T[1]) dy = 0.02*(Ymax-Ymin) try: Plot.set_xlim(Xmin-dx,Xmax+dx) Plot.set_ylim(Ymin-dy,Ymax+dy) except: pass if Peaks == None: normcl = mpcls.Normalize(Ymin,Ymax) acolor = mpl.cm.get_cmap(G2frame.ContourColor) wx.BeginBusyCursor() if XYlist.shape[0]>1: if G2frame.Waterfall: for xylist in XYlist: ymin = np.amin(xylist.T[1]) ymax = np.amax(xylist.T[1]) normcl = mpcls.Normalize(ymin,ymax) colorRange = xylist.T[1] segs = np.reshape(np.hstack((xylist[:-1],xylist[1:])),(-1,2,2)) line = mplC.LineCollection(segs,cmap=acolor,norm=normcl) line.set_array(colorRange) Plot.add_collection(line) axcb = Page.figure.colorbar(line) axcb.set_label(plotType) else: #ok lines = mplC.LineCollection(XYlist,cmap=acolor) lines.set_array(np.arange(XYlist.shape[0])) Plot.add_collection(lines) axcb = Page.figure.colorbar(lines) axcb.set_label('PDF number') lgndlist = [] if G2frame.Legend: # make short names from choices dropping PDF and AZM and then extension labels = [os.path.splitext(i[3:i.find('Azm')].strip())[0] for i in choices] numlines = len(labels) # create an empty labeled line for each label with color from color map for i,lbl in enumerate(labels): color = acolor(int(0.5+acolor.N*i/(numlines-1.))) lgndlist.append(mpl.lines.Line2D([], [], color=color, label=lbl)) Plot.legend(handles=lgndlist,loc='best') else: if G2frame.Waterfall: colorRange = XYlist[0].T[1] segs = np.reshape(np.hstack((XYlist[0][:-1],XYlist[0][1:])),(-1,2,2)) line = mplC.LineCollection(segs,cmap=acolor,norm=normcl) line.set_array(colorRange) Plot.add_collection(line) axcb = Page.figure.colorbar(line) axcb.set_label('Intensity') else: #ok line = mplC.LineCollection(XYlist,color=colors[0]) Plot.add_collection(line) wx.EndBusyCursor() if plotType == 'G(R)' and numbDen: Xb = [0.,5.] Yb = [0.,-20.*np.pi*numbDen] Plot.plot(Xb,Yb,color='k',dashes=(5,5)) Plot.set_xlim([0.,PDFdata['Rmax']]) elif plotType == 'F(Q)': Xb = [0.,5.0] Yb = [0.,-20.*np.pi*numbDen] Plot.plot(Xb,Yb,color='k',dashes=(5,5)) Plot.axhline(0.,color='k') elif plotType == 'S(Q)': Plot.axhline(1.,color='k') else: G2frame.Lines = [] X = XYlist[0].T[0] Y = XYlist[0].T[1] Plot.plot(X,Y,color='b',picker=3) if 'calc' in Peaks and len(Peaks['calc']): XC,YC= Peaks['calc'] Plot.plot(XC,YC,color='g') G2frame.Lines.append(Plot.axvline(peaks['Limits'][0],color='g',dashes=(5,5),picker=2.)) G2frame.Lines.append(Plot.axvline(peaks['Limits'][1],color='r',dashes=(5,5),picker=2.)) for peak in Peaks['Peaks']: G2frame.Lines.append(Plot.axvline(peak[0],color='r',picker=2.)) Xb = [0.,peaks['Limits'][1]] Yb = [0.,Xb[1]*peaks['Background'][1][1]] Plot.plot(Xb,Yb,color='k',dashes=(5,5)) # elif G2frame.Legend: # Plot.legend(loc='best') if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) xylim = [] Page.toolbar.push_current() Page.toolbar.draw() else: Page.canvas.draw() ################################################################################ ##### PlotCalib ################################################################################ def PlotCalib(G2frame,Inst,XY,Sigs,newPlot=False): '''plot of CW or TOF peak calibration ''' global Plot def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3g'%(xpos,Title,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1) found = [] xlim = Plot.get_xlim() wid = xlim[1]-xlim[0] found = XY[np.where(np.fabs(XY.T[0]-xpos) < 0.005*wid)] if len(found): pos = found[0][1] if 'C' in Inst['Type'][0]: Page.SetToolTipString('position=%.4f'%(pos)) else: Page.SetToolTipString('position=%.2f'%(pos)) else: Page.SetToolTipString('') xylim = [] Title = 'Position calibration' new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(Title,'mpl') if not new: if not newPlot: xylim = copy.copy(lim) else: newPlot = True Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar Plot.set_title(Title) Plot.set_xlabel(r'd-spacing',fontsize=14) if 'C' in Inst['Type'][0]: Plot.set_ylabel(r'$\mathsf{\Delta(2\theta)}$',fontsize=14) else: Plot.set_ylabel(r'$\mathsf{\Delta}T/T$',fontsize=14) for ixy,xyw in enumerate(XY): if len(xyw) > 2: X,Y,W = xyw else: X,Y = xyw W = 0. Yc = G2lat.Dsp2pos(Inst,X) if 'C' in Inst['Type'][0]: Y = Y-Yc E = Sigs[ixy] bin = W/2. else: Y = (Y-Yc)/Yc E = Sigs[ixy]/Yc bin = W/(2.*Yc) if E: Plot.errorbar(X,Y,ecolor='k',yerr=E) if ixy: Plot.plot(X,Y,'kx',picker=3) else: Plot.plot(X,Y,'kx',label='peak') if W: if ixy: Plot.plot(X,bin,'b+') else: Plot.plot(X,bin,'b+',label='bin width') Plot.plot(X,-bin,'b+') Plot.axhline(0.,color='r',linestyle='--') Plot.legend(loc='best') if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) # xylim = [] Page.toolbar.push_current() Page.toolbar.draw() else: Page.canvas.draw() ################################################################################ ##### PlotXY ################################################################################ def PlotXY(G2frame,XY,XY2=[],labelX='X',labelY='Y',newPlot=False, Title='',lines=False,names=[],names2=[],vertLines=[]): '''simple plot of xy data :param wx.Frame G2frame: The main GSAS-II tree "window" :param list XY: a list of X,Y array pairs; len(X) = len(Y) :param list XY2: a secondary list of X,Y pairs :param str labelX: label for X-axis :param str labelY: label for Y-axis :param bool newPlot: =True if new plot is to be made :param str Title: title for plot :param bool lines: = True if lines desired for XY plot; XY2 always plotted as lines :param list names: legend names for each XY plot as list a of str values :param list names2: legend names for each XY2 plot as list a of str values :param list vertLines: lists of vertical line x-positions; can be one for each XY :returns: nothing ''' global xylim def OnKeyPress(event): if event.key == 'u': if Page.Offset[1] < 100.: Page.Offset[1] += 1. elif event.key == 'd': if Page.Offset[1] > 0.: Page.Offset[1] -= 1. elif event.key == 'l': Page.Offset[0] -= 1. elif event.key == 'r': Page.Offset[0] += 1. elif event.key == 'o': Page.Offset = [0,0] elif event.key == 's': if len(XY): G2IO.XYsave(G2frame,XY,labelX,labelY,names) if len(XY2): G2IO.XYsave(G2frame,XY2,labelX,labelY,names2) elif event.key == 'g': mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid'] Draw() def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('X =%9.3f %s =%9.3f'%(xpos,Title,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1) def Draw(): global xylim Plot.clear() Plot.set_title(Title) Plot.set_xlabel(r''+labelX,fontsize=14) Plot.set_ylabel(r''+labelY,fontsize=14) colors = ['xkcd:blue','xkcd:red','xkcd:green','xkcd:cyan','xkcd:magenta','xkcd:black', 'xkcd:pink','xkcd:brown','xkcd:teal','xkcd:orange','xkcd:grey','xkcd:violet',] NC = len(colors) Page.keyPress = OnKeyPress Xmax = 0. Ymax = 0. for ixy,xy in enumerate(XY): X,Y = XY[ixy] Xmax = max(Xmax,max(X)) Ymax = max(Ymax,max(Y)) if lines: dX = Page.Offset[0]*(ixy)*Xmax/500. dY = Page.Offset[1]*(ixy)*Ymax/100. if len(names): Plot.plot(X+dX,Y+dY,colors[ixy%NC],picker=False,label=names[ixy]) else: Plot.plot(X+dX,Y+dY,colors[ixy%NC],picker=False) else: Plot.plot(X,Y,marker='+',color=colors[ixy%NC],picker=False) if len(vertLines): for ixy,X in enumerate(vertLines): dX = Page.Offset[0]*(ixy)*Xmax/500. for x in X: Plot.axvline(x+dX,color=colors[ixy%NC],dashes=(5,5),picker=False) if XY2 is not None and len(XY2): for ixy,xy in enumerate(XY2): X,Y = XY2[ixy] dX = Page.Offset[0]*(ixy+1)*Xmax/500. dY = Page.Offset[1]*(ixy+1)*Ymax/100. if len(names2): Plot.plot(X+dX,Y+dY,colors[ixy%NC],picker=False,label=names2[ixy]) else: Plot.plot(X+dX,Y+dY,colors[ixy%NC],picker=False) if len(names): Plot.legend(names,loc='best') if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) xylim = [] Page.toolbar.push_current() Page.toolbar.draw() Page.canvas.draw() else: Page.canvas.draw() new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(Title,'mpl') Page.Offset = [0,0] if not new: if not newPlot: xylim = copy.copy(lim) else: newPlot = True Page.canvas.mpl_connect('key_press_event', OnKeyPress) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Offset = [0,0] if lines: Page.Choice = (' key press','l: offset left','r: offset right','d: offset down', 'u: offset up','o: reset offset','g: toggle grid','s: save data as csv file') else: Page.Choice = None Draw() ################################################################################ ##### PlotXYZ ################################################################################ def PlotXYZ(G2frame,XY,Z,labelX='X',labelY='Y',newPlot=False,Title='',zrange=None,color=None,buttonHandler=None): '''simple contour plot of xyz data :param wx.Frame G2frame: The main GSAS-II tree "window" :param list XY: a list of X,Y arrays :param list Z: a list of Z values for each X,Y pair :param str labelX: label for X-axis :param str labelY: label for Y-axis :param bool newPlot: =True if new plot is to be made :param str Title: title for plot :param list zrange: [zmin,zmax]; default=None to use limits in Z :param str color: one of mpl.cm.dated.keys(); default=None to use G2frame.ContourColor :returns: nothing ''' def OnKeyPress(event): if event.key == 'u': G2frame.Cmax = min(1.0,G2frame.Cmax*1.2) elif event.key == 'd': G2frame.Cmax = max(0.0,G2frame.Cmax*0.8) elif event.key == 'o': G2frame.Cmax = 1.0 elif event.key == 'g': mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid'] elif event.key == 'i': choice = ['nearest','bilinear','bicubic','spline16','spline36','hanning', 'hamming','hermite','kaiser','quadric','catrom','gaussian','bessel', 'mitchell','sinc','lanczos'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Interpolation',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.Interpolate = choice[sel] else: G2frame.Interpolate = 'nearest' dlg.Destroy() elif event.key == 's': choice = [m for m in mpl.cm.datad.keys()] # if not m.endswith("_r") choice.sort() dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.ContourColor = choice[sel] else: G2frame.ContourColor = GSASIIpath.GetConfigValue('Contour_color','RdYlGn') dlg.Destroy() wx.CallAfter(PlotXYZ,G2frame,XY,Z,labelX,labelY,False,Title) def OnMotion(event): xpos = event.xdata if xpos and Xmin 1.: if 0 <= xpos < len(resNames): resName = resNames[int(xpos+.5)-1] else: resName = '' SetCursor(Page) try: if 0 <= xpos < len(resNames): G2frame.G2plotNB.status.SetStatusText('Residue: %s score: %.2f'%(resName,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select AA error plot first',1) def OnPick(event): xpos = event.mouseevent.xdata if xpos and pickHandler: xpos = int(xpos+.5) if 0 <= xpos < len(resNames): resName = resNames[xpos] else: resName = '' pickHandler(resName) def Draw(): global Plot1,Plot2 Plot.clear() Plot.set_title(Title) Plot.set_axis_off() Plot1 = Page.figure.add_subplot(211) Plot1.set_ylabel(r'Error score 1',fontsize=14) Plot1.set_xlabel(r'Residue',fontsize=14) colors = list(np.where(np.array(Probs1)>thresh[0][1],'r','b')) resNums = np.arange(len(resNames)) Plot1.bar(resNums,Probs1,color=colors,linewidth=0,picker=1) if thresh is not None: for item in thresh[0]: Plot1.axhline(item,dashes=(5,5),picker=False) Plot2 = Page.figure.add_subplot(212,sharex=Plot1) Plot2.set_ylabel(r'Error score 2',fontsize=14) Plot2.set_xlabel(r'Residue',fontsize=14) colors = list(np.where(np.array(Probs2)>thresh[1][1],'r','b')) Plot2.bar(resNums,Probs2,color=colors,linewidth=0,picker=1) if thresh is not None: for item in thresh[1]: Plot2.axhline(item,dashes=(5,5),picker=False) Page.xylim = [Plot1.get_xlim(),Plot1.get_ylim(),Plot2.get_ylim()] Page.canvas.draw() new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(Title,'mpl') Page.canvas.mpl_connect('pick_event', OnPick) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Draw() ################################################################################ ##### PlotStrain ################################################################################ def PlotStrain(G2frame,data,newPlot=False): '''plot of strain data, used for diagnostic purposes ''' def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('d-spacing =%9.5f Azimuth =%9.3f'%(ypos,xpos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select Strain pattern first',1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Strain','mpl') if not new: if not newPlot: xylim = copy.copy(lim) else: newPlot = True Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar Plot.set_title('Strain') Plot.set_ylabel(r'd-spacing',fontsize=14) Plot.set_xlabel(r'Azimuth',fontsize=14) # colors=['b','g','r','c','m','k'] colors = ['xkcd:blue','xkcd:red','xkcd:green','xkcd:cyan','xkcd:magenta','xkcd:black', 'xkcd:pink','xkcd:brown','xkcd:teal','xkcd:orange','xkcd:grey','xkcd:violet',] NC = len(colors) for N,item in enumerate(data['d-zero']): Y,X = np.array(item['ImtaObs']) #plot azimuth as X & d-spacing as Y Plot.plot(X,Y,marker='+',color=colors[N%NC],picker=False) Y,X = np.array(item['ImtaCalc']) Plot.plot(X,Y,colors[N%NC],picker=False) Plot.plot([0.,360.],[item['Dcalc'],item['Dcalc']],colors[5],dashes=(5,5)) if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) xylim = [] Page.toolbar.push_current() Page.toolbar.draw() else: Page.canvas.draw() ################################################################################ ##### PlotBarGraph ################################################################################ def PlotBarGraph(G2frame,Xarray,Xname='',Yname='Number',Title='',PlotName=None,ifBinned=False,maxBins=None): 'Needs a description' def OnPageChanged(event): PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection()) if PlotText == PlotName: PlotBarGraph(G2frame,Xarray,Xname,Title,PlotText) def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('X =%9.3f Number =%9.3g'%(xpos,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select %s first'%PlotName,1) if PlotName is None or not len(Xarray): return new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(PlotName,'mpl') if new: G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None if ifBinned: Dbins,Bins = Xarray nBins = len(Dbins) wid = Dbins[1]-Dbins[0] else: nBins= min(40,max(10,len(Xarray)//10)) if maxBins is not None: nBins = min(nBins,maxBins) Bins,Dbins = np.histogram(Xarray,nBins) wid = Dbins[1]-Dbins[0] Dbins = Dbins[:-1] Plot.set_title(Title) Plot.set_xlabel(Xname,fontsize=14) Plot.set_ylabel(Yname,fontsize=14) Plot.bar(Dbins,Bins,width=wid,align='edge',facecolor='red',edgecolor='black') Page.canvas.draw() ################################################################################ ##### PlotSASDSizeDist ################################################################################ def PlotSASDSizeDist(G2frame): 'Needs a description' def OnPageChanged(event): PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection()) if 'Powder' in PlotText: PlotPatterns(G2frame,plotType='SASD',newPlot=True) elif 'Size' in PlotText: PlotSASDSizeDist(G2frame) elif 'Pair' in PlotText: PlotSASDPairDist(G2frame) def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('diameter =%9.3f f(D) =%9.3g'%(xpos,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select Size pattern first',1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Size Distribution','mpl') if new: G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None PatternId = G2frame.PatternId data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Models')) Bins,Dbins,BinMag = data['Size']['Distribution'] Plot.set_title('Size Distribution') Plot.set_xlabel(r'$D, \AA$',fontsize=14) Plot.set_ylabel(r'$Volume\ distribution,\ f(D)$',fontsize=14) if data['Size']['logBins']: Plot.set_xscale("log",nonposx='mask') Plot.set_xlim([np.min(2.*Bins)/2.,np.max(2.*Bins)*2.]) Plot.bar(2.*Bins-Dbins,BinMag,2.*Dbins,facecolor='white',edgecolor='green') #plot diameters # colors=['b','r','c','m','k'] colors = ['xkcd:blue','xkcd:red','xkcd:green','xkcd:cyan','xkcd:magenta','xkcd:black', 'xkcd:pink','xkcd:brown','xkcd:teal','xkcd:orange','xkcd:grey','xkcd:violet',] NC = len(colors) if 'Size Calc' in data: Rbins,Dist = data['Size Calc'] for i in range(len(Rbins)): if len(Rbins[i]): Plot.plot(2.*Rbins[i],Dist[i],color=colors[i%NC]) #plot diameters Page.canvas.draw() ################################################################################ ##### PlotSASDPairDist ################################################################################ def PlotSASDPairDist(G2frame): 'Needs a description' def OnPageChanged(event): PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection()) if 'Powder' in PlotText: PlotPatterns(G2frame,plotType='SASD',newPlot=True) elif 'Size' in PlotText: PlotSASDSizeDist(G2frame) elif 'Pair' in PlotText: PlotSASDPairDist(G2frame) def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('pair dist =%9.3f f(D) =%9.3g'%(xpos,ypos),1) except TypeError: G2frame.G2plotNB.status.SetStatusText('Select Pair pattern first',1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Pair Distribution','mpl') if new: G2frame.G2plotNB.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED,OnPageChanged) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None PatternId = G2frame.PatternId data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Models')) if len(data['Pair']['Distribution']): Bins,Dbins,BinMag = data['Pair']['Distribution'] Plot.set_title('Pair Distribution') Plot.set_xlabel(r'$R, \AA$',fontsize=14) Plot.set_ylabel(r'$Pair\ distribution,\ P(R)$',fontsize=14) Plot.bar(Bins-Dbins,BinMag,Dbins,facecolor='white',edgecolor='green') #plot diameters if 'Pair Calc' in data['Pair']: [Rbins,Dist] = data['Pair']['Pair Calc'].T Plot.plot(Rbins,Dist,color='r') #plot radii Page.canvas.draw() ################################################################################ ##### PlotPowderLines ################################################################################ def PlotPowderLines(G2frame): ''' plotting of powder lines (i.e. no powder pattern) as sticks ''' global Plot def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position SetCursor(Page) G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f '%(xpos,),1) if G2frame.PickId and G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Index Peak List','Unit Cells List']: found = [] if len(G2frame.HKL): xlim = Plot.get_xlim() wid = xlim[1]-xlim[0] found = G2frame.HKL[np.where(np.fabs(G2frame.HKL.T[-1]-xpos) < 0.002*wid)] if len(found): h,k,l = found[0][:3] Page.SetToolTipString('%d,%d,%d'%(int(h),int(k),int(l))) else: Page.SetToolTipString('') new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Powder Lines','mpl') if new: Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None Plot.set_title('Powder Pattern Lines') Plot.set_xlabel(r'$\mathsf{2\theta}$',fontsize=14) PatternId = G2frame.PatternId peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Index Peak List'))[0] for peak in peaks: Plot.axvline(peak[0],color='b') for hkl in G2frame.HKL: Plot.axvline(hkl[-2],color='r',dashes=(5,5)) xmin = peaks[0][0] xmax = peaks[-1][0] delt = xmax-xmin xlim = [max(0,xmin-delt/20.),min(180.,xmax+delt/20.)] Plot.set_xlim(xlim) Page.canvas.draw() Page.toolbar.push_current() ################################################################################ ##### PlotPeakWidths ################################################################################ def PlotPeakWidths(G2frame,PatternName=None): ''' Plotting of instrument broadening terms as function of 2-theta Seen when "Instrument Parameters" chosen from powder pattern data tree. Parameter PatternName allows the PWDR to be referenced as a string rather than a wx tree item, defined in G2frame.PatternId. ''' # sig = lambda Th,U,V,W: 1.17741*math.sqrt(U*tand(Th)**2+V*tand(Th)+W)*math.pi/18000. # gam = lambda Th,X,Y: (X/cosd(Th)+Y*tand(Th))*math.pi/18000. # 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.) # gamFW2 = lambda s,g: math.sqrt(s**2+(0.4654996*g)**2)+.5345004*g #Ubaldo Bafile - private communication def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata G2frame.G2plotNB.status.SetStatusText('q =%.3f%s %sq/q =%.4f'%(xpos,Angstr+Pwrm1,GkDelta,ypos),1) def OnKeyPress(event): if event.key == 'g': mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid'] elif event.key == 's': # write the function values (not peaks) onto a file dlg = wx.FileDialog(G2frame, 'Choose CSV file to write', G2G.GetExportPath(G2frame), wildcard='column-separated file (*.csv)|.csv', style=wx.FD_CHANGE_DIR|wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() else: return finally: dlg.Destroy() fp = open(filename,'w') fp.write("# Peak widths. Def. are default values from InstParms file, fit are from refined Instrument Parameters\n") if 'C' in Parms['Type'][0]: Write2csv(fp,['Q', 'Gauss-def','Lorenz-def,total-def', 'Gauss-fit','Lorenz-fit,total-fit'] ,header=True) for vals in zip(Q,Y,Z,W,Yf,Zf,Wf): Write2csv(fp,vals) else: Write2csv(fp,['Q', 'Gauss-def','Lorenz-def', 'Gauss-fit','Lorenz-fit',] ,header=True) for vals in zip(Q,S,G,Sf,Gf): Write2csv(fp,vals) fp.close() wx.CallAfter(PlotPeakWidths,G2frame,PatternName) if PatternName: G2frame.PatternId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, PatternName) PatternId = G2frame.PatternId limitID = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits') if limitID: limits = G2frame.GPXtree.GetItemPyData(limitID)[:2] else: return Parms,Parms2 = G2frame.GPXtree.GetItemPyData( \ G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters')) if 'PKS' in Parms['Type'][0]: return elif 'T' in Parms['Type'][0]: difC = Parms['difC'][0] else: lam = G2mth.getWave(Parms) try: # PATCH: deal with older peak lists, before changed to dict to implement TOF peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'))['peaks'] except TypeError: print ("Your peak list needs reformatting...",end='') item = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List') G2frame.GPXtree.SelectItem(item) item = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters') G2frame.GPXtree.SelectItem(item) print ("done") return xylim = [] new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Peak Widths','mpl') Page.Choice = (' key press','g: toggle grid','s: save as .csv file') Page.keyPress = OnKeyPress if not new: if not G2frame.G2plotNB.allowZoomReset: # save previous limits xylim = copy.copy(lim) else: Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.canvas.mpl_connect('key_press_event', OnKeyPress) # save information needed to reload from tree and redraw G2frame.G2plotNB.RegisterRedrawRoutine(G2frame.G2plotNB.lastRaisedPlotTab, PlotPeakWidths,(G2frame,G2frame.GPXtree.GetItemText(G2frame.PatternId))) TreeItemText = G2frame.GPXtree.GetItemText(G2frame.PatternId) G2frame.G2plotNB.status.SetStatusText('histogram: '+TreeItemText,1) Page.SetToolTipString('') X = [] Y = [] Z = [] W = [] if 'C' in Parms['Type'][0]: Plot.figure.suptitle(TreeItemText) Plot.set_title('Instrument and sample peak widths') Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14) Plot.set_ylabel(r'$\Delta Q/Q, \Delta d/d$',fontsize=14) Xmin,Xmax = limits[1] X = np.linspace(Xmin,Xmax,num=101,endpoint=True) Q = 4.*np.pi*npsind(X/2.)/lam Z = np.ones_like(X) data = G2mth.setPeakparms(Parms,Parms2,X,Z) s = np.sqrt(data[4])*np.pi/18000. #var -> sig(radians) g = data[6]*np.pi/18000. #centideg -> radians G = G2pwd.getgamFW(g,s) #/2. #delt-theta from TCH fxn Y = sq8ln2*s/nptand(X/2.) Z = g/nptand(X/2.) W = G/nptand(X/2.) Plot.plot(Q,Y,color='r',label='Gaussian') Plot.plot(Q,Z,color='g',label='Lorentzian') Plot.plot(Q,W,color='b',label='G+L') fit = G2mth.setPeakparms(Parms,Parms2,X,Z,useFit=True) sf = np.sqrt(fit[4])*np.pi/18000. gf = fit[6]*np.pi/18000. Gf = G2pwd.getgamFW(gf,sf) #/2. Yf = sq8ln2*sf/nptand(X/2.) Zf = gf/nptand(X/2.) Wf = Gf/nptand(X/2.) Plot.plot(Q,Yf,color='r',dashes=(5,5),label='Gaussian fit') Plot.plot(Q,Zf,color='g',dashes=(5,5),label='Lorentzian fit') Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit') Xp = [] Yp = [] Zp = [] Wp = [] for peak in peaks: Xp.append(4.0*math.pi*sind(peak[0]/2.0)/lam) try: s = math.sqrt(peak[4])*math.pi/18000. except ValueError: s = 0.01 g = peak[6]*math.pi/18000. G = G2pwd.getgamFW(g,s) #/2. Yp.append(sq8ln2*s/tand(peak[0]/2.)) Zp.append(g/tand(peak[0]/2.)) Wp.append(G/tand(peak[0]/2.)) if len(peaks): Plot.plot(Xp,Yp,'+',color='r',label='G peak') Plot.plot(Xp,Zp,'+',color='g',label='L peak') Plot.plot(Xp,Wp,'+',color='b',label='G+L peak') legend = Plot.legend(loc='best') SetupLegendPick(legend,new) Page.canvas.draw() else: #'T'OF Plot.set_title('Instrument and sample peak coefficients') Plot.set_xlabel(r'$Q, \AA^{-1}$',fontsize=14) Plot.set_ylabel(r'$\alpha, \beta, \Delta Q/Q, \Delta d/d$',fontsize=14) Xmin,Xmax = limits[1] T = np.linspace(Xmin,Xmax,num=101,endpoint=True) Z = np.ones_like(T) data = G2mth.setPeakparms(Parms,Parms2,T,Z) ds = T/difC Q = 2.*np.pi/ds A = data[4] B = data[6] S = 1.17741*np.sqrt(data[8])/T G = data[10]/T Plot.plot(Q,A,color='r',label='Alpha') Plot.plot(Q,B,color='g',label='Beta') Plot.plot(Q,S,color='b',label='Gaussian') Plot.plot(Q,G,color='m',label='Lorentzian') fit = G2mth.setPeakparms(Parms,Parms2,T,Z) ds = T/difC Q = 2.*np.pi/ds Af = fit[4] Bf = fit[6] Sf = 1.17741*np.sqrt(fit[8])/T Gf = fit[10]/T Plot.plot(Q,Af,color='r',dashes=(5,5),label='Alpha fit') Plot.plot(Q,Bf,color='g',dashes=(5,5),label='Beta fit') Plot.plot(Q,Sf,color='b',dashes=(5,5),label='Gaussian fit') Plot.plot(Q,Gf,color='m',dashes=(5,5),label='Lorentzian fit') Tp = [] Ap = [] Bp = [] Sp = [] Gp = [] Wp = [] Qp = [] for peak in peaks: Tp.append(peak[0]) Ap.append(peak[4]) Bp.append(peak[6]) Qp.append(2.*np.pi*difC/peak[0]) Sp.append(1.17741*np.sqrt(peak[8])/peak[0]) Gp.append(peak[10]/peak[0]) if Qp: Plot.plot(Qp,Ap,'+',color='r',label='Alpha peak') Plot.plot(Qp,Bp,'+',color='g',label='Beta peak') Plot.plot(Qp,Sp,'+',color='b',label='Gaussian peak') Plot.plot(Qp,Gp,'+',color='m',label='Lorentzian peak') Plot.legend(loc='best') if xylim and not G2frame.G2plotNB.allowZoomReset: # this restores previous plot limits (but I'm not sure why there are two .push_current calls) Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) Page.toolbar.push_current() Page.toolbar.draw() else: Page.canvas.draw() ################################################################################ ##### PlotSizeStrainPO ################################################################################ def PlotSizeStrainPO(G2frame,data,hist='',Start=False): '''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase ''' def OnPick(event): if 'Inv. pole figure' not in plotType: return ind = event.ind[0] h,k,l = RefSets[ind] msg = '%d,%d,%d=%.2f'%(h,k,l,Rmd[ind]) Page.SetToolTipString(msg) def rp2xyz(r,p): z = npcosd(r) xy = np.sqrt(1.-z**2) return xy*npcosd(p),xy*npsind(p),z def OnMotion(event): if 'Inv. pole figure' not in plotType: return if event.xdata and event.ydata: #avoid out of frame errors xpos = event.xdata ypos = event.ydata r = xpos**2+ypos**2 if r <= 1.0: if 'Eq. area' in plotType: r,p = 2.*npasind(np.sqrt(r)*sq2),npatan2d(xpos,ypos) else: r,p = 2.*npatand(np.sqrt(r)),npatan2d(xpos,ypos) if p<0.: p += 360. ipf = lut(r*np.pi/180.,p*np.pi/180.) p = 90.-p if p<0.: p += 360. xyz = np.inner(Amat,np.array([rp2xyz(r,p)])) y,x,z = list(xyz/np.max(np.abs(xyz))) G2frame.G2plotNB.status.SetStatusText( 'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z),1) import scipy.interpolate as si generalData = data['General'] SGData = generalData['SGData'] if Start: #initialize the spherical harmonics qlmn arrays ptx.pyqlmninit() Start = False cell = generalData['Cell'][1:] Amat,Bmat = G2lat.cell2AB(cell[:6]) useList = data['Histograms'] phase = generalData['Name'] plotType = generalData['Data plot type'] plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.', 'St. proj. Inv. pole figure':'','Eq. area Inv. pole figure':''} for ptype in plotDict: G2frame.G2plotNB.Delete(ptype) if plotType in ['None'] or not useList: return if hist == '': hist = list(useList.keys())[0] if plotType in ['Mustrain','Size']: new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(plotType,'3d') else: new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(plotType,'mpl') if not new: if not Page.IsShown(): Page.Show() else: Page.canvas.mpl_connect('pick_event', OnPick) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = None G2frame.G2plotNB.status.SetStatusText('',1) PHI = np.linspace(0.,360.,40,True) PSI = np.linspace(0.,180.,40,True) X = np.outer(npcosd(PHI),npsind(PSI)) Y = np.outer(npsind(PHI),npsind(PSI)) Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI)) try: #temp patch instead of 'mustrain' for old files with 'microstrain' if plotDict[plotType]: coeff = useList[hist][plotDict[plotType]] except KeyError: return if plotType in ['Mustrain','Size']: diam = 0.5 if plotType == 'Mustrain': diam = 1.0 if coeff[0] == 'isotropic': X *= diam*coeff[1][0] Y *= diam*coeff[1][0] Z *= diam*coeff[1][0] elif coeff[0] == 'uniaxial': def uniaxCalc(xyz,iso,aniso,axes): Z = np.array(axes) cp = abs(np.dot(xyz,Z)) sp = np.sqrt(1.-cp**2) R = iso*aniso/np.sqrt((iso*cp)**2+(aniso*sp)**2) return R*xyz*diam iso,aniso = coeff[1][:2] axes = np.inner(Amat,np.array(coeff[3])) axes /= nl.norm(axes) Shkl = np.array(coeff[1]) XYZ = np.dstack((X,Y,Z)) XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes)) X,Y,Z = np.dsplit(XYZ,3) X = X[:,:,0] Y = Y[:,:,0] Z = Z[:,:,0] elif coeff[0] == 'ellipsoidal': def ellipseCalc(xyz,E,R): XYZ = xyz*E.T return np.inner(XYZ.T,R)*diam S6 = coeff[4] Sij = G2lat.U6toUij(S6) E,R = nl.eigh(Sij) XYZ = np.dstack((X,Y,Z)) XYZ = np.nan_to_num(np.apply_along_axis(ellipseCalc,2,XYZ,E,R)) X,Y,Z = np.dsplit(XYZ,3) X = X[:,:,0] Y = Y[:,:,0] Z = Z[:,:,0] elif coeff[0] == 'generalized': def genMustrain(xyz,SGData,A,Shkl): uvw = np.inner(Amat.T,xyz) Strm = np.array(G2spc.MustrainCoeff(uvw,SGData)) Sum = np.sum(np.multiply(Shkl,Strm)) Sum = np.where(Sum > 0.01,Sum,0.01) Sum = np.sqrt(Sum) return Sum*xyz Shkl = np.array(coeff[4]) if np.any(Shkl): XYZ = np.dstack((X,Y,Z)) XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,Amat,Shkl)) X,Y,Z = np.dsplit(XYZ,3) X = X[:,:,0] Y = Y[:,:,0] Z = Z[:,:,0] if np.any(X) and np.any(Y) and np.any(Z): np.seterr(all='ignore') Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1) xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T XYZlim = [min(xyzlim[0]),max(xyzlim[1])] if 'x' in generalData['3Dproj']: Plot.contour(X,Y,Z,10,zdir='x',offset=XYZlim[0]) if 'y' in generalData['3Dproj']: Plot.contour(X,Y,Z,10,zdir='y',offset=XYZlim[1]) if 'z' in generalData['3Dproj']: Plot.contour(X,Y,Z,10,zdir='z',offset=XYZlim[0]) Plot.set_xlim3d(XYZlim) Plot.set_ylim3d(XYZlim) Plot.set_zlim3d(XYZlim) try: Plot.set_aspect('equal') except: #broken in mpl 3.1.1; worked in mpl 3.0.3 pass # Plot.autoscale() if plotType == 'Size': Plot.set_title('Crystallite size for '+phase+'\n'+coeff[0]+' model') Plot.set_xlabel(r'X, $\mu$m') Plot.set_ylabel(r'Y, $\mu$m') Plot.set_zlabel(r'Z, $\mu$m') else: Plot.set_title(r'$\mu$strain for '+phase+'\n'+coeff[0]+' model') Plot.set_xlabel(r'X, $\mu$strain') Plot.set_ylabel(r'Y, $\mu$strain') Plot.set_zlabel(r'Z, $\mu$strain') elif plotType in ['Preferred orientation',]: h,k,l = generalData['POhkl'] if coeff[0] == 'MD': print ('March-Dollase preferred orientation plot') else: PH = np.array(generalData['POhkl']) phi,beta = G2lat.CrsAng(PH,cell[:6],SGData) SHCoef = {} for item in coeff[5]: L,N = eval(item.strip('C')) SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item] ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) X = np.linspace(0,90.0,26) Y = G2lat.polfcal(ODFln,'0',X,0.0) Plot.plot(X,Y,color='k',label=str(PH)) Plot.legend(loc='best') Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase+'\n'+hist) Plot.set_xlabel(r'$\psi$',fontsize=16) Plot.set_ylabel('MRD',fontsize=14) elif 'Inv. pole figure' in plotType: sq2 = 1.0/math.sqrt(2.0) Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) rId = G2gd.GetGPXtreeItemId(G2frame,Id,'Reflection Lists') RefData = G2frame.GPXtree.GetItemPyData(rId)[phase] if 'Type' not in RefData or 'RefList' not in RefData: G2G.G2MessageBox(G2frame,'Reflection list not ready','RefData error') return Type = RefData['Type'] Refs = RefData['RefList'].T ns = 0 if RefData['Super']: ns = 1 if 'C' in Type: obsRMD = Refs[12+ns] else: obsRMD = Refs[15+ns] Phi = [] Beta = [] Rmd = [] Ops = np.array([Op[0].T for Op in SGData['SGOps']]) refSets = [np.inner(Ops,hkl) for hkl in Refs[:3].T] for ir,refSet in enumerate(refSets): refSet = np.vstack((refSet,-refSet)) #add Friedel pairs refSet = [np.where(ref[2]<0,-1.*ref,ref) for ref in refSet] #take +l of each pair then remove duplicates refSet = [str(ref).strip('[]').replace('-0',' 0') for ref in refSet] refSet = [np.fromstring(item,sep=' ') for item in set(refSet)] refSets[ir] = refSet RefSets = [] for ir,refSet in enumerate(refSets): r,beta,phi = G2lat.HKL2SpAng(refSet,cell[:6],SGData) #radius, inclination, azimuth phi *= np.pi/180. beta *= np.pi/180. Phi += list(phi) Beta += list(beta) Rmd += len(phi)*[obsRMD[ir],] RefSets += refSet RefSets = np.array(RefSets) Beta = np.abs(np.array(Beta)) Phi = np.array(Phi) Phi=np.where(Phi<0.,Phi+2.*np.pi,Phi) Rmd = np.array(Rmd) Rmd = np.where(Rmd<0.,0.,Rmd) if 'Eq. area' in plotType: x,y = np.sin(Beta/2.)*np.cos(Phi)/sq2,np.sin(Beta/2.)*np.sin(Phi)/sq2 else: x,y = np.tan(Beta/2.)*np.cos(Phi),np.tan(Beta/2.)*np.sin(Phi) npts = 201 X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts)) R,P = np.sqrt(X**2+Y**2).flatten(),npatan2d(Y,X).flatten() P=np.where(P<0.,P+360.,P) if 'Eq. area' in plotType: R = np.where(R <= 1.,2.*npasind(R*sq2),0.0) else: R = np.where(R <= 1.,2.*npatand(R),0.0) Z = np.zeros_like(R) try: sfac = 0.1 while True: try: lut = si.SmoothSphereBivariateSpline(Beta,Phi,Rmd,s=sfac) break except ValueError: sfac *= 1.05 Z = [lut(ri*np.pi/180.,p*np.pi/180.) for ri,p in zip(list(R),list(P))] # print ('IVP for histogramn: %s: interpolate sfactor: %.2f'%(hist,sfac)) except AttributeError: G2frame.G2plotNB.Delete(plotType) G2G.G2MessageBox(G2frame,'IVP interpolate error: scipy needs to be 0.11.0 or newer', 'IVP error') return Z = np.reshape(Z,(npts,npts)) try: CS = Plot.contour(Y,X,Z,aspect='equal') Plot.clabel(CS,fontsize=9,inline=1) except ValueError: pass acolor = mpl.cm.get_cmap(G2frame.ContourColor) Img = Plot.imshow(Z.T,aspect='equal',cmap=acolor,extent=[-1,1,-1,1]) Plot.plot(y,x,'+',picker=3) Page.figure.colorbar(Img) Plot.axis('off') Plot.set_title('0 0 1 Inverse pole figure for %s\n%s'%(phase,hist)) Page.canvas.draw() ################################################################################ ##### PlotTexture ################################################################################ def PlotTexture(G2frame,data,Start=False): '''Pole figure, inverse pole figure plotting. dict generalData contains all phase info needed which is in data ''' shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) # PatternId = G2frame.PatternId generalData = data['General'] SGData = generalData['SGData'] pName = generalData['Name'] textureData = generalData['SH Texture'] G2frame.G2plotNB.Delete('Texture') if not textureData['Order']: return #no plot!! SHData = generalData['SH Texture'] SHCoef = SHData['SH Coeff'][1] cell = generalData['Cell'][1:7] Amat,Bmat = G2lat.cell2AB(cell) sq2 = 1.0/math.sqrt(2.0) def rp2xyz(r,p): z = npcosd(r) xy = np.sqrt(1.-z**2) return xy*npsind(p),xy*npcosd(p),z def OnMotion(event): SHData = data['General']['SH Texture'] if event.xdata and event.ydata: #avoid out of frame errors xpos = event.xdata ypos = event.ydata if 'Inverse' in SHData['PlotType']: r = xpos**2+ypos**2 if r <= 1.0: if 'equal' in G2frame.Projection: r,p = 2.*npasind(np.sqrt(r)*sq2),npatan2d(xpos,ypos) else: r,p = 2.*npatand(np.sqrt(r)),npatan2d(xpos,ypos) ipf = G2lat.invpolfcal(IODFln,SGData,np.array([r,]),np.array([p,])) xyz = np.inner(Amat,np.array([rp2xyz(r,p)])) y,x,z = list(xyz/np.max(np.abs(xyz))) G2frame.G2plotNB.status.SetStatusText( 'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z),1) elif 'Axial' in SHData['PlotType']: pass else: #ordinary pole figure z = xpos**2+ypos**2 if z <= 1.0: z = np.sqrt(z) if 'equal' in G2frame.Projection: r,p = 2.*npasind(z*sq2),npatan2d(ypos,xpos) else: r,p = 2.*npatand(z),npatan2d(ypos,xpos) pf = G2lat.polfcal(ODFln,SamSym[textureData['Model']],np.array([r,]),np.array([p,])) G2frame.G2plotNB.status.SetStatusText('phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf),1) def OnPick(event): pick = event.artist Dettext = pick.get_gid() Page.SetToolTipString(Dettext) #TODO: add histogram positions to polefigures if '3D' in SHData['PlotType']: new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Texture','3d') else: new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Texture','mpl') if not new: if not Page.IsShown(): Page.Show() else: Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.canvas.mpl_connect('pick_event', OnPick) Page.Choice = None G2frame.G2plotNB.status.SetStatusText('') G2frame.G2plotNB.status.SetStatusWidths([150,-1]) PH = np.array(SHData['PFhkl']) phi,beta = G2lat.CrsAng(PH,cell,SGData) ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) if not np.any(ODFln): return PX = np.array(SHData['PFxyz']) gam = atan2d(PX[0],PX[1]) xy = math.sqrt(PX[0]**2+PX[1]**2) xyz = math.sqrt(PX[0]**2+PX[1]**2+PX[2]**2) psi = asind(xy/xyz) IODFln = G2lat.Glnh(Start,SHCoef,psi,gam,SamSym[textureData['Model']]) if 'Axial' in SHData['PlotType']: X = np.linspace(0,90.0,26) Y = G2lat.polfcal(ODFln,SamSym[textureData['Model']],X,0.0) Plot.plot(X,Y,color='k',label=str(SHData['PFhkl'])) Plot.legend(loc='best') h,k,l = SHData['PFhkl'] Plot.set_title('%d %d %d Axial distribution for %s'%(h,k,l,pName)) Plot.set_xlabel(r'$\psi$',fontsize=16) Plot.set_ylabel('MRD',fontsize=14) else: npts = 201 if 'Inverse' in SHData['PlotType']: X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts)) R,P = np.sqrt(X**2+Y**2).flatten(),npatan2d(Y,X).flatten() if 'equal' in G2frame.Projection: R = np.where(R <= 1.,2.*npasind(R*sq2),0.0) else: R = np.where(R <= 1.,2.*npatand(R),0.0) Z = np.zeros_like(R) Z = G2lat.invpolfcal(IODFln,SGData,R,P) Z = np.reshape(Z,(npts,npts)) try: CS = Plot.contour(Y,X,Z,aspect='equal') Plot.clabel(CS,fontsize=9,inline=1) except ValueError: pass acolor = mpl.cm.get_cmap(G2frame.ContourColor) Img = Plot.imshow(Z.T,aspect='equal',cmap=acolor,extent=[-1,1,-1,1]) Page.figure.colorbar(Img) x,y,z = SHData['PFxyz'] Plot.axis('off') Plot.set_title('%d %d %d Inverse pole figure for %s'%(int(x),int(y),int(z),pName)) Plot.set_xlabel(G2frame.Projection.capitalize()+' projection') elif '3D' in SHData['PlotType']: PSI,GAM = np.mgrid[0:31,0:31] PSI = PSI.flatten()*6. GAM = GAM.flatten()*12. P = G2lat.polfcal(ODFln,SamSym[textureData['Model']],PSI,GAM).reshape((31,31)) GAM = np.linspace(0.,360.,31,True) PSI = np.linspace(0.,180.,31,True) X = np.outer(npsind(GAM),npsind(PSI))*P.T Y = np.outer(npcosd(GAM),npsind(PSI))*P.T Z = np.outer(np.ones(np.size(GAM)),npcosd(PSI))*P.T h,k,l = SHData['PFhkl'] if np.any(X) and np.any(Y) and np.any(Z): np.seterr(all='ignore') Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1) np.seterr(all='ignore') xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T XYZlim = [min(xyzlim[0]),max(xyzlim[1])] if 'x' in generalData['3Dproj']: Plot.contour(X,Y,Z,10,zdir='x',offset=XYZlim[0]) if 'y' in generalData['3Dproj']: Plot.contour(X,Y,Z,10,zdir='y',offset=XYZlim[1]) if 'z' in generalData['3Dproj']: Plot.contour(X,Y,Z,10,zdir='z',offset=XYZlim[0]) Plot.set_xlim3d(XYZlim) Plot.set_ylim3d(XYZlim) Plot.set_zlim3d(XYZlim) try: Plot.set_aspect('equal') except: #broken in mpl 3.1.1; worked in mpl 3.0.3 pass Plot.set_title('%d %d %d Pole distribution for %s'%(h,k,l,pName)) Plot.set_xlabel(r'X, MRD') Plot.set_ylabel(r'Y, MRD') Plot.set_zlabel(r'Z, MRD') else: X,Y = np.meshgrid(np.linspace(1.,-1.,npts),np.linspace(-1.,1.,npts)) R,P = np.sqrt(X**2+Y**2).flatten(),npatan2d(X,Y).flatten() if 'equal' in G2frame.Projection: R = np.where(R <= 1.,2.*npasind(R*sq2),0.0) else: R = np.where(R <= 1.,2.*npatand(R),0.0) Z = np.zeros_like(R) Z = G2lat.polfcal(ODFln,SamSym[textureData['Model']],R,P) Z = np.reshape(Z,(npts,npts)) try: CS = Plot.contour(Y,X,Z) Plot.clabel(CS,fontsize=9,inline=1) except ValueError: pass acolor = mpl.cm.get_cmap(G2frame.ContourColor) Img = Plot.imshow(Z.T,aspect='equal',cmap=acolor,extent=[-1,1,-1,1]) Page.figure.colorbar(Img) if 'det Angles' in textureData and textureData['ShoDet']: Rdet = np.array([item[1] for item in textureData['det Angles']]) Pdet = np.array([item[2] for item in textureData['det Angles']]) if 'equal' in G2frame.Projection: Rdet = npsind(Rdet/2.)/sq2 else: Rdet = nptand(Rdet/2.) Xdet = list(npcosd(Pdet)*Rdet) Ydet = list(npsind(Pdet)*Rdet) for i,[x,y] in enumerate(zip(Xdet,Ydet)): Plot.plot(x,-y,'k+',picker=5,gid=textureData['det Angles'][i][0]) h,k,l = SHData['PFhkl'] Plot.axis('off') Plot.set_title('%d %d %d Pole figure for %s'%(h,k,l,pName)) Page.canvas.draw() ################################################################################ ##### Plot Modulation ################################################################################ def ModulationPlot(G2frame,data,atom,ax,off=0): 'Needs a description' global Off,Atom,Ax,Slab,Off Off = off Atom = atom Ax = ax def OnMotion(event): xpos = event.xdata if xpos: #avoid out of frame mouse position ypos = event.ydata ix = int(round(xpos*10)) iy = int(round((Slab.shape[0]-1)*(ypos+0.5-Off*0.005))) SetCursor(Page) try: G2frame.G2plotNB.status.SetStatusText('t =%9.3f %s =%9.3f %s=%9.3f'%(xpos,GkDelta+Ax,ypos,Gkrho,Slab[iy,ix]/8.),1) # GSASIIpath.IPyBreak() except (TypeError,IndexError): G2frame.G2plotNB.status.SetStatusText('Select '+Title+' pattern first',1) def OnPlotKeyPress(event): global Off,Atom,Ax if event.key == '0': Off = 0 elif event.key in ['+','=']: Off += 1 elif event.key == '-': Off -= 1 elif event.key in ['l','r',] and mapData['Flip']: roll = 1 if event.key == 'l': roll = -1 rho = Map['rho'] Map['rho'] = np.roll(rho,roll,axis=3) wx.CallAfter(ModulationPlot,G2frame,data,Atom,Ax,Off) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Modulation','mpl') if not new: if not Page.IsShown(): Page.Show() else: Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.canvas.mpl_connect('key_press_event', OnPlotKeyPress) G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar General = data['General'] cx,ct,cs,cia = General['AtomPtrs'] mapData = General['Map'] if mapData['Flip']: Page.Choice = ['+: shift up','-: shift down','0: reset shift','l: move left','r: move right'] else: Page.Choice = ['+: shift up','-: shift down','0: reset shift'] Page.keyPress = OnPlotKeyPress Map = General['4DmapData'] MapType = mapData['MapType'] rhoSize = np.array(Map['rho'].shape) atxyz = np.array(atom[cx:cx+3]) Spos = atom[-1]['SS1']['Spos'] tau = np.linspace(0.,2.,101) wave = np.zeros((3,101)) if len(Spos): scof = [] ccof = [] waveType = Spos[0] for i,spos in enumerate(Spos[1:]): if waveType in ['ZigZag','Block'] and not i: Tminmax = spos[0][:2] XYZmax = np.array(spos[0][2:5]) if waveType == 'Block': wave = G2mth.posBlock(tau,Tminmax,XYZmax).T elif waveType == 'ZigZag': wave = G2mth.posZigZag(tau,Tminmax,XYZmax).T else: scof.append(spos[0][:3]) ccof.append(spos[0][3:]) wave += G2mth.posFourier(tau,np.array(scof),np.array(ccof)) #does all the Fourier terms together if mapData['Flip']: Title = 'Charge flip' else: Title = MapType Title += ' map for atom '+atom[0]+ \ ' at %.4f %.4f %.4f'%(atxyz[0],atxyz[1],atxyz[2]) ix = -np.array(np.rint(rhoSize[:3]*atxyz)+1,dtype='i') ix += (rhoSize[:3]//2) ix = ix%rhoSize[:3] rho = np.roll(np.roll(np.roll(Map['rho'],ix[0],axis=0),ix[1],axis=1),ix[2],axis=2) ix = rhoSize[:3]//2 ib = 4 hdx = [2,2,2] #this needs to be something for an offset correction on atom positions if Ax == 'x': Doff = (hdx[0]+Off)*.005 slab = np.sum(np.sum(rho[:,ix[1]-ib:ix[1]+ib,ix[2]-ib:ix[2]+ib,:],axis=2),axis=1) Plot.plot(tau,wave[0]) elif Ax == 'y': Doff = (hdx[1]+Off)*.005 slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,:,ix[2]-ib:ix[2]+ib,:],axis=2),axis=0) Plot.plot(tau,wave[1]) elif Ax == 'z': Doff = (hdx[2]+Off)*.005 slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,ix[1]-ib:ix[1]+ib,:,:],axis=1),axis=0) Plot.plot(tau,wave[2]) Plot.set_title(Title) Plot.set_xlabel('t') Plot.set_ylabel(r'$\mathsf{\Delta}$%s'%(Ax)) Slab = np.hstack((slab,slab,slab)) acolor = mpl.cm.get_cmap('RdYlGn') if 'delt' in MapType: Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Doff,.5+Doff),cmap=acolor) else: Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Doff,.5+Doff)) Plot.set_ylim([-0.25,0.25]) Page.canvas.draw() ################################################################################ ##### PlotCovariance ################################################################################ def PlotCovariance(G2frame,Data): '''Plots the covariance matrix. Also shows values for parameters and their standard uncertainties (esd's) or the correlation between variables. ''' def OnPlotKeyPress(event): if event.key == 's': choice = [m for m in mpl.cm.datad.keys()] # if not m.endswith("_r") choice.sort() dlg = wx.SingleChoiceDialog(G2frame,'Select','Color scheme',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() G2frame.VcovColor = choice[sel] else: G2frame.VcovColor = 'RdYlGn' dlg.Destroy() elif event.key == 'p': covFile = open(os.path.splitext(G2frame.GSASprojectfile)[0]+'.cov','w') covFile.write(128*'*' + '\n') covFile.write('*' + 126*' ' + '*\n') covFile.write('*{:^126}*\n'.format('Covariance Matrix')) covFile.write('*' + 126*' ' + '*\n') covFile.write(128*'*' + '\n\n\n\n') llen = len(Page.varyList) for start in range(0, llen, 8): # split matrix into batches of 7 columns if llen >= start + 8: stop = start + 8 else: stop = llen covFile.write(12*' ' + '\t') for idx in range(start, stop): covFile.write('{:^12}\t'.format(Page.varyList[idx])) covFile.write('\n\n') for line in range(llen): covFile.write('{:>12}\t'.format(Page.varyList[line])) for idx in range(start, stop): covFile.write('{: 12.6f}\t'.format(Page.covArray[line][idx])) covFile.write('\n') covFile.write('\n\n\n') covFile.close() wx.CallAfter(PlotCovariance,G2frame,Data) def OnMotion(event): if event.button: ytics = imgAx.get_yticks() ytics = np.where(ytics180.,PhiPsi-360.,PhiPsi) Phi,Psi = PhiPsi.T Plot.plot(Phi,Psi,'ro',picker=5) Plot.set_xlim((-180.,180.)) Plot.set_ylim((-180.,180.)) else: if len(Coeff): X,Y = np.meshgrid(np.linspace(0.,360.,45),np.linspace(0.,360.,45)) Z = np.array([-G2mth.calcRamaEnergy(x,y,Coeff)[1] for x,y in zip(X.flatten(),Y.flatten())]) Plot.contour(X,Y,np.reshape(Z,(45,45))) Img = Plot.imshow(rama,aspect='equal',cmap=acolor,interpolation='nearest', extent=[0,360,0,360],origin='lower') if len(PhiPsi): Phi,Psi = PhiPsi.T Plot.plot(Phi,Psi,'ro',picker=5) Plot.set_xlim((0.,360.)) Plot.set_ylim((0.,360.)) Plot.set_title('Ramachandran for '+RamaName+' in '+phaseName) Plot.set_xlabel(r'$\phi$',fontsize=16) Plot.set_ylabel(r'$\psi$',fontsize=16) Page.figure.colorbar(Img) Page.canvas.draw() ################################################################################ ##### PlotSeq ################################################################################ def PlotSelectedSequence(G2frame,ColumnList,TableGet,SelectX,fitnum=None,fitvals=None): '''Plot a result from a sequential refinement :param wx.Frame G2frame: The main GSAS-II tree "window" :param list ColumnList: list of int values corresponding to columns selected as y values :param function TableGet: a function that takes a column number as argument and returns the column label, the values and there ESDs (or None) :param function SelectX: a function that returns a selected column number (or None) as the X-axis selection ''' global Title,xLabel,yLabel xLabel = yLabel = Title = '' def OnMotion(event): if event.xdata and event.ydata: #avoid out of frame errors xpos = event.xdata ypos = event.ydata msg = '%5.3f %.6g'%(xpos,ypos) Page.SetToolTipString(msg) def OnKeyPress(event): global Title,xLabel,yLabel if event.key == 's': G2frame.seqXaxis = G2frame.seqXselect() wx.CallAfter(Draw) elif event.key == 't': dlg = G2G.MultiStringDialog(G2frame,'Set titles & labels',[' Title ',' x-Label ',' y-Label '], [Title,xLabel,yLabel]) if dlg.Show(): Title,xLabel,yLabel = dlg.GetValues() dlg.Destroy() Draw() elif event.key == 'l': G2frame.seqLines = not G2frame.seqLines Draw() def Draw(): global Title,xLabel,yLabel G2frame.G2plotNB.status.SetStatusText( 'press L to toggle lines, S to select X axis, T to change titles (reselect column to show?)',1) Plot.clear() # colors=['b','g','r','c','m','k'] colors = ['xkcd:blue','xkcd:red','xkcd:green','xkcd:cyan','xkcd:magenta','xkcd:black', 'xkcd:pink','xkcd:brown','xkcd:teal','xkcd:orange','xkcd:grey','xkcd:violet',] NC = len(colors) uselist = G2frame.SeqTable.GetColValues(1) X = np.arange(0,G2frame.SeqTable.GetNumberRows(),1) xName = 'Data sequence number' if G2frame.seqXaxis is not None: try: # fails if selected X column is no longer in table xName,X,Xsig = Page.seqTableGet(G2frame.seqXaxis) if G2frame.seqReverse and not G2frame.seqXaxis: X = X[::-1] except: print('X column no longer in table, resetting') G2frame.seqXaxis = None for ic,col in enumerate(Page.seqYaxisList): Ncol = colors[ic%NC] name,Y,sig = Page.seqTableGet(col) if G2frame.seqReverse and not G2frame.seqXaxis: Y = Y[::-1] sig = sig[::-1] # deal with missing (None) values in arrays Xnew = [] Ynew = [] Ysnew = [] gotsig = False for i in range(len(X)): if not uselist[i]: continue if X[i] is None or Y[i] is None: continue Xnew.append(X[i]) Ynew.append(Y[i]) if sig and sig[i]: gotsig = True Ysnew.append(sig[i]) else: Ysnew.append(0.0) if gotsig: if G2frame.seqLines: Plot.errorbar(Xnew,Ynew,yerr=Ysnew,color=Ncol,label=name) else: Plot.errorbar(Xnew,Ynew,yerr=Ysnew,label=name,linestyle='None',color=Ncol,marker='x') else: Plot.plot(Xnew,Ynew,color=Ncol) Plot.plot(Xnew,Ynew,marker='o',color=Ncol,label=name) if Page.fitvals: # TODO: deal with fitting of None values if G2frame.seqReverse and not G2frame.seqXaxis: Page.fitvals = Page.fitvals[::-1] Plot.plot(X,Page.fitvals,label='Fit',color=colors[(ic+2)%NC]) Plot.legend(loc='best') if Title: Plot.set_title(Title) else: Plot.set_title('') if xLabel: Plot.set_xlabel(xLabel) else: Plot.set_xlabel(xName) if yLabel: Plot.set_ylabel(yLabel) else: Plot.set_ylabel('Parameter values') Page.canvas.draw() G2frame.seqXselect = SelectX try: G2frame.seqXaxis except: G2frame.seqXaxis = None if fitnum is None: label = 'Sequential refinement' else: label = 'Parametric fit #'+str(fitnum+1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(label,'mpl') if not new: if not Page.IsShown(): Page.Show() else: Page.canvas.mpl_connect('key_press_event', OnKeyPress) Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.Choice = ['l - toggle lines','s - select x-axis','t - change titles',] Page.keyPress = OnKeyPress Page.seqYaxisList = ColumnList Page.seqTableGet = TableGet Page.fitvals = fitvals Draw() ################################################################################ ##### PlotExposedImage & PlotImage ################################################################################ def PlotExposedImage(G2frame,newPlot=False,event=None): '''General access module for 2D image plotting ''' plotNo = G2frame.G2plotNB.nb.GetSelection() if plotNo < 0: return # no plots if G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Powder Image': PlotImage(G2frame,newPlot,event,newImage=True) elif G2frame.G2plotNB.nb.GetPageText(plotNo) == '2D Integration': PlotIntegration(G2frame,newPlot,event) def OnStartMask(G2frame): '''Initiate the start of a Frame or Polygon map, etc. Called from a menu command (GSASIIimgGUI) or from OnImPlotKeyPress. Variable G2frame.MaskKey contains a single letter ('f' or 'p', etc.) that determines what type of mask is created. :param wx.Frame G2frame: The main GSAS-II tree "window" ''' Masks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Masks')) if G2frame.MaskKey == 'f': new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) if Masks['Frames']: Masks['Frames'] = [] PlotImage(G2frame,newImage=True) G2frame.MaskKey = 'f' Page.figure.suptitle('Defining Frame mask (use right-mouse to end)',color='g',fontweight='bold') Page.canvas.draw() elif G2frame.MaskKey == 'p': Masks['Polygons'].append([]) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.figure.suptitle('Defining Polygon mask (use right-mouse to end)',color='r',fontweight='bold') Page.canvas.draw() elif G2frame.MaskKey == 'a': new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.figure.suptitle('Left-click to create an arc mask',color='r',fontweight='bold') Page.canvas.draw() elif G2frame.MaskKey == 'x': new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.figure.suptitle('Left-click to create an x-line mask',color='r',fontweight='bold') Page.canvas.draw() elif G2frame.MaskKey == 'y': new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.figure.suptitle('Left-click to create an y-line mask',color='r',fontweight='bold') Page.canvas.draw() elif G2frame.MaskKey == 'r': new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.figure.suptitle('Left-click to create a ring mask',color='r',fontweight='bold') Page.canvas.draw() elif G2frame.MskDelete: new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.figure.suptitle('select spot mask to delete',color='r',fontweight='bold') Page.canvas.draw() G2imG.UpdateMasks(G2frame,Masks) def OnStartNewDzero(G2frame): '''Initiate the start of adding a new d-zero to a strain data set :param wx.Frame G2frame: The main GSAS-II tree "window" :param str eventkey: a single letter ('a') that triggers the addition of a d-zero. ''' G2frame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',0) G2frame.PickId = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Stress/Strain') data = G2frame.GPXtree.GetItemPyData(G2frame.PickId) return data def ToggleMultiSpotMask(G2frame): '''Turns on and off MultiSpot selection mode; displays a subtitle on plot the is cleared by the next PlotImage call ''' new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) if G2frame.MaskKey == 's': G2frame.MaskKey = '' Page.Choice[-1] = 's: start multiple spot mask mode' wx.CallAfter(PlotImage,G2frame,newImage=True) else: G2frame.MaskKey = 's' (x0,y0),(x1,y1) = Plot.get_position().get_points() Page.Choice[-1] = 's: stop multiple spot mask mode' ShowSpotMaskInfo(G2frame,Page) def ShowSpotMaskInfo(G2frame,Page): if G2frame.MaskKey == 's': Page.figure.suptitle('Multiple spot mode on (size={}), press s or right-click to end' .format(G2frame.spotSize),color='r',fontweight='bold') else: Page.figure.suptitle('New spot size={}'.format(G2frame.spotSize), color='r',fontweight='bold') Page.canvas.draw() def ComputeArc(angI,angO,wave,azm0=0,azm1=362): '''Computes arc/ring arrays in with inner and outer radii from angI,angO and beginning and ending azimuths azm0,azm1 (optional). Returns the inner and outer ring/arc arrays. ''' Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.)) xy1 = [] xy2 = [] aR = [azm0,azm1,max(3,int(0.5+azm1-azm0))] # number of points should be at least 3 if azm1-azm0 > 180: aR[2] /= 2 # for more than 180 degrees, steps can be 2 deg. Azm = np.linspace(*aR) for azm in Azm: xy1.append(G2img.GetDetectorXY(Dsp(angI,wave),azm,Data)) #what about hyperbola xy2.append(G2img.GetDetectorXY(Dsp(angO,wave),azm,Data)) #what about hyperbola return np.array(xy1).T,np.array(xy2).T def UpdatePolygon(pick,event,polygon): '''Update a polygon (or frame) in response to the location of the mouse. Delete the selected point if moved on top of another. With right button add a point after the current button. ''' Xpos,Ypos = [event.xdata,event.ydata] if event.button == 1: # find distance to closest point other than selected point dlist = [np.sqrt((x-Xpos)**2 + (y-Ypos)**2) for i,(x,y) in enumerate(polygon)] dlist[pick.pointNumber] = max(dlist) dmin = min(dlist) cp = dlist.index(min(dlist)) # closest point if dmin < 1.5 and cp != pick.pointNumber: del polygon[pick.pointNumber] else: polygon[pick.pointNumber] = [Xpos,Ypos] polygon[-1] = polygon[0][:] elif event.button == 3: polygon.insert(pick.pointNumber+1,[Xpos,Ypos]) def PlotImage(G2frame,newPlot=False,event=None,newImage=True): '''Plot of 2D detector images as contoured plot. Also plot calibration ellipses, masks, etc. Plots whatever is in G2frame.ImageZ :param wx.Frame G2frame: main GSAS-II frame :param bool newPlot: if newPlot is True, the plot is reset (zoomed out, etc.) :param event: matplotlib mouse event (or None) :param bool newImage: If True, the Figure is cleared and redrawn ''' from matplotlib.patches import Ellipse,Circle import numpy.ma as ma G2frame.ShiftDown = False G2frame.cid = None #Dsp = lambda tth,wave: wave/(2.*npsind(tth/2.)) global Data,Masks,StrSta,Plot1,Page # RVD: these are needed for multiple image controls/masks # colors=['b','g','r','c','m','k'] colors = ['xkcd:blue','xkcd:red','xkcd:green','xkcd:cyan','xkcd:magenta','xkcd:black', 'xkcd:pink','xkcd:brown','xkcd:teal','xkcd:orange','xkcd:grey','xkcd:violet',] NC = len(colors) Data = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) G2frame.spotSize = GSASIIpath.GetConfigValue('Spot_mask_diameter',1.0) G2frame.spotString = '' # patch if 'invert_x' not in Data: Data['invert_x'] = False Data['invert_y'] = True # end patch Masks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Masks')) try: #may be absent StrSta = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Stress/Strain')) except TypeError: #is missing StrSta = {} def OnImMotion(event): Page.SetToolTipString('') sizexy = Data['size'] if event.xdata and event.ydata and len(G2frame.ImageZ): #avoid out of frame errors Page.SetToolTipString('%8.2f %8.2fmm'%(event.xdata,event.ydata)) SetCursor(Page) item = G2frame.itemPicked pixelSize = Data['pixelSize'] scalex = 1000./pixelSize[0] #microns --> 1/mm scaley = 1000./pixelSize[1] if item and G2frame.GPXtree.GetItemText(G2frame.PickId) == 'Image Controls': if 'Text' in str(item): Page.SetToolTipString('%8.3f %8.3fmm'%(event.xdata,event.ydata)) else: xcent,ycent = Data['center'] xpos = event.xdata-xcent ypos = event.ydata-ycent tth,azm = G2img.GetTthAzm(event.xdata,event.ydata,Data) if 'Lazm' in str(item) or 'Uazm' in str(item) and not Data['fullIntegrate']: Page.SetToolTipString('%6d deg'%(azm)) elif 'Itth' in str(item) or 'Otth' in str(item): Page.SetToolTipString('%8.3f deg'%(tth)) elif 'linescan' in str(item): Data['linescan'][1] = azm G2frame.scanazm.SetValue(azm) Page.SetToolTipString('%6.1f deg'%(azm)) else: xcent,ycent = Data['center'] xpos = event.xdata ypos = event.ydata radius = np.sqrt((xpos-xcent)**2+(ypos-ycent)**2) xpix = int(xpos*scalex) ypix = int(ypos*scaley) Int = 0 if (0 <= xpix < sizexy[0]) and (0 <= ypix < sizexy[1]): Int = G2frame.ImageZ[ypix][xpix] tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data) Q = 2.*math.pi/dsp if G2frame.StrainKey: G2frame.G2plotNB.status.SetStatusText('d-zero pick active',0) elif G2frame.MaskKey in ['p','f']: G2frame.G2plotNB.status.SetStatusText('Polygon/frame mask pick - LB next point, RB close polygon',1) else: G2frame.G2plotNB.status.SetStatusText( \ 'Radius=%.3fmm, 2-th=%.3fdeg, dsp=%.3fA, Q=%.5fA-1, azm=%.2fdeg, I=%6d'%(radius,tth,dsp,Q,azm,Int),1) def OnImPlotKeyRelease(event): if event.key == 'shift': G2frame.ShiftDown = False def OnImPlotKeyPress(event): try: treeItem = G2frame.GPXtree.GetItemText(G2frame.PickId) except TypeError: return if treeItem == 'Masks': if event.key in [str(i) for i in range(10)]+['.']: G2frame.spotString += event.key return elif G2frame.spotString: try: size = float(G2frame.spotString) G2frame.spotSize = size print('Spot size set to {} mm'.format(size)) ShowSpotMaskInfo(G2frame,Page) except: print('Spot size {} invalid'.format(G2frame.spotString)) G2frame.spotString = '' if event.key == 's': # turn multiple spot mode on/off ToggleMultiSpotMask(G2frame) return elif event.key == ' ': # space key: ask for spot size dlg = G2G.SingleFloatDialog(G2frame.G2plotNB,'Spot Size', 'Enter new value for spot size', G2frame.spotSize,[.1,50]) if dlg.ShowModal() == wx.ID_OK: G2frame.spotSize = dlg.GetValue() print('Spot size set to {} mm'.format(G2frame.spotSize)) ShowSpotMaskInfo(G2frame,Page) dlg.Destroy() elif event.key == 't': try: # called from menu? Xpos,Ypos = event.xdata,event.ydata except AttributeError: G2G.G2MessageBox(G2frame.G2plotNB, 'You must use the "{}" key from the keyboard'.format(event.key), 'Keyboard only') return if not (event.xdata and event.ydata): return spot = [event.xdata,event.ydata,G2frame.spotSize] Masks['Points'].append(spot) artist = Circle(spot[:2],radius=spot[2]/2,fc='none',ec='r',picker=3) Page.figure.gca().add_artist(artist) artist.itemNumber = len(Masks['Points'])-1 artist.itemType = 'Spot' G2imG.UpdateMasks(G2frame,Masks) Page.canvas.draw() return elif event.key in ['l','p','f','a','r','x','y']: G2frame.MaskKey = event.key OnStartMask(G2frame) elif event.key == 'd': G2frame.MskDelete = True OnStartMask(G2frame) elif event.key == 'shift': G2frame.ShiftDown = True elif treeItem == 'Stress/Strain': if event.key in ['a',]: G2frame.StrainKey = event.key OnStartNewDzero(G2frame) wx.CallAfter(PlotImage,G2frame,newImage=False) elif treeItem == 'Image Controls': if event.key in ['c',]: Xpos = event.xdata if not Xpos: #got point out of frame return Ypos = event.ydata dlg = wx.MessageDialog(G2frame,'Are you sure you want to change the center?', 'Center change',style=wx.OK|wx.CANCEL) try: if dlg.ShowModal() == wx.ID_OK: print ('move center to: %.3f,%.3f'%(Xpos,Ypos)) Data['center'] = [Xpos,Ypos] G2imG.UpdateImageControls(G2frame,Data,Masks) wx.CallAfter(PlotImage,G2frame,newPlot=False) finally: dlg.Destroy() return elif event.key in ['d',]: # set dmin from plot position if not (event.xdata and event.ydata): return xpos = event.xdata ypos = event.ydata tth,azm,D,dsp = G2img.GetTthAzmDsp(xpos,ypos,Data) G2frame.calibDmin.SetValue(dsp) elif event.key in ['x',]: Data['invert_x'] = not Data['invert_x'] elif event.key in ['y',]: Data['invert_y'] = not Data['invert_y'] elif event.key in ['s',] and Data['linescan'][0]: Page.plotStyle['logPlot'] = False Page.plotStyle['sqrtPlot'] = not Page.plotStyle['sqrtPlot'] elif event.key in ['n',] and Data['linescan'][0]: Page.plotStyle['sqrtPlot'] = False Page.plotStyle['logPlot'] = not Page.plotStyle['logPlot'] elif event.key in ['+','=','-',] and Data['linescan'][0]: if event.key in ['+','=']: Data['linescan'][1] += 0.5 else: Data['linescan'][1] -= 0.5 xlim = Plot1.get_xlim() azm = Data['linescan'][1]-AzmthOff xy = G2img.GetLineScan(G2frame.ImageZ,Data) Plot1.cla() olderr = np.seterr(invalid='ignore') #get around sqrt/log(-ve) error if Page.plotStyle['logPlot']: xy[1] = np.log(xy[1]) elif Page.plotStyle['sqrtPlot']: xy[1] = np.sqrt(xy[1]) np.seterr(invalid=olderr['invalid']) Plot1.plot(xy[0],xy[1]) Plot1.set_xlim(xlim) Plot1.set_xscale("linear") Plot1.set_title('Line scan at azm= %6.1f'%(azm+AzmthOff)) Page.canvas.draw() else: return wx.CallAfter(PlotImage,G2frame,newPlot=True) def OnImPick(event): 'A object has been picked' def OnDragIntBound(event): 'Respond to the dragging of one of the integration boundaries' if event.xdata is None or event.ydata is None: # mouse is outside window. Could abort the movement, # for now ignore the movement until it moves back in return tth,azm,D,dsp = G2img.GetTthAzmDsp(event.xdata,event.ydata,Data) itemPicked = str(G2frame.itemPicked) if 'Itth' in itemPicked: Data['IOtth'][0] = max(tth,0.001) elif 'Otth' in itemPicked: Data['IOtth'][1] = tth elif 'Lazm' in itemPicked: Data['LRazimuth'][0] = int(azm) Data['LRazimuth'][0] %= 360 elif 'Uazm' in itemPicked: Data['LRazimuth'][1] = int(azm) Data['LRazimuth'][1] %= 360 elif 'linescan' in itemPicked: Data['linescan'][1] = azm else: return if Data['LRazimuth'][0] > Data['LRazimuth'][1]: Data['LRazimuth'][1] += 360 if Data['fullIntegrate']: Data['LRazimuth'][1] = Data['LRazimuth'][0]+360 #if Data['IOtth'][0] > Data['IOtth'][1]: # Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0] # compute arcs, etc LRAzim = Data['LRazimuth'] #NB: integers AzmthOff = Data['azmthOff'] IOtth = Data['IOtth'] wave = Data['wavelength'] dspI = wave/(2.0*sind(IOtth[0]/2.0)) ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola) dspO = wave/(2.0*sind(IOtth[1]/2.0)) ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse Azm = np.arange(LRAzim[0],LRAzim[1]+1.)-AzmthOff if ellI: xyI = [] for azm in Azm: xy = G2img.GetDetectorXY(dspI,azm,Data) if np.any(xy): xyI.append(xy) if len(xyI): xyI = np.array(xyI) arcxI,arcyI = xyI.T if ellO: xyO = [] for azm in Azm: xy = G2img.GetDetectorXY(dspO,azm,Data) if np.any(xy): xyO.append(xy) if len(xyO): xyO = np.array(xyO) arcxO,arcyO = xyO.T Page.canvas.restore_region(savedplot) if 'Itth' in itemPicked: pick.set_data([arcxI,arcyI]) elif 'Otth' in itemPicked: pick.set_data([arcxO,arcyO]) elif 'Lazm' in itemPicked: pick.set_data([[arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]]]) elif 'Uazm' in itemPicked: pick.set_data([[arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]]]) elif 'linescan' in itemPicked: xlim = Plot1.get_xlim() azm = Data['linescan'][1]-AzmthOff dspI = wave/(2.0*sind(0.1/2.0)) xyI = G2img.GetDetectorXY(dspI,azm,Data) dspO = wave/(2.0*sind(60./2.0)) xyO = G2img.GetDetectorXY(dspO,azm,Data) pick.set_data([[xyI[0],xyO[0]],[xyI[1],xyO[1]]]) xy = G2img.GetLineScan(G2frame.ImageZ,Data) Plot1.cla() olderr = np.seterr(invalid='ignore') #get around sqrt/log(-ve) error if Page.plotStyle['logPlot']: xy[1] = np.log(xy[1]) elif Page.plotStyle['sqrtPlot']: xy[1] = np.sqrt(xy[1]) np.seterr(invalid=olderr['invalid']) Plot1.plot(xy[0],xy[1]) Plot1.set_xlim(xlim) Plot1.set_xscale("linear") Plot1.set_title('Line scan at azm= %6.1f'%(azm+AzmthOff)) Page.canvas.draw() Page.figure.gca().draw_artist(pick) Page.canvas.blit(Page.figure.gca().bbox) def OnDragMask(event): 'Respond to the dragging of a mask' if event.xdata is None or event.ydata is None: # mouse is outside window. Could abort the movement, # for now ignore the movement until it moves back in return Xpos,Ypos = [event.xdata,event.ydata] #if Page.toolbar._active: return # zoom/pan selected Page.canvas.restore_region(savedplot) try: pickType = pick.itemType except: pickType = None if pickType == "Spot": itemNum = G2frame.itemPicked.itemNumber if event.button == 1: if G2frame.ShiftDown: r = math.sqrt((Xpos-Masks['Points'][itemNum][0])**2+ (Ypos-Masks['Points'][itemNum][1])**2) pick.radius = r else: x = Masks['Points'][itemNum][0]+Xpos-XposBeforeDrag y = Masks['Points'][itemNum][1]+Ypos-YposBeforeDrag pick.center=[x,y] Page.figure.gca().draw_artist(pick) elif pickType.startswith('Ring'): wave = Data['wavelength'] itemNum = G2frame.itemPicked.itemNumber if event.button == 1: angO = angI = G2img.GetTth(Xpos,Ypos,Data) if pickType == 'RingInner': angO += Masks['Rings'][itemNum][1] else: angI -= Masks['Rings'][itemNum][1] Masks['Rings'][itemNum][0] = (angO+angI)/2 elif event.button == 3: ang = G2img.GetTth(Xpos,Ypos,Data) t = 2*abs(ang - Masks['Rings'][itemNum][0]) angI = Masks['Rings'][itemNum][0] - t/2. angO = Masks['Rings'][itemNum][0] + t/2. Masks['Rings'][itemNum][1] = t (x1,y1),(x2,y2) = ComputeArc(angI,angO,wave) pI,pO = G2frame.ringList[pick.itemNumber] pI.set_data((x1,y1)) pO.set_data((x2,y2)) Page.figure.gca().draw_artist(pI) Page.figure.gca().draw_artist(pO) elif pickType.startswith('Arc'): wave = Data['wavelength'] itemNum = G2frame.itemPicked.itemNumber tth,azm,thick = Masks['Arcs'][itemNum] tthN,azmN,D,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data) if event.button == 1: if pickType == 'ArcInner': angO = angI = tthN angO += thick off = 0 Masks['Arcs'][itemNum][0] = (angO + angI)/2 elif pickType == 'ArcOuter': angO = angI = tthN angI -= thick off = 0 Masks['Arcs'][itemNum][0] = (angO + angI)/2 elif pickType == 'ArcLower': angO = tth + thick/2 angI = tth - thick/2 off = azmN - azm[0] elif pickType == 'ArcUpper': angO = tth + thick/2 angI = tth - thick/2 off = azmN - azm[1] azm[0] += off azm[1] += off elif event.button == 3: if pickType == 'ArcInner' or pickType == 'ArcOuter': t = 2*abs(tthN - tth) angI = tth - t/2. angO = tth + t/2. Masks['Arcs'][itemNum][2] = t off = 0 elif pickType == 'ArcLower': angO = tth + thick/2 angI = tth - thick/2 off = azmN - azm[0] elif pickType == 'ArcUpper': angO = tth + thick/2 angI = tth - thick/2 off = azmN - azm[1] newRange = azm[1] - azm[0] - 2*off if newRange < 2 or newRange > 358: return # don't let the azimuthal range get too small or large azm[0] += off azm[1] -= off (x1,y1),(x2,y2) = ComputeArc(angI,angO,wave,*azm) pI,pO,pL,pU = G2frame.arcList[pick.itemNumber] pI.set_data((x2,y2)) pO.set_data((x1,y1)) pL.set_data(([x1[0],x2[0]],[y1[0],y2[0]])) pU.set_data(([x1[-1],x2[-1]],[y1[-1],y2[-1]])) Page.figure.gca().draw_artist(pI) Page.figure.gca().draw_artist(pO) Page.figure.gca().draw_artist(pL) Page.figure.gca().draw_artist(pU) elif pickType == 'Polygon': # respond to drag polygon = Masks['Polygons'][pick.itemNumber][:] UpdatePolygon(pick,event,polygon) xl,yl = np.hsplit(np.array(polygon),2) artist = Plot.plot(xl,yl,'r+')[0] # points Page.figure.gca().add_artist(artist) artist = G2frame.polyList[pick.itemNumber] artist.set_data((xl,yl)) # lines Page.figure.gca().draw_artist(artist) elif pickType == 'Frame': polygon = Masks['Frames'][:] UpdatePolygon(pick,event,polygon) xl,yl = np.hsplit(np.array(polygon),2) artist = Plot.plot(xl,yl,'g+')[0] # points Page.figure.gca().add_artist(artist) artist = G2frame.frameArtist artist.set_data((xl,yl)) # lines Page.figure.gca().draw_artist(artist) else: # non-dragable object return Page.canvas.blit(Page.figure.gca().bbox) if G2frame.itemPicked is not None: return if G2frame.GPXtree.GetItemText(G2frame.PickId) == 'Image Controls': G2frame.itemPicked = pick = event.artist G2frame.mousePicked = event.mouseevent # prepare to animate move of integration ranges Page = G2frame.G2plotNB.nb.GetPage(plotNum) saveLinestyle = pick.get_linestyle() pick.set_linestyle(':') # set line as dotted Page.figure.gca() Page.canvas.draw() # refresh without dotted line & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragIntBound) pick.set_linestyle(saveLinestyle) # back to original elif G2frame.GPXtree.GetItemText(G2frame.PickId) == 'Masks': # prepare to animate dragging of mask G2frame.itemPicked = pick = event.artist G2frame.mousePicked = event.mouseevent XposBeforeDrag,YposBeforeDrag = [event.mouseevent.xdata,event.mouseevent.ydata] #GSASIIpath.IPyBreak() Page = G2frame.G2plotNB.nb.GetPage(plotNum) try: pickType = pick.itemType except: # should not happen anymore pickType = None if pickType == 'Spot': pl = [pick,] elif pickType.startswith('Ring'): pl = G2frame.ringList[pick.itemNumber] elif pickType.startswith('Arc'): pl = G2frame.arcList[pick.itemNumber] elif pickType == 'Polygon': pl = [G2frame.polyList[pick.itemNumber]] elif pickType == 'Frame': pl = [G2frame.frameArtist,] else: print('picktype {} should not happen!'.format(pickType)) GSASIIpath.IPyBreak() saveLinestyle = [p.get_linestyle() for p in pl] for p in pl: p.set_linestyle('dotted') # set line as dotted Page.canvas.draw() # refresh without dotted line & save bitmap savedplot = Page.canvas.copy_from_bbox(Page.figure.gca().bbox) G2frame.cid = Page.canvas.mpl_connect('motion_notify_event', OnDragMask) for p,s in zip(pl,saveLinestyle): p.set_linestyle(s) # set back to original def OnImRelease(event): '''Called when the mouse is released inside an image plot window ''' global Page try: treeItem = G2frame.GPXtree.GetItemText(G2frame.PickId) except TypeError: return if Data.get('linescan',[False,0.])[0]: Page.xlim1 = Plot1.get_xlim() new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) if G2frame.cid is not None: # if there is a drag connection, delete it Page.canvas.mpl_disconnect(G2frame.cid) G2frame.cid = None if treeItem not in ['Image Controls','Masks','Stress/Strain']: return if treeItem == 'Masks' and G2frame.spotString: try: size = float(G2frame.spotString) G2frame.spotSize = size print('Spot size set to {} mm'.format(size)) ShowSpotMaskInfo(G2frame,Page) except: print('Spot size {} invalid'.format(G2frame.spotString)) G2frame.spotString = '' pixelSize = Data['pixelSize'] scalex = 1000./pixelSize[0] scaley = 1000./pixelSize[1] # pixLimit = Data['pixLimit'] #can be too tight pixLimit = 20 #this makes the search box 40x40 pixels if G2frame.itemPicked is None and treeItem == 'Image Controls' and len(G2frame.ImageZ): # nothing being dragged, add calibration point (left mouse) or launch calibration (right) Xpos = event.xdata if not (Xpos and G2frame.ifGetRing): #got point out of frame return Ypos = event.ydata if Ypos and not Page.toolbar._active: #make sure zoom/pan not selected if event.button == 1: Xpix = Xpos*scalex Ypix = Ypos*scaley if event.key == 'shift': #force selection at cursor position xpos = Xpix ypos = Ypix I = J = 10 else: xpos,ypos,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix) if I and J: xpos += .5 #shift to pixel center ypos += .5 xpos /= scalex #convert to mm ypos /= scaley Data['ring'].append([xpos,ypos]) elif event.button == 3: G2frame.GetStatusBar().SetStatusText('Calibrating...',0) if G2img.ImageCalibrate(G2frame,Data): G2frame.GetStatusBar().SetStatusText('Calibration successful - Show ring picks to check',0) print ('Calibration successful') else: G2frame.GetStatusBar().SetStatusText('Calibration failed - Show ring picks to diagnose',0) print ('Calibration failed') G2frame.ifGetRing = False G2imG.UpdateImageControls(G2frame,Data,Masks) return wx.CallAfter(PlotImage,G2frame,newImage=False) return elif G2frame.MaskKey and treeItem == 'Masks': # nothing being dragged, create a new mask Xpos,Ypos = [event.xdata,event.ydata] if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected return if G2frame.MaskKey == 's': if event.button == 3: ToggleMultiSpotMask(G2frame) else: if G2frame.ShiftDown: #force user selection sig = G2frame.spotSize else: #optimize spot pick pixLimit = 5 Xpix,Ypix = Xpos*scalex,Ypos*scaley Xpix,Ypix,I,J = G2img.ImageLocalMax(G2frame.ImageZ,pixLimit,Xpix,Ypix) ind = [int(Xpix),int(Ypix)] nxy = 15 ImMax = np.max(G2frame.ImageZ) result = G2img.FitImageSpots(G2frame.ImageZ,ImMax,ind,pixelSize,nxy,G2frame.spotSize) if result: Xpos,Ypos,sig = result else: print ('Not a spot') return spot = [Xpos,Ypos,sig] Masks['Points'].append(spot) artist = Circle((Xpos,Ypos),radius=spot[2]/2,fc='none',ec='r',picker=3) Page.figure.gca().add_artist(artist) artist.itemNumber = len(Masks['Points'])-1 artist.itemType = 'Spot' G2imG.UpdateMasks(G2frame,Masks) Page.canvas.draw() return elif G2frame.MaskKey == 'r': if event.button == 1: tth = G2img.GetTth(Xpos,Ypos,Data) t = GSASIIpath.GetConfigValue('Ring_mask_thickness',0.1) Masks['Rings'].append([tth,t]) G2imG.UpdateMasks(G2frame,Masks) G2frame.MaskKey = '' wx.CallAfter(PlotImage,G2frame,newImage=True) return elif G2frame.MaskKey == 'a': if event.button == 1: tth,azm = G2img.GetTthAzm(Xpos,Ypos,Data) azm = int(azm) t = GSASIIpath.GetConfigValue('Ring_mask_thickness',0.1) a = GSASIIpath.GetConfigValue('Arc_mask_azimuth',10.0) Masks['Arcs'].append([tth,[azm-a/2.,azm+a/2.],t]) G2imG.UpdateMasks(G2frame,Masks) G2frame.MaskKey = '' wx.CallAfter(PlotImage,G2frame,newImage=True) return elif G2frame.MaskKey in ['p','f']: if G2frame.MaskKey =='p': polygon = Masks['Polygons'][-1] color = 'r' lbl = 'Polygon' else: polygon = Masks['Frames'] color = 'g' lbl = 'Frame' if event.button == 3: # close the polygon/frame if len(polygon) <= 2: # too few points if G2frame.MaskKey =='p': del Masks['Polygons'][-1] else: Masks['Frames'] = [] G2G.G2MessageBox(G2frame.G2plotNB,lbl+' deleted -- not enough points', 'too few points') else: polygon.append(polygon[0][:]) # G2frame.G2plotNB.status.SetStatusText('Polygon closed',) # BHT: never gets seen G2frame.MaskKey = '' G2imG.UpdateMasks(G2frame,Masks) wx.CallAfter(PlotImage,G2frame,newImage=True) return else: G2frame.G2plotNB.status.SetStatusText('New '+lbl+' point: %.1f,%.1f'%(Xpos,Ypos),1) if len(polygon): xpr,ypr = polygon[-1] Plot.plot((xpr,Xpos),(ypr,Ypos),color) Plot.plot(Xpos,Ypos,color+'+') Page.canvas.draw() polygon.append([Xpos,Ypos]) #G2imG.UpdateMasks(G2frame,Masks) return elif G2frame.MaskKey in ['x','y']: Xpix,Ypix = int(Xpos*scalex),int(Ypos*scaley) if G2frame.MaskKey == 'y': Masks['Ylines'].append(Xpix) else: Masks['Xlines'].append(Ypix) G2imG.UpdateMasks(G2frame,Masks) wx.CallAfter(PlotImage,G2frame,newImage=True) return G2imG.UpdateMasks(G2frame,Masks) wx.CallAfter(PlotImage,G2frame,newImage=False) elif G2frame.MskDelete: G2frame.MskDelete = False if G2frame.itemPicked: del Masks['Points'][G2frame.itemPicked.itemNumber] G2imG.UpdateMasks(G2frame,Masks) wx.CallAfter(PlotImage,G2frame,newImage=True) elif treeItem == 'Stress/Strain' and G2frame.StrainKey: Xpos,Ypos = [event.xdata,event.ydata] if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected return dsp = G2img.GetDsp(Xpos,Ypos,Data) StrSta['d-zero'].append({'Dset':dsp,'Dcalc':0.0,'pixLimit':10,'cutoff':0.5,'Ivar':0.0, 'ImxyObs':[[],[]],'ImxyCalc':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0]}) R,r = G2img.MakeStrStaRing(StrSta['d-zero'][-1],G2frame.ImageZ,Data) if not len(R): del StrSta['d-zero'][-1] G2frame.ErrorDialog('Strain peak selection','WARNING - No points found for this ring selection') StrSta['d-zero'] = G2mth.sortArray(StrSta['d-zero'],'Dset',reverse=True) G2frame.StrainKey = '' G2imG.UpdateStressStrain(G2frame,StrSta) wx.CallAfter(PlotImage,G2frame,newPlot=False) else: # start here after dragging of integration range lines or a mask Xpos,Ypos = [event.xdata,event.ydata] if not Xpos or not Ypos or Page.toolbar._active: #got point out of frame or zoom/pan selected return tth,azm,dsp = G2img.GetTthAzmDsp(Xpos,Ypos,Data)[:3] itemPicked = str(G2frame.itemPicked) try: pickType = G2frame.itemPicked.itemType except: pickType = '?' if G2frame.ifGetRing: #delete a calibration ring pick xypos = [Xpos,Ypos] rings = Data['ring'] for ring in rings: if np.allclose(ring,xypos,.01,0): rings.remove(ring) elif 'Line2D' in itemPicked and treeItem == 'Image Controls': if 'Itth' in itemPicked: Data['IOtth'][0] = max(tth,0.001) elif 'Otth' in itemPicked: Data['IOtth'][1] = tth elif 'Lazm' in itemPicked: Data['LRazimuth'][0] = int(azm) elif 'Uazm' in itemPicked and not Data['fullIntegrate']: Data['LRazimuth'][1] = int(azm) Data['LRazimuth'][0] %= 360 Data['LRazimuth'][1] %= 360 if Data['LRazimuth'][0] > Data['LRazimuth'][1]: Data['LRazimuth'][1] += 360 if Data['fullIntegrate']: Data['LRazimuth'][1] = Data['LRazimuth'][0]+360 if Data['IOtth'][0] > Data['IOtth'][1]: Data['IOtth'][0],Data['IOtth'][1] = Data['IOtth'][1],Data['IOtth'][0] if Data['binType'] == 'Q': wave = Data['wavelength'] IOtth = [4.*math.pi*sind(Data['IOtth'][0]/2.)/wave,4.*math.pi*sind(Data['IOtth'][1]/2.)/wave] G2frame.InnerTth.SetValue(IOtth[0]) G2frame.OuterTth.SetValue(IOtth[1]) else: G2frame.InnerTth.SetValue(Data['IOtth'][0]) G2frame.OuterTth.SetValue(Data['IOtth'][1]) G2frame.Lazim.SetValue(Data['LRazimuth'][0]) G2frame.Razim.SetValue(Data['LRazimuth'][1]) elif pickType == "Spot" and treeItem == 'Masks': spotnum = G2frame.itemPicked.itemNumber if event.button == 1: if G2frame.ShiftDown: Masks['Points'][spotnum] = list(G2frame.itemPicked.center) + [2.*G2frame.itemPicked.radius,] else: # update the selected circle mask with the last drawn values Masks['Points'][spotnum][0:2] = G2frame.itemPicked.center elif event.button == 3: del Masks['Points'][spotnum] G2imG.UpdateMasks(G2frame,Masks) elif pickType.startswith('Ring') and treeItem == 'Masks': G2imG.UpdateMasks(G2frame,Masks) # changes saved during animation elif pickType.startswith('Arc') and treeItem == 'Masks': G2imG.UpdateMasks(G2frame,Masks) # changes saved during animation elif pickType == 'Polygon' and treeItem == 'Masks': polygon = Masks['Polygons'][G2frame.itemPicked.itemNumber] UpdatePolygon(G2frame.itemPicked,event,polygon) G2imG.UpdateMasks(G2frame,Masks) elif pickType == 'Frame' and treeItem == 'Masks': UpdatePolygon(G2frame.itemPicked,event,Masks['Frames']) G2imG.UpdateMasks(G2frame,Masks) else: # nothing was done, nothing was changed, don't replot G2frame.itemPicked = None return wx.CallAfter(PlotImage,G2frame,newImage=True) G2frame.itemPicked = None # PlotImage execution starts here if not len(G2frame.ImageZ): return xylim = [] new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=newImage) if Data.get('linescan',[False,0.])[0]: Plot.set_visible(False) GS_kw = {'width_ratios':[1,2],} # try: Plot1,Plot = Page.figure.subplots(1,2,gridspec_kw=GS_kw) # except AttributeError: # figure.Figure.subplots added in MPL 2.2 # Plot1,Plot = MPLsubplots(Page.figure, 1,2, gridspec_kw=GS_kw) Plot1.set_title('Line scan at azm= %6.1f'%Data['linescan'][1]) Plot1.set_xlabel(r'$\mathsf{2\Theta}$',fontsize=12) Plot1.set_ylabel('Intensity',fontsize=12) xy = G2img.GetLineScan(G2frame.ImageZ,Data) olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error if Page.plotStyle['logPlot']: xy[1] = np.log(xy[1]) Plot1.set_ylabel('log(Intensity)',fontsize=12) elif Page.plotStyle['sqrtPlot']: Plot1.set_ylabel(r'$\sqrt{Intensity}$',fontsize=12) xy[1] = np.sqrt(xy[1]) np.seterr(invalid=olderr['invalid']) Plot1.plot(xy[0],xy[1]) if newImage: G2frame.MaskKey = '' # subtitle will be removed, so turn off mode if not new: if not newPlot: xylim = lim else: Page.canvas.mpl_connect('key_press_event', OnImPlotKeyPress) Page.canvas.mpl_connect('key_release_event', OnImPlotKeyRelease) Page.canvas.mpl_connect('motion_notify_event', OnImMotion) Page.canvas.mpl_connect('pick_event', OnImPick) Page.canvas.mpl_connect('button_release_event', OnImRelease) Page.Choice = None Title = G2frame.GPXtree.GetItemText(G2frame.Image)[4:] G2frame.G2plotNB.status.DestroyChildren() #get rid of special stuff on status bar Plot.set_title(Title) try: if G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Image Controls',]: Page.Choice = [' key press','c: set beam center','d: set dmin','x: flip x','y: flip y',] if Data.get('linescan',[False,0.])[0]: Page.Choice += ['s: toggle sqrt plot line scan','n: toggle log plot line scan'] Page.keyPress = OnImPlotKeyPress elif G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Masks',]: Page.Choice = [' key press','a: arc mask','r: ring mask', 'x: x line mask','y: y line mask', 'p: polygon mask','f: frame mask', 't: add spot mask at mouse position', 'd: select spot mask to delete with mouse', ' typing a number sets diameter of new spot masks', ' (space) input the spot mask diameter'] Page.Choice.append('s: start multiple spot mask mode') # this must be the last choice Page.keyPress = OnImPlotKeyPress elif G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Stress/Strain',]: Page.Choice = (' key press','a: add new ring',) Page.keyPress = OnImPlotKeyPress except TypeError: pass size,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(G2frame.Image) imScale = 1 maxpix = 2048 if len(G2frame.ImageZ) > maxpix: imScale = len(G2frame.ImageZ)//maxpix sizexy = Data['size'] pixelSize = Data['pixelSize'] Xmax = sizexy[0]*pixelSize[0]/1000. Ymax = sizexy[1]*pixelSize[1]/1000. xlim = (0,Xmax) ylim = (Ymax,0) Imin,Imax = Data['range'][1] acolor = mpl.cm.get_cmap(Data['color']) xcent,ycent = Data['center'] Plot.set_xlabel('Image x-axis, mm',fontsize=12) Plot.set_ylabel('Image y-axis, mm',fontsize=12) #do threshold mask - "real" mask - others are just bondaries Zlim = Masks['Thresholds'][1] wx.BeginBusyCursor() try: if newImage: Imin,Imax = Data['range'][1] MA = ma.masked_outside(G2frame.ImageZ,Zlim[0],Zlim[1]) try: MaskA = ma.getmaskarray(MA)^Masks['SpotMask']['spotMask'] MA = ma.array(MA,mask=MaskA) except KeyError: # should not be needed if initializtion is proper if GSASIIpath.GetConfigValue('debug'): print('SpotMask missing') MaskA = ma.getmaskarray(MA) except TypeError: # needed if spotMasks set to initial value (None) if GSASIIpath.GetConfigValue('debug'): print('spotMask is None') MaskA = ma.getmaskarray(MA) for xline in Masks.get('Xlines',[]): MaskA[xline,:] = True for yline in Masks.get('Ylines',[]): MaskA[:,yline] = True A = G2img.ImageCompress(MA,imScale) AM = G2img.ImageCompress(MaskA,imScale) Plot.imshow(AM,aspect='equal',cmap='Reds', interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Ymax,0]) Page.ImgObj = Plot.imshow(A,aspect='equal',cmap=acolor, interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Ymax,0]) Plot.plot(xcent,ycent,'x') if Data['showLines']: # draw integration range arc/circles/lines LRAzim = Data['LRazimuth'] #NB: integers Nazm = Data['outAzimuths'] delAzm = float(LRAzim[1]-LRAzim[0])/Nazm AzmthOff = Data['azmthOff'] IOtth = Data['IOtth'] wave = Data['wavelength'] dspI = wave/(2.0*sind(IOtth[0]/2.0)) ellI = G2img.GetEllipse(dspI,Data) #=False if dsp didn't yield an ellipse (ugh! a parabola or a hyperbola) dspO = wave/(2.0*sind(IOtth[1]/2.0)) ellO = G2img.GetEllipse(dspO,Data) #Ditto & more likely for outer ellipse Azm = np.arange(LRAzim[0],LRAzim[1]+1.)-AzmthOff if ellI: xyI = [] for azm in Azm: xy = G2img.GetDetectorXY(dspI,azm,Data) if np.any(xy): xyI.append(xy) if len(xyI): xyI = np.array(xyI) arcxI,arcyI = xyI.T Plot.plot(arcxI,arcyI,picker=3,label='Itth') if ellO: xyO = [] for azm in Azm: xy = G2img.GetDetectorXY(dspO,azm,Data) if np.any(xy): xyO.append(xy) if len(xyO): xyO = np.array(xyO) arcxO,arcyO = xyO.T Plot.plot(arcxO,arcyO,picker=3,label='Otth') if ellO and ellI: Plot.plot([arcxI[0],arcxO[0]],[arcyI[0],arcyO[0]],picker=3,label='Lazm') Plot.plot([arcxI[-1],arcxO[-1]],[arcyI[-1],arcyO[-1]],picker=3,label='Uazm') for i in range(Nazm): cake = LRAzim[0]+i*delAzm-AzmthOff if Data.get('centerAzm',False): cake += delAzm/2. ind = np.searchsorted(Azm,cake) Plot.plot([arcxI[ind],arcxO[ind]],[arcyI[ind],arcyO[ind]],color='k',dashes=(5,5)) if 'linescan' in Data and Data['linescan'][0] and G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Image Controls',]: azm = Data['linescan'][1]-Data['azmthOff'] IOtth = [0.1,60.] wave = Data['wavelength'] dspI = wave/(2.0*sind(IOtth[0]/2.0)) xyI = G2img.GetDetectorXY(dspI,azm,Data) dspO = wave/(2.0*sind(IOtth[1]/2.0)) xyO = G2img.GetDetectorXY(dspO,azm,Data) Plot.plot([xyI[0],xyO[0]],[xyI[1],xyO[1]],picker=3,label='linescan') if G2frame.PickId and G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Image Controls',]: for xring,yring in Data['ring']: Plot.plot(xring,yring,'r+',picker=3) if Data['setRings']: N = 0 for ring in Data['rings']: xring,yring = np.array(ring).T[:2] Plot.plot(xring,yring,'.',color=colors[N%NC]) N += 1 for ellipse in Data['ellipses']: #what about hyperbola? cent,phi,[width,height],col = ellipse if width > 0: #ellipses Plot.add_artist(Ellipse([cent[0],cent[1]],2*width,2*height,phi,ec=col,fc='none')) Plot.text(cent[0],cent[1],'+',color=col,ha='center',va='center') if G2frame.PickId and G2frame.GPXtree.GetItemText(G2frame.PickId) in ['Stress/Strain',]: for N,ring in enumerate(StrSta['d-zero']): if 'ImxyCalc' in ring: xringc,yringc = ring['ImxyCalc'] Plot.plot(xringc,yringc,colors[N%NC]) xring,yring = ring['ImxyObs'] Plot.plot(xring,yring,'.',colors[N%NC]) # display the Masks if 'Frames' not in Masks: Masks['Frames'] = [] # patch for i,spot in enumerate(Masks['Points']): # drawing spot masks if len(spot): x,y,d = spot artist = Circle((x,y),radius=d/2,fc='none',ec='r',picker=3) Plot.add_artist(artist) artist.itemNumber = i artist.itemType = 'Spot' G2frame.ringList = [] for iring,ring in enumerate(Masks['Rings']): # drawing spot masks if ring: tth,thick = ring wave = Data['wavelength'] (x1,y1),(x2,y2) = ComputeArc(tth-thick/2.,tth+thick/2.,wave) artistO, = Plot.plot(x1,y1,'r',picker=3) artistO.itemNumber = iring artistO.itemType = 'RingOuter' artistI, = Plot.plot(x2,y2,'r',picker=3) artistI.itemNumber = iring artistI.itemType = 'RingInner' G2frame.ringList.append([artistI,artistO]) G2frame.arcList = [] for iarc,arc in enumerate(Masks['Arcs']): # drawing arc masks if arc: tth,azm,thick = arc wave = Data['wavelength'] (x1,y1),(x2,y2) = ComputeArc(tth-thick/2.,tth+thick/2.,wave,azm[0],azm[1]) arcList = [] arcList.append(Plot.plot(x2,y2,'r',picker=3)[0]) # 'inner' arcList[-1].itemNumber = iarc arcList[-1].itemType = 'ArcInner' arcList.append(Plot.plot(x1,y1,'r',picker=3)[0]) # 'outer' arcList[-1].itemNumber = iarc arcList[-1].itemType = 'ArcOuter' arcList.append(Plot.plot([x1[0],x2[0]],[y1[0],y2[0]],'r',picker=3)[0]) # 'lower' arcList[-1].itemNumber = iarc arcList[-1].itemType = 'ArcLower' arcList.append(Plot.plot([x1[-1],x2[-1]],[y1[-1],y2[-1]],'r',picker=3)[0]) # 'upper' arcList[-1].itemNumber = iarc arcList[-1].itemType = 'ArcUpper' G2frame.arcList.append(arcList) G2frame.polyList = [] for ipoly,polygon in enumerate(Masks['Polygons']): if not polygon: continue # ignore if empty if polygon[0] != polygon[-1]: print('Closing polygon {}'.format(ipoly)) polygon.append(polygon[0][:]) xl,yl = np.hsplit(np.array(polygon),2) G2frame.polyList.append(Plot.plot(xl,yl,'r')[0]) # line for i,(x,y) in enumerate(zip(xl[:-1],yl[:-1])): artist = Plot.plot(x,y,'r+',picker=10)[0] # point (plus sign) artist.itemNumber = ipoly artist.itemType = 'Polygon' artist.pointNumber = i G2frame.frameArtist = [] if Masks['Frames']: polygon = Masks['Frames'] if polygon[0] != polygon[-1]: print('Closing frame mask') polygon.append(polygon[0][:]) xl,yl = np.hsplit(np.array(polygon),2) G2frame.frameArtist = Plot.plot(xl,yl,'g')[0] for i,(x,y) in enumerate(zip(xl[:-1],yl[:-1])): artist = Plot.plot(x,y,'g+',picker=10)[0] # point (plus sign) artist.itemType = 'Frame' artist.pointNumber = i if newImage: Page.figure.colorbar(Page.ImgObj) Plot.set_xlim(xlim) Plot.set_ylim(ylim) if Data.get('linescan',[False,0.])[0]: Plot1.set_xlim(Data['IOtth']) if Data['invert_x']: Plot.invert_xaxis() if Data['invert_y']: Plot.invert_yaxis() if not newPlot and xylim: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) if Data.get('linescan',[False,0.])[0]: try: Plot1.set_xlim(Page.xlim1) except: pass xylim = [] Page.toolbar.push_current() Page.toolbar.draw() # patch for wx 2.9 on Mac, to force a redraw i,j= wx.__version__.split('.')[0:2] if int(i)+int(j)/10. > 2.8 and 'wxOSX' in wx.PlatformInfo: Page.canvas.draw() else: Page.canvas.draw() finally: wx.EndBusyCursor() ################################################################################ ##### PlotIntegration ################################################################################ def PlotIntegration(G2frame,newPlot=False,event=None): '''Plot of 2D image after image integration with 2-theta and azimuth as coordinates ''' def OnMotion(event): Page.SetToolTipString('') SetCursor(Page) azm = event.ydata tth = event.xdata if azm and tth: G2frame.G2plotNB.status.SetStatusText(\ 'Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm),1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Integration','mpl') if not new: if not newPlot: xylim = copy.copy(lim) else: Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.views = False Page.Choice = None Data = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) image = G2frame.Integrate[0] xsc = G2frame.Integrate[1] ysc = G2frame.Integrate[2] Imin,Imax = Data['range'][1] acolor = mpl.cm.get_cmap(Data['color']) Plot.set_title(G2frame.GPXtree.GetItemText(G2frame.Image)[4:]) Plot.set_ylabel('azimuth',fontsize=12) Plot.set_xlabel('2-theta',fontsize=12) Img = Plot.imshow(image,cmap=acolor,vmin=Imin,vmax=Imax,interpolation='nearest', \ extent=[ysc[0],ysc[-1],xsc[-1],xsc[0]],aspect='auto') Page.figure.colorbar(Img) # if Data['ellipses']: # for ellipse in Data['ellipses']: # x,y = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color # tth,azm = G2img.GetTthAzm(x,y,Data) ## azm = np.where(azm < 0.,azm+360,azm) # Plot.plot(tth,azm,'b,') if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) xylim = [] Page.toolbar.push_current() Page.toolbar.draw() else: Page.canvas.draw() ################################################################################ ##### PlotTRImage ################################################################################ def PlotTRImage(G2frame,tax,tay,taz,newPlot=False): '''a test plot routine - not normally used ''' def OnMotion(event): Page.SetToolTipString('') SetCursor(Page) azm = event.xdata tth = event.ydata if azm and tth: G2frame.G2plotNB.status.SetStatusText(\ 'Detector 2-th =%9.3fdeg, azm = %7.2fdeg'%(tth,azm),1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Transformed Powder Image','mpl') if not new: if not newPlot: xylim = copy.copy(lim) else: Page.canvas.mpl_connect('motion_notify_event', OnMotion) Page.views = False Page.Choice = None Data = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) Imin,Imax = Data['range'][1] step = (Imax-Imin)/5. V = np.arange(Imin,Imax,step) acolor = mpl.cm.get_cmap(Data['color']) Plot.set_title(G2frame.GPXtree.GetItemText(G2frame.Image)[4:]) Plot.set_xlabel('azimuth',fontsize=12) Plot.set_ylabel('2-theta',fontsize=12) Plot.contour(tax,tay,taz,V,cmap=acolor) if Data['showLines']: IOtth = Data['IOtth'] if Data['fullIntegrate']: LRAzim = [-180,180] else: LRAzim = Data['LRazimuth'] #NB: integers Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[0],IOtth[0]],picker=True) Plot.plot([LRAzim[0],LRAzim[1]],[IOtth[1],IOtth[1]],picker=True) if not Data['fullIntegrate']: Plot.plot([LRAzim[0],LRAzim[0]],[IOtth[0],IOtth[1]],picker=True) Plot.plot([LRAzim[1],LRAzim[1]],[IOtth[0],IOtth[1]],picker=True) if Data['setRings']: rings = np.concatenate((Data['rings']),axis=0) for xring,yring,dsp in rings: x,y = G2img.GetTthAzm(xring,yring,Data) Plot.plot(y,x,'r+') if Data['ellipses']: for ellipse in Data['ellipses']: ring = np.array(G2img.makeIdealRing(ellipse[:3])) #skip color x,y = np.hsplit(ring,2) tth,azm = G2img.GetTthAzm(x,y,Data) Plot.plot(azm,tth,'b,') if not newPlot: Page.toolbar.push_current() Plot.set_xlim(xylim[0]) Plot.set_ylim(xylim[1]) xylim = [] Page.toolbar.push_current() Page.toolbar.draw() else: Page.canvas.draw() ################################################################################ ##### PlotStructure ################################################################################ def PlotStructure(G2frame,data,firstCall=False,pageCallback=None): '''Crystal structure plotting package. Can show structures as balls, sticks, lines, thermal motion ellipsoids and polyhedra. Magnetic moments shown as black/red arrows according to spin state :param wx.Frame G2frame: main GSAS-II window :param dict data: dict with plotting information (see :ref:Phase Tree object) :param bool firstCall: If True, this is the initial call and causes the plot to be shown twice (needed for Mac and possibly linux) :param function pageCallback: a callback function to update items on the parent page. Currently implemented for RB Models tab only ''' def FindPeaksBonds(XYZ): rFact = data['Drawing'].get('radiusFactor',0.85) #data['Drawing'] could be empty! Bonds = [[] for x in XYZ] for i,xyz in enumerate(XYZ): Dx = XYZ-xyz dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1)) IndB = ma.nonzero(ma.masked_greater(dist,rFact*2.2)) for j in IndB[0]: Bonds[i].append(Dx[j]/2.) Bonds[j].append(-Dx[j]/2.) return Bonds def OnKeyBox(event): mode = cb.GetValue() if mode in ['jpeg','bmp','tiff',]: try: import Image as Im except ImportError: try: from PIL import Image as Im except ImportError: print ("PIL/pillow Image module not present. Cannot save images without this") raise Exception("PIL/pillow Image module not found") projFile = G2frame.GSASprojectfile if projFile: Fname = (os.path.splitext(projFile)[0]+'.'+mode).replace('*','+') else: dlg = wx.FileDialog(G2frame, 'Choose graphics save file',G2G.GetExportPath(G2frame), wildcard='Graphics file (*.'+mode+')|*.'+mode,style=wx.FD_OPEN| wx.FD_CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: Fname = dlg.GetPath() finally: dlg.Destroy() size = Page.canvas.GetSize() if Fname: GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1) if mode in ['jpeg',]: Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB, GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) else: Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB, GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) try: im.frombytes(Pix) except AttributeError: im.fromstring(Pix) im = im.transpose(Im.FLIP_TOP_BOTTOM) im.save(Fname,mode) cb.SetValue(' save as/key:') G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1) else: event.key = cb.GetValue()[0] cb.SetValue(' save as/key:') wx.CallAfter(OnKey,event) Page.canvas.SetFocus() # redirect the Focus from the button back to the plot def OnKey(event): #on key UP!! keyBox = False try: keyCode = event.GetKeyCode() if keyCode > 255: keyCode = 0 key = chr(keyCode) except AttributeError: #if from OnKeyBox above keyBox = True key = str(event.key).upper() indx = drawingData['selectedAtoms'] cx,ct = drawingData['atomPtrs'][:2] if key in ['C']: drawingData['viewPoint'] = [np.array([.5,.5,.5]),[0,0]] drawingData['viewDir'] = [0,0,1] drawingData['oldxy'] = [] V0 = np.array([0,0,1]) V = np.inner(Amat,V0) V /= np.sqrt(np.sum(V**2)) A = np.arccos(np.sum(V*V0)) Q = G2mth.AV2Q(A,[0,1,0]) drawingData['Quaternion'] = Q SetViewPointText(drawingData['viewPoint'][0]) SetViewDirText(drawingData['viewDir']) G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) elif key in ['N']: drawAtoms = drawingData['Atoms'] if not len(drawAtoms): #no atoms return pI = drawingData['viewPoint'][1] if not len(pI): pI = [0,0] if indx: try: pI[0] = indx[pI[1]] Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3] except IndexError: pI = [0,0] Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3] pI[1] += 1 pI[1] %= len(indx) txt = ' in selection' else: pI[0] += 1 pI[0] %= len(drawAtoms) Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3] txt = '' drawingData['viewPoint'] = [np.array([Tx,Ty,Tz]),pI] SetViewPointText(drawingData['viewPoint'][0]) G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+txt,1) elif key in ['K'] and generalData['Map']['MapType']: drawingData['showSlice'] = not drawingData.get('showSlice',False) SetShowCS(drawingData['showSlice']) elif key in ['P']: drawAtoms = drawingData['Atoms'] if not len(drawAtoms): #no atoms return pI = drawingData['viewPoint'][1] if not len(pI): pI = [0,0] if indx: try: pI[0] = indx[pI[1]] Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3] except IndexError: pI = [0,0] Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3] pI[1] -= 1 pI[1] %= len(indx) txt = ' in selection' else: pI[0] -= 1 pI[0] %= len(drawAtoms) Tx,Ty,Tz = drawAtoms[pI[0]][cx:cx+3] txt = '' drawingData['viewPoint'] = [np.array([Tx,Ty,Tz]),pI] SetViewPointText(drawingData['viewPoint'][0]) G2frame.G2plotNB.status.SetStatusText('View point at atom '+drawAtoms[pI[0]][ct-1]+txt,1) elif key in ['U','D','L','R'] and mapData['Flip'] == True: dirDict = {'U':[0,1],'D':[0,-1],'L':[-1,0],'R':[1,0]} SetMapRoll(dirDict[key]) if 'rho' in generalData.get('4DmapData',{}): Set4DMapRoll(dirDict[key]) SetPeakRoll(dirDict[key]) SetMapPeaksText(mapPeaks) elif key in ['M',]and generalData['Modulated']: #make a movie file try: import imageio except ImportError: G2G.G2MessageBox(G2frame, 'This command requires the Python imageio package to be installed', 'missing package') return from PIL import Image as Im Fname = generalData['Name']+'.gif' size = Page.canvas.GetSize() G2frame.tau = 0.0 data['Drawing']['Atoms'],Fade = G2mth.ApplyModulation(data,G2frame.tau) #modifies drawing atom array! SetDrawAtomsText(data['Drawing']['Atoms']) G2phG.FindBondsDraw(data) #rebuild bonds & polygons Draw('key down',Fade) fps = GSASIIpath.GetConfigValue('Movie_fps',10) duration = GSASIIpath.GetConfigValue('Movie_time',5) #sec steps = duration*fps delt = 1./steps with imageio.get_writer(Fname, mode='I',fps=fps) as writer: G2frame.tau = 0. for i in range(steps): G2frame.G2plotNB.status.SetStatusText('Modulation tau = %.2f'%(G2frame.tau),1) data['Drawing']['Atoms'],Fade = G2mth.ApplyModulation(data,G2frame.tau) #modifies drawing atom array! SetDrawAtomsText(data['Drawing']['Atoms']) G2phG.FindBondsDraw(data) #rebuild bonds & polygons Draw('key down',Fade) GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1) Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB, GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) try: im.frombytes(Pix) except AttributeError: im.fromstring(Pix) im = im.transpose(Im.FLIP_TOP_BOTTOM) writer.append_data(np.array(im)) G2frame.tau += delt return elif key in ['+','-','=','0']: if keyBox: OnKeyPressed(event) return Draw('key up') def OnKeyPressed(event): #On key down for repeating operation - used to change tau... try: keyCode = event.GetKeyCode() if keyCode > 255: keyCode = 0 key = chr(keyCode) except AttributeError: #if from OnKeyBox above key = str(event.key).upper() if key in ['+','-','=','0']: if generalData['Modulated']: tstep = 1./36 #0.05 if key == '0': G2frame.tau = 0. elif key in ['+','=']: G2frame.tau += tstep elif key == '-': G2frame.tau -= tstep G2frame.tau %= 1. #force 0-1 range; makes loop G2frame.G2plotNB.status.SetStatusText('Modulation tau = %.4f'%(G2frame.tau),1) data['Drawing']['Atoms'],Fade = G2mth.ApplyModulation(data,G2frame.tau) #modifies drawing atom array! SetDrawAtomsText(data['Drawing']['Atoms']) G2phG.FindBondsDraw(data) #rebuild bonds & polygons if not np.any(Fade): Fade += 1 Draw('key down',Fade) else: #TODO sequential result movie here SeqId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'Sequential results') if SeqId: Seqdata = G2frame.GPXtree.GetItemPyData(SeqId) histNames = Seqdata['histNames'] if key == '0': G2frame.seq = 0 elif key in ['=','+']: G2frame.seq += 1 elif key in ['-','_']: G2frame.seq -= 1 G2frame.seq %= len(histNames) #makes loop G2frame.G2plotNB.status.SetStatusText('Seq. data file: %s'%(histNames[G2frame.seq]),1) pId = data['pId'] SGData = generalData['SGData'] pfx = str(pId)+'::' phfx = '%d:%d:'%(pId,G2frame.seq) seqData = Seqdata[histNames[G2frame.seq]] parmDict = seqData['parmDict'] cellA = G2lat.cellDijFill(pfx,phfx,SGData,parmDict) global cell, Vol, Amat, Bmat, A4mat, B4mat cell = G2lat.A2cell(cellA) Vol = G2lat.calc_V(cellA) Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse Gmat,gmat = G2lat.cell2Gmat(cell) A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) data['Drawing']['Atoms'] = G2mth.ApplySeqData(data,seqData) SetDrawAtomsText(data['Drawing']['Atoms']) G2phG.FindBondsDrawCell(data,cell) #rebuild bonds & polygons Draw('key down') else: pass def GetTruePosition(xy,Add=False): View = GL.glGetIntegerv(GL.GL_VIEWPORT) Proj = GL.glGetDoublev(GL.GL_PROJECTION_MATRIX) Model = GL.glGetDoublev(GL.GL_MODELVIEW_MATRIX) Zmax = 1. if Add: Indx = GetSelectedAtoms() if G2frame.phaseDisplay.GetPageText(getSelection()) == 'Map peaks': peakList = data['Map Peaks'] for i,peak in enumerate(peakList): x,y,z = peak[1:4] X,Y,Z = GLU.gluProject(x,y,z,Model,Proj,View) XY = [int(X),int(View[3]-Y)] if np.allclose(xy,XY,atol=10) and Z < Zmax: Zmax = Z try: Indx.remove(i) ClearSelectedAtoms() for Id in Indx: SetSelectedAtoms(Id,Add) except: SetSelectedAtoms(i,Add) G2frame.G2plotNB.status.SetStatusText( ' Selected peak: {:.3f} @ ({:.3f},{:.3f},{:.3f})' .format(*peak[0:4]),1) return elif G2frame.phaseDisplay.GetPageText(getSelection()) == 'Draw Atoms': atomList = drawAtoms cx = G2phG.getAtomPtrs(data,True)[0] sympt = cx+3 else: atomList = data['Atoms'] cx = G2phG.getAtomPtrs(data)[0] sympt = None for i,atom in enumerate(atomList): x,y,z = atom[cx:cx+3] X,Y,Z = GLU.gluProject(x,y,z,Model,Proj,View) XY = [int(X),int(View[3]-Y)] if np.allclose(xy,XY,atol=10) and Z < Zmax: Zmax = Z try: Indx.remove(i) ClearSelectedAtoms() for Id in Indx: SetSelectedAtoms(Id,Add) except: SetSelectedAtoms(i,Add) lbl = atom[0] if sympt: lbl += ' ' + atom[sympt] G2frame.G2plotNB.status.SetStatusText( ' Selected atom: {}'.format(lbl),1) return def OnMouseDown(event): xy = event.GetPosition() if event.ShiftDown(): if event.LeftIsDown(): GetTruePosition(xy) elif event.RightIsDown(): GetTruePosition(xy,True) Draw('Shift atom select') else: drawingData['oldxy'] = list(xy) def OnMouseMove(event): if event.ShiftDown(): #don't want any inadvertant moves when picking return newxy = event.GetPosition() if event.Dragging(): if event.AltDown() and rbObj: if event.LeftIsDown(): SetRBRotation(newxy) Q = rbObj['Orient'][0] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) elif event.RightIsDown(): SetRBTranslation(newxy) Tx,Ty,Tz = rbObj['Orig'][0] G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f'%(Tx,Ty,Tz),1) elif event.MiddleIsDown(): SetRBRotationZ(newxy) Q = rbObj['Orient'][0] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) Draw('move') elif not event.ControlDown(): if event.LeftIsDown(): SetRotation(newxy) Q = drawingData['Quaternion'] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) elif event.RightIsDown(): SetTranslation(newxy) Tx,Ty,Tz = drawingData['viewPoint'][0] rho = G2mth.getRho([Tx,Ty,Tz],mapData) G2frame.G2plotNB.status.SetStatusText('New view point: %.4f, %.4f, %.4f; density: %.4f'%(Tx,Ty,Tz,rho),1) elif event.MiddleIsDown(): SetRotationZ(newxy) Q = drawingData['Quaternion'] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) Draw('move') elif drawingData.get('showSlice'): View = GL.glGetIntegerv(GL.GL_VIEWPORT) Tx,Ty,Tz = drawingData['viewPoint'][0] tx,ty,tz = GLU.gluProject(Tx,Ty,Tz) Cx,Cy,Cz = GLU.gluUnProject(newxy[0],View[3]-newxy[1],tz) rho = G2mth.getRho([Cx,Cy,Cz],mapData) contlevels = contourSet.get_array() contstr = str(contlevels).strip('[]') G2frame.G2plotNB.status.SetStatusText('Cursor position: %.4f, %.4f, %.4f; density: %.4f, contours at: %s'%(Cx,Cy,Cz,rho,contstr),1) def OnMouseWheel(event): if event.ShiftDown(): return drawingData['cameraPos'] += event.GetWheelRotation()/24. drawingData['cameraPos'] = max(10,min(500,drawingData['cameraPos'])) G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(drawingData['cameraPos']),1) page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Options': G2frame.phaseDisplay.cameraPosTxt.SetLabel('Camera Position: '+'%.2f'%(drawingData['cameraPos'])) G2frame.phaseDisplay.cameraSlider.SetValue(drawingData['cameraPos']) Draw('wheel') def getSelection(): try: return G2frame.phaseDisplay.GetSelection() except: G2frame.G2plotNB.status.SetStatusText('Select this from Phase data window!',1) return 0 def SetViewPointText(VP): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Options': G2frame.phaseDisplay.viewPoint.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2])) def SetShowCS(CS): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Options': G2frame.phaseDisplay.showCS.SetValue(CS) def SetRBOrigText(): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'RB Models': for i,sizer in enumerate(G2frame.testRBObjSizers['Xsizers']): sizer.SetValue(testRBObj['rbObj']['Orig'][0][i]) if pageCallback: try: pageCallback() except: pass def SetRBOrienText(): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'RB Models': for i,sizer in enumerate(G2frame.testRBObjSizers['Osizers']): sizer.SetLabel('%8.5f'%(testRBObj['rbObj']['Orient'][0][i])) if pageCallback: try: pageCallback() except: pass def SetViewDirText(VD): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Options': G2frame.phaseDisplay.viewDir.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2])) def SetMapPeaksText(mapPeaks): data['Map Peaks'] = mapPeaks page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Map peaks': G2frame.MapPeaksTable.SetData(data['Map Peaks']) panel = G2frame.phaseDisplay.GetPage(page).GetChildren() names = [child.GetName() for child in panel] try: panel[names.index('GridWindow')].Refresh() except ValueError: #different wx versions! panel[names.index('grid window')].Refresh() def SetDrawAtomsText(drawAtoms): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Atoms': table = G2frame.atomTable.GetData() for i,atom in enumerate(drawAtoms): if generalData['Type'] == 'magnetic': table[i][2:8] = atom[2:8] else: table[i][2:5] = atom[2:5] G2frame.atomTable.SetData(table) panel = G2frame.phaseDisplay.GetPage(page).GetChildren() names = [child.GetName() for child in panel] try: panel[names.index('GridWindow')].Refresh() except ValueError: #different wx versions! panel[names.index('grid window')].Refresh() def ClearSelectedAtoms(): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Atoms': G2frame.phaseDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Draw Atoms elif G2frame.phaseDisplay.GetPageText(page) == 'Map peaks': G2frame.phaseDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms elif G2frame.phaseDisplay.GetPageText(page) == 'Atoms': G2frame.phaseDisplay.GetPage(page).ClearSelection() #this is the Atoms grid in Atoms def SetSelectedAtoms(ind,Add=False): page = getSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Atoms': G2frame.phaseDisplay.GetPage(page).SelectRow(ind,Add) #this is the Atoms grid in Draw Atoms elif G2frame.phaseDisplay.GetPageText(page) == 'Map peaks': G2frame.phaseDisplay.GetPage(page).SelectRow(ind,Add) elif G2frame.phaseDisplay.GetPageText(page) == 'Atoms': Id = drawAtoms[ind][-3] for i,atom in enumerate(atomData): if atom[-1] == Id: G2frame.phaseDisplay.GetPage(page).SelectRow(i,Add) #this is the Atoms grid in Atoms def GetSelectedAtoms(): page = getSelection() Ind = [] if page: if G2frame.phaseDisplay.GetPageText(page) == 'Draw Atoms': Ind = G2frame.phaseDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Draw Atoms elif G2frame.phaseDisplay.GetPageText(page) == 'Map peaks': Ind = G2frame.phaseDisplay.GetPage(page).GetSelectedRows() elif G2frame.phaseDisplay.GetPageText(page) == 'Atoms': Ind = G2frame.phaseDisplay.GetPage(page).GetSelectedRows() #this is the Atoms grid in Atoms return Ind def SetBackground(): R,G,B,A = Page.camera['backColor'] GL.glClearColor(R,G,B,A) GL.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT) def SetLights(): GL.glEnable(GL.GL_DEPTH_TEST) GL.glShadeModel(GL.GL_SMOOTH) GL.glEnable(GL.GL_LIGHTING) GL.glEnable(GL.GL_LIGHT0) GL.glLightModeli(GL.GL_LIGHT_MODEL_TWO_SIDE,0) GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[.1,.1,.1,1]) GL.glLightfv(GL.GL_LIGHT0,GL.GL_DIFFUSE,[.8,.8,.8,1]) # glLightfv(GL_LIGHT0,GL_SPECULAR,[1,1,1,1]) # glLightfv(GL_LIGHT0,GL_POSITION,[0,0,1,1]) def GetRoll(newxy,rhoshape): Q = drawingData['Quaternion'] dxy = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,newxy+[0,])) dxy = np.array(dxy*rhoshape) roll = np.where(dxy>0.5,1,np.where(dxy<-.5,-1,0)) return roll def SetMapRoll(newxy): rho = generalData['Map']['rho'] roll = GetRoll(newxy,rho.shape) generalData['Map']['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2) drawingData['oldxy'] = list(newxy) def Set4DMapRoll(newxy): rho = generalData['4DmapData']['rho'] if len(rho): roll = GetRoll(newxy,rho.shape[:3]) generalData['4DmapData']['rho'] = np.roll(np.roll(np.roll(rho,roll[0],axis=0),roll[1],axis=1),roll[2],axis=2) def SetPeakRoll(newxy): rho = generalData['Map']['rho'] roll = GetRoll(newxy,rho.shape) steps = 1./np.array(rho.shape) dxy = roll*steps for peak in mapPeaks: peak[1:4] += dxy peak[1:4] %= 1. peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2)) def SetTranslation(newxy): #first get translation vector in screen coords. oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy drawingData['oldxy'] = list(newxy) V = np.array([-dxy[0],dxy[1],0.]) #then transform to rotated crystal coordinates & apply to view point Q = drawingData['Quaternion'] V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V)) Tx,Ty,Tz = drawingData['viewPoint'][0] Tx += V[0]*0.01 Ty += V[1]*0.01 Tz += V[2]*0.01 drawingData['viewPoint'][0] = np.array([Tx,Ty,Tz]) SetViewPointText([Tx,Ty,Tz]) def SetRBTranslation(newxy): #first get translation vector in screen coords. if 'fixOrig' in rbObj: if rbObj['fixOrig']: return oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy drawingData['oldxy'] = list(newxy) V = np.array([-dxy[0],dxy[1],0.]) #then transform to rotated crystal coordinates & apply to RB origin Q = drawingData['Quaternion'] V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V)) Tx,Ty,Tz = rbObj['Orig'][0] Tx -= V[0]*0.01 Ty -= V[1]*0.01 Tz -= V[2]*0.01 rbObj['Orig'][0][:] = Tx,Ty,Tz SetRBOrigText() def SetRotation(newxy): 'Perform a rotation in x-y space due to a left-mouse drag' #first get rotation vector in screen coords. & angle increment oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! drawingData['oldxy'] = list(newxy) V = np.array([dxy[1],dxy[0],0.]) A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) if not A: return # nothing changed, nothing to do # next transform vector back to xtal coordinates via inverse quaternion # & make new quaternion Q = drawingData['Quaternion'] V = G2mth.prodQVQ(G2mth.invQ(Q),np.inner(Bmat,V)) DQ = G2mth.AVdeg2Q(A,V) Q = G2mth.prodQQ(Q,DQ) drawingData['Quaternion'] = Q # finally get new view vector - last row of rotation matrix VD = np.inner(Bmat,G2mth.Q2Mat(Q)[2]) VD /= np.sqrt(np.sum(VD**2)) drawingData['viewDir'] = VD SetViewDirText(VD) def SetRotationZ(newxy): #first get rotation vector (= view vector) in screen coords. & angle increment View = GL.glGetIntegerv(GL.GL_VIEWPORT) cent = [View[2]/2,View[3]/2] oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! drawingData['oldxy'] = list(newxy) V = drawingData['viewDir'] A = [0,0] A[0] = dxy[1]*.25 A[1] = dxy[0]*.25 if newxy[0] > cent[0]: A[0] *= -1 if newxy[1] < cent[1]: A[1] *= -1 # next transform vector back to xtal coordinates & make new quaternion Q = drawingData['Quaternion'] V = np.inner(Amat,V) Qx = G2mth.AVdeg2Q(A[0],V) Qy = G2mth.AVdeg2Q(A[1],V) Q = G2mth.prodQQ(Q,Qx) Q = G2mth.prodQQ(Q,Qy) drawingData['Quaternion'] = Q def SetRBRotation(newxy): #first get rotation vector in screen coords. & angle increment oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return drawingData['oldxy'] = list(newxy) V = np.array([dxy[1],dxy[0],0.]) A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) # next transform vector back to xtal coordinates via inverse quaternion # & make new quaternion Q = rbObj['Orient'][0] #rotate RB to Cart QC = drawingData['Quaternion'] #rotate Cart to drawing V = G2mth.prodQVQ(G2mth.invQ(QC),V) V = G2mth.prodQVQ(G2mth.invQ(Q),V) DQ = G2mth.AVdeg2Q(A,V) Q = G2mth.prodQQ(Q,DQ) rbObj['Orient'][0][:] = Q SetRBOrienText() def SetRBRotationZ(newxy): #first get rotation vector (= view vector) in screen coords. & angle increment View = GL.glGetIntegerv(GL.GL_VIEWPORT) cent = [View[2]/2,View[3]/2] oldxy = drawingData['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return drawingData['oldxy'] = list(newxy) V = drawingData['viewDir'] A = [0,0] A[0] = dxy[1]*.25 A[1] = dxy[0]*.25 if newxy[0] < cent[0]: A[0] *= -1 if newxy[1] > cent[1]: A[1] *= -1 # next transform vector back to RB coordinates & make new quaternion Q = rbObj['Orient'][0] #rotate RB to cart V = np.inner(Amat,V) V = -G2mth.prodQVQ(G2mth.invQ(Q),V) Qx = G2mth.AVdeg2Q(A[0],V) Qy = G2mth.AVdeg2Q(A[1],V) Q = G2mth.prodQQ(Q,Qx) Q = G2mth.prodQQ(Q,Qy) rbObj['Orient'][0][:] = Q SetRBOrienText() def RenderBox(): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(2) GL.glEnable(GL.GL_BLEND) GL.glBlendFunc(GL.GL_SRC_ALPHA,GL.GL_ONE_MINUS_SRC_ALPHA) GL.glEnable(GL.GL_LINE_SMOOTH) GL.glBegin(GL.GL_LINES) for line,color in zip(uEdges,uColors): GL.glColor3ubv(color) GL.glVertex3fv(line[0]) GL.glVertex3fv(line[1]) GL.glEnd() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_LINE_SMOOTH) GL.glDisable(GL.GL_BLEND) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderUnitVectors(x,y,z): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(2) GL.glEnable(GL.GL_BLEND) GL.glBlendFunc(GL.GL_SRC_ALPHA,GL.GL_ONE_MINUS_SRC_ALPHA) GL.glEnable(GL.GL_LINE_SMOOTH) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glScalef(1/cell[0],1/cell[1],1/cell[2]) GL.glBegin(GL.GL_LINES) for line,color in list(zip(uEdges,uColors))[:3]: GL.glColor3ubv(color) GL.glVertex3fv(-line[1]/2.) GL.glVertex3fv(line[1]/2.) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_LINE_SMOOTH) GL.glDisable(GL.GL_BLEND) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderPlane(plane,color): fade = list(color) + [.25,] GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_AMBIENT_AND_DIFFUSE,fade) GL.glShadeModel(GL.GL_FLAT) GL.glEnable(GL.GL_BLEND) GL.glBlendFunc(GL.GL_SRC_ALPHA,GL.GL_ONE_MINUS_SRC_ALPHA) GL.glPushMatrix() GL.glShadeModel(GL.GL_SMOOTH) GL.glPolygonMode(GL.GL_FRONT_AND_BACK,GL.GL_FILL) GL.glFrontFace(GL.GL_CW) GL.glBegin(GL.GL_POLYGON) for vertex in plane: GL.glVertex3fv(vertex) GL.glEnd() GL.glPopMatrix() GL.glDisable(GL.GL_BLEND) GL.glShadeModel(GL.GL_SMOOTH) def RenderViewPlane(plane,Z,width,height): global txID GL.glShadeModel(GL.GL_FLAT) newTX = False if not txID: txID = GL.glGenTextures(1) newTX = True GL.glBindTexture(GL.GL_TEXTURE_2D, txID) GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT,1) GL.glEnable(GL.GL_BLEND) GL.glBlendFunc(GL.GL_SRC_ALPHA,GL.GL_ONE_MINUS_SRC_ALPHA) GL.glEnable(GL.GL_TEXTURE_2D) GL.glPushMatrix() GL.glLoadIdentity() GL.glShadeModel(GL.GL_SMOOTH) GL.glPolygonMode(GL.GL_FRONT_AND_BACK,GL.GL_FILL) GL.glFrontFace(GL.GL_CW) GL.glTexEnvf(GL.GL_TEXTURE_ENV, GL.GL_TEXTURE_ENV_MODE, GL.GL_REPLACE) GL.glTexEnvf(GL.GL_TEXTURE_ENV, GL.GL_ALPHA_SCALE, 1.0) GL.glTexParameteri(GL.GL_TEXTURE_2D, GL.GL_TEXTURE_BASE_LEVEL, 0) GL.glTexParameteri(GL.GL_TEXTURE_2D, GL.GL_TEXTURE_MAX_LEVEL, 0) if newTX: GL.glTexImage2D(GL.GL_TEXTURE_2D,0,GL.GL_RGBA,width,height,0,GL.GL_RGBA,GL.GL_UNSIGNED_BYTE,Z) else: GL.glTexSubImage2D(GL.GL_TEXTURE_2D,0,0,0,width,height,GL.GL_RGBA,GL.GL_UNSIGNED_BYTE,Z) GL.glBegin(GL.GL_POLYGON) for vertex,evertex in zip(plane,eBox): GL.glTexCoord2fv(evertex) GL.glVertex3fv(vertex) GL.glEnd() GL.glPopMatrix() GL.glDisable(GL.GL_TEXTURE_2D) GL.glDisable(GL.GL_BLEND) GL.glShadeModel(GL.GL_SMOOTH) def RenderSphere(x,y,z,radius,color): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) q = GLU.gluNewQuadric() GLU.gluSphere(q,radius,20,10) GL.glPopMatrix() def RenderDots(XYZ,RC): GL.glEnable(GL.GL_COLOR_MATERIAL) XYZ = np.array(XYZ) GL.glPushMatrix() for xyz,rc in zip(XYZ,RC): x,y,z = xyz r,c = rc GL.glColor3fv(c/255.) GL.glPointSize(r*50) GL.glBegin(GL.GL_POINTS) GL.glVertex3fv(xyz) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderSmallSphere(x,y,z,radius,color): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) q = GLU.gluNewQuadric() GLU.gluSphere(q,radius,4,2) GL.glPopMatrix() def RenderEllipsoid(x,y,z,ellipseProb,E,R4,color): s1,s2,s3 = E GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) GL.glMultMatrixf(R4.T) GL.glEnable(GL.GL_NORMALIZE) GL.glScale(s1,s2,s3) q = GLU.gluNewQuadric() GLU.gluSphere(q,ellipseProb,20,10) GL.glDisable(GL.GL_NORMALIZE) GL.glPopMatrix() def RenderBonds(x,y,z,Bonds,radius,color,slice=20): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) for bond in Bonds: GL.glPushMatrix() Dx = np.inner(Amat,bond) Z = np.sqrt(np.sum(Dx**2)) if Z: azm = atan2d(-Dx[1],-Dx[0]) phi = acosd(Dx[2]/Z) GL.glRotate(-azm,0,0,1) GL.glRotate(phi,1,0,0) q = GLU.gluNewQuadric() GLU.gluCylinder(q,radius,radius,Z,slice,2) GL.glPopMatrix() GL.glPopMatrix() def RenderMoment(x,y,z,Moment,color,slice=20): Dx = np.inner(Amat,Moment/ABC)/2. Z = np.sqrt(np.sum(Dx**2)) if Z: GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) GL.glTranslate(-Dx[0],-Dx[1],-Dx[2]) azm = atan2d(-Dx[1],-Dx[0]) phi = acosd(Dx[2]/Z) GL.glRotate(-azm,0,0,1) GL.glRotate(phi,1,0,0) q = GLU.gluNewQuadric() GLU.gluQuadricOrientation(q,GLU.GLU_INSIDE) GLU.gluDisk(q,0.,.1,slice,1) GLU.gluQuadricOrientation(q,GLU.GLU_OUTSIDE) GLU.gluCylinder(q,.1,.1,2.*Z,slice,2) GL.glTranslate(0,0,2*Z) GLU.gluQuadricOrientation(q,GLU.GLU_INSIDE) GLU.gluDisk(q,.1,.2,slice,1) GLU.gluQuadricOrientation(q,GLU.GLU_OUTSIDE) GLU.gluCylinder(q,.2,0.,.4,slice,2) GL.glPopMatrix() def RenderLines(x,y,z,Bonds,color): GL.glShadeModel(GL.GL_FLAT) xyz = np.array([x,y,z]) GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(1) GL.glColor3fv(color) GL.glPushMatrix() GL.glBegin(GL.GL_LINES) for bond in Bonds: GL.glVertex3fv(xyz) GL.glVertex3fv(xyz+bond) GL.glEnd() GL.glColor4ubv([0,0,0,0]) GL.glPopMatrix() GL.glDisable(GL.GL_COLOR_MATERIAL) GL.glShadeModel(GL.GL_SMOOTH) def RenderPolyhedra(x,y,z,Faces,color): GL.glShadeModel(GL.GL_FLAT) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glShadeModel(GL.GL_SMOOTH) GL.glMultMatrixf(B4mat.T) for face,norm in Faces: GL.glPolygonMode(GL.GL_FRONT_AND_BACK,GL.GL_FILL) GL.glFrontFace(GL.GL_CW) GL.glNormal3fv(norm) GL.glBegin(GL.GL_TRIANGLES) for vert in face: GL.glVertex3fv(vert) GL.glEnd() GL.glPopMatrix() GL.glShadeModel(GL.GL_SMOOTH) def RenderMapPeak(x,y,z,color,den): GL.glShadeModel(GL.GL_FLAT) xyz = np.array([x,y,z]) GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(3) GL.glColor3fv(2*color*den/255) GL.glPushMatrix() GL.glBegin(GL.GL_LINES) for vec in mapPeakVecs: GL.glVertex3fv(vec[0]+xyz) GL.glVertex3fv(vec[1]+xyz) GL.glEnd() GL.glColor4ubv([0,0,0,0]) GL.glPopMatrix() GL.glDisable(GL.GL_COLOR_MATERIAL) GL.glShadeModel(GL.GL_SMOOTH) def RenderBackbone(Backbone,BackboneColor,radius): GL.glPushMatrix() GL.glMultMatrixf(B4mat.T) GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glShadeModel(GL.GL_SMOOTH) # gle.gleSetJoinStyle(TUBE_NORM_EDGE | TUBE_JN_ANGLE | TUBE_JN_CAP) # gle.glePolyCylinder(Backbone,BackboneColor,radius) GL.glPopMatrix() GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderLabel(x,y,z,label,r,color,matRot): ''' color wx.Colour object ''' GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) GL.glDisable(GL.GL_LIGHTING) # GL.glWindowPos3f(0,0,0) GL.glMultMatrixf(matRot) GL.glRotate(180,1,0,0) #fix to flip about x-axis text = gltext.Text(text=' '+label,font=Font,foreground=color) text.draw_text(scale=0.025) GL.glEnable(GL.GL_LIGHTING) GL.glPopMatrix() def RenderMap(rho,rhoXYZ,indx,Rok): GL.glShadeModel(GL.GL_FLAT) cLevel = drawingData['contourLevel'] XYZ = [] RC = [] for i,xyz in enumerate(rhoXYZ): if not Rok[i]: x,y,z = xyz I,J,K = indx[i] alpha = 1.0 if cLevel < 1.: alpha = min(1.0,(abs(rho[I,J,K])/mapData['rhoMax']-cLevel)/(1.-cLevel)) if rho[I,J,K] < 0.: XYZ.append(xyz) RC.append([0.2*alpha,2*Or]) else: XYZ.append(xyz) RC.append([0.2*alpha,2*Gr]) RenderDots(XYZ,RC) GL.glShadeModel(GL.GL_SMOOTH) def Draw(caller='',Fade=[]): #useful debug? # if caller: # print (caller,generalData['Name']) # end of useful debug vdWRadii = generalData['vdWRadii'] mapData = generalData['Map'] D4mapData = generalData.get('4DmapData',{}) pageName = '' page = getSelection() if page: pageName = G2frame.phaseDisplay.GetPageText(page) rhoXYZ = [] rho = [] FourD = False if len(D4mapData.get('rho',[])): #preferentially select 4D map if there FourD = True # rho = D4mapData['rho'][:,:,:,int(G2frame.tau*10)] #pick current tau 3D slice elif len(mapData['rho']): #ordinary 3D map rho = mapData['rho'] if len(rho): VP = drawingData['viewPoint'][0]-np.array([.5,.5,.5]) contLevel = drawingData['contourLevel']*mapData['rhoMax'] if 'delt-F' in mapData['MapType'] or 'N' in mapData.get('Type',''): rho = ma.array(rho,mask=(np.abs(rho)=0,VP%steps,VP%steps-steps) Vsteps = -np.array(VP/steps,dtype='i') rho = np.roll(np.roll(np.roll(rho,Vsteps[0],axis=0),Vsteps[1],axis=1),Vsteps[2],axis=2) indx = np.array(ma.nonzero(rho)).T rhoXYZ = indx*steps+VP-incre Nc = max(len(rhoXYZ),1) rcube = 2000.*Vol/(ForthirdPI*Nc) rmax = math.exp(math.log(rcube)/3.)**2 radius = min(drawingData.get('mapSize',10.)**2,rmax) view = drawingData['viewPoint'][0] Rok = np.sum(np.inner(Amat,rhoXYZ-view).T**2,axis=1)>radius Ind = GetSelectedAtoms() VS = np.array(Page.canvas.GetSize()) aspect = float(VS[0])/float(VS[1]) cPos = drawingData['cameraPos'] Zclip = drawingData['Zclip']*cPos/200. Q = drawingData['Quaternion'] # Move view point on selection of a single peak, if enabled if pageName == 'Map peaks' and len(Ind) == 1 and drawingData['peakMoveView']: ind = Ind[0] mag,x,y,z = mapPeaks[:,:4][ind] drawingData['viewPoint'][0][:] = [x,y,z] Tx,Ty,Tz = drawingData['viewPoint'][0] cx,ct,cs,ci = drawingData['atomPtrs'] bondR = drawingData['bondRadius'] SymFade = drawingData.get('SymFade',False) G,g = G2lat.cell2Gmat(cell) GS = G GS[0][1] = GS[1][0] = math.sqrt(GS[0][0]*GS[1][1]) GS[0][2] = GS[2][0] = math.sqrt(GS[0][0]*GS[2][2]) GS[1][2] = GS[2][1] = math.sqrt(GS[1][1]*GS[2][2]) ellipseProb = G2lat.criticalEllipse(drawingData['ellipseProb']/100.) SetBackground() GL.glInitNames() GL.glPushName(0) GL.glMatrixMode(GL.GL_PROJECTION) GL.glLoadIdentity() GL.glViewport(0,0,VS[0],VS[1]) GLU.gluPerspective(20.,aspect,cPos-Zclip,cPos+Zclip) GLU.gluLookAt(0,0,cPos,0,0,0,0,1,0) SetLights() GL.glMatrixMode(GL.GL_MODELVIEW) GL.glLoadIdentity() matRot = G2mth.Q2Mat(Q) matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) GL.glMultMatrixf(matRot.T) GL.glMultMatrixf(A4mat.T) GL.glTranslate(-Tx,-Ty,-Tz) drawingData['modelView'] = GL.glGetDoublev(GL.GL_MODELVIEW_MATRIX) if drawingData['showABC']: x,y,z = drawingData['viewPoint'][0] RenderUnitVectors(x,y,z) Backbones = {} BackboneColor = [] # glEnable(GL_BLEND) # glBlendFunc(GL_SRC_ALPHA,GL_ONE_MINUS_SRC_ALPHA) if not len(Fade): atmFade = np.ones(len(drawingData['Atoms'])) else: atmFade = Fade for iat,atom in enumerate(drawingData['Atoms']): x,y,z = atom[cx:cx+3] Bonds = atom[-2] Faces = atom[-1] try: atNum = generalData['AtomTypes'].index(atom[ct]) except ValueError: atNum = -1 CL = atom[cs+2] if not atmFade[iat]: continue atColor = atmFade[iat]*np.array(CL)/255. if SymFade and atom[cs-1] != '1': atColor *= .5 if drawingData['showRigidBodies'] and atom[ci] in rbAtmDict: bndColor = Or/255. else: bndColor = atColor if iat in Ind and G2frame.phaseDisplay.GetPageText(getSelection()) != 'Map peaks': atColor = np.array(Gr)/255. # color += [.25,] radius = 0.5 if atom[cs] != '': try: GL.glLoadName(atom[-3]) except: #problem with old files - missing code pass if 'balls' in atom[cs]: vdwScale = drawingData['vdwScale'] ballScale = drawingData['ballScale'] if atNum < 0: radius = 0.3 elif 'H' == atom[ct]: if drawingData['showHydrogen']: if 'vdW' in atom[cs] and atNum >= 0: radius = vdwScale*vdWRadii[atNum] else: radius = ballScale*drawingData['sizeH'] else: radius = 0.0 else: if 'vdW' in atom[cs]: radius = vdwScale*vdWRadii[atNum] else: radius = ballScale*BondRadii[atNum] RenderSphere(x,y,z,radius,atColor) if 'sticks' in atom[cs]: RenderBonds(x,y,z,Bonds,bondR,bndColor) elif 'ellipsoids' in atom[cs]: RenderBonds(x,y,z,Bonds,bondR,bndColor) if atom[cs+3] == 'A': Uij = atom[cs+5:cs+11] U = np.multiply(G2spc.Uij2U(Uij),GS) U = np.inner(Amat,np.inner(U,Amat).T) E,R = nl.eigh(U) R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) E = np.sqrt(E) if atom[ct] == 'H' and not drawingData['showHydrogen']: pass else: RenderEllipsoid(x,y,z,ellipseProb,E,R4,atColor) else: if atom[ct] == 'H' and not drawingData['showHydrogen']: pass else: radius = ellipseProb*math.sqrt(abs(atom[cs+4])) RenderSphere(x,y,z,radius,atColor) elif 'lines' in atom[cs]: radius = 0.1 RenderLines(x,y,z,Bonds,bndColor) elif atom[cs] == 'sticks': radius = 0.1 RenderBonds(x,y,z,Bonds,bondR,bndColor) elif atom[cs] == 'polyhedra': RenderPolyhedra(x,y,z,Faces,atColor) elif atom[cs] == 'backbone': if atom[ct-1].split()[0] in ['C','N']: if atom[2] not in Backbones: Backbones[atom[2]] = [] Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z])))) BackboneColor.append(list(atColor)) if generalData['Type'] == 'magnetic': magMult = drawingData.get('magMult',1.0) SymOp = int(atom[cs-1].split('+')[0]) OpNum = G2spc.GetOpNum(SymOp,SGData)-1 Moment = np.array(atom[cx+3:cx+6])*magMult color = (Wt-Bc)/255. if not SGData['SGGray'] and SpnFlp[OpNum] < 0: color = Rd/255. if SymFade and atom[cs-1] != '1': color *= .5 RenderMoment(x,y,z,Moment,color) if atom[cs+1] == 'type': RenderLabel(x,y,z,' '+atom[ct],radius,wxGreen,matRot) elif atom[cs+1] == 'name': RenderLabel(x,y,z,' '+atom[ct-1],radius,wxGreen,matRot) elif atom[cs+1] == 'number': RenderLabel(x,y,z,' '+str(iat),radius,wxGreen,matRot) elif atom[cs+1] == 'residue' and atom[ct-1] in ['CA','CA A']: RenderLabel(x,y,z,' '+atom[ct-4],radius,wxGreen,matRot) elif atom[cs+1] == '1-letter' and atom[ct-1] in ['CA','CA A']: RenderLabel(x,y,z,' '+atom[ct-3],radius,wxGreen,matRot) elif atom[cs+1] == 'chain' and atom[ct-1] in ['CA','CA A']: RenderLabel(x,y,z,' '+atom[ct-2],radius,wxGreen,matRot) # glDisable(GL_BLEND) if not FourD and len(rhoXYZ): #no green dot map for 4D - it's wrong! RenderMap(rho,rhoXYZ,indx,Rok) if len(Ind) == 1 and pageName == 'Map peaks': # one peak has been selected, show as selected by draw options PeakDistRadius = drawingData['PeakDistRadius'] atomsExpandRadius = drawingData['atomsExpandRadius'] atomsdistRadius = drawingData['atomsDistRadius'] ind = Ind[0] mag,x,y,z = mapPeaks[:,:4][ind] RenderMapPeak(x,y,z,Gr,1.0) # distances to other peaks within PeakDistRadius A if PeakDistRadius > 0: XYZ = mapPeaks.T[1:4].T Dx = XYZ-(x,y,z) dist = np.sqrt(np.sum(np.inner(Dx,Amat)**2,axis=1)) for i in ma.nonzero(ma.masked_greater(dist,PeakDistRadius))[0]: lbl = '{:.2f}'.format(dist[i]) RenderLines(x,y,z,[Dx[i]],Gr) lx,ly,lz = (x,y,z)+(Dx[i]/2) RenderLabel(lx,ly,lz,lbl,radius,wxGreen,matRot) [mag,x1,y1,z1] = mapPeaks[:,:4][i] if mag > 0.: RenderMapPeak(x1,y1,z1,Wt,mag/peakMax) else: RenderMapPeak(x1,y1,z1,Or,-2*mag/peakMax) # find and display atoms within atomsExpandRadius A if atomsExpandRadius > 0: xyzA = np.array((x,y,z)) cx,ct,cs,ci = G2phG.getAtomPtrs(data) cellArray = G2lat.CellBlock(1) radDict = dict(zip(*G2phG.getAtomRadii(data))) Names = [] Atoms = [] Radii = [] Color = [] for atomB in data['Atoms']: xyzB = np.array(atomB[cx:cx+3]) color = np.array(generalData['Color'][generalData['AtomTypes'].index(atomB[ct])])/255. result = G2spc.GenAtom(xyzB,SGData,False,6*[0.],True) for item in result: for xyz in cellArray+np.array(item[0]): dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2)) if 0 < dist <= max(atomsdistRadius,atomsExpandRadius): ax,ay,az = xyz RenderSphere(ax,ay,az,radius,color) Atoms.append(xyz) Radii.append(radDict[atomB[ct]]) Names.append(atomB[0]) Color.append(color) if dist < atomsdistRadius: RenderLines(x,y,z,[xyz-xyzA],Gr) lx,ly,lz = (xyzA+xyz)/2 lbl = '{:.2f}'.format(dist) RenderLabel(lx,ly,lz,lbl,radius,wxGreen,matRot) ax,ay,az = xyz RenderLabel(ax,ay,az,' '+atomB[0],radius,wxGreen,matRot) # find bonds bondData = [[] for i in range(len(Atoms))] Atoms = np.array(Atoms) Radii = np.array(Radii) for i,atom in enumerate(Atoms): Dx = Atoms-atom sumR = Radii + Radii[i] dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5) IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms for j in IndB[0]: bondData[i].append(Dx[j]*Radii[i]/sumR[j]) bondData[j].append(-Dx[j]*Radii[j]/sumR[j]) # draw bonds bondR = drawingData['bondRadius'] for i,xyz in enumerate(Atoms): ax,ay,az = xyz RenderBonds(ax,ay,az,bondData[i],bondR,Color[i]) elif len(mapPeaks): XYZ = mapPeaks.T[1:4].T mapBonds = FindPeaksBonds(XYZ) for ind,[mag,x,y,z] in enumerate(mapPeaks[:,:4]): if ind in Ind and pageName == 'Map peaks': RenderMapPeak(x,y,z,Gr,1.0) else: if mag > 0.: RenderMapPeak(x,y,z,Wt,mag/peakMax) else: RenderMapPeak(x,y,z,Or,-2*mag/peakMax) if showBonds: RenderLines(x,y,z,mapBonds[ind],Wt) if len(testRBObj) and pageName == 'RB Models': XYZ = G2mth.UpdateRBXYZ(Bmat,testRBObj['rbObj'],testRBObj['rbData'],testRBObj['rbType'])[0] rbBonds = FindPeaksBonds(XYZ) for ind,[x,y,z] in enumerate(XYZ): aType = testRBObj['rbAtTypes'][ind] name = ' '+aType+str(ind) color = np.array(testRBObj['AtInfo'][aType][1]) RenderSphere(x,y,z,0.2,color/255.) RenderBonds(x,y,z,rbBonds[ind],0.03,Gr) RenderLabel(x,y,z,name,0.2,wxOrange,matRot) if len(mcsaModels) > 1 and pageName == 'MC/SA': #skip the default MD entry for ind,[x,y,z] in enumerate(mcsaXYZ): aType = mcsaTypes[ind] name = ' '+aType+str(ind) color = np.array(MCSA['AtInfo'][aType][1]) RenderSphere(x,y,z,0.2,color/255.) RenderBonds(x,y,z,mcsaBonds[ind],0.03,Gr/255.) RenderLabel(x,y,z,name,0.2,wxOrange,matRot) if Backbones: for chain in Backbones: Backbone = Backbones[chain] RenderBackbone(Backbone,BackboneColor,bondR) if drawingData['unitCellBox']: RenderBox() if drawingData['Plane'][1]: H,phase,stack,phase,color = drawingData['Plane'] Planes = G2lat.PlaneIntercepts(Amat,H,phase,stack) for plane in Planes: RenderPlane(plane,color) if drawingData.get('showSlice',False): global contourSet,Zslice if len(D4mapData.get('rho',[])): #preferentially select 4D map if there modQ = np.array(generalData['SuperVec'][0]) rho = D4mapData['rho'] elif len(mapData['rho']): #ordinary 3D map rho = mapData['rho'] else: return Rmax = np.max(rho)*drawingData['contourMax'] import matplotlib.pyplot as plt Model = GL.glGetDoublev(GL.GL_MODELVIEW_MATRIX) invModel = nl.inv(Model) msize = 5. #-5A - 5A slice mRes = generalData['Map']['GridStep'] npts = int(2*msize/mRes) VP = np.array(drawingData['viewPoint'][0]) SX,SY = np.meshgrid(np.linspace(-1.,1.,npts),np.linspace(-1.,1.,npts)) SXYZ = msize*np.dstack((SX,SY,np.zeros_like(SX))) SXYZ = np.reshape(np.inner(SXYZ,invModel[:3,:3].T)+VP[nxs,nxs,:],(-1,3)) if FourD: SXYZT = np.vstack((SXYZ.T,np.inner(SXYZ,modQ)+G2frame.tau)).T Zslice = np.reshape(map_coordinates(rho,(SXYZT%1.*rho.shape).T,order=1,mode='wrap'),(npts,npts)) else: Zslice = np.reshape(map_coordinates(rho,(SXYZ%1.*rho.shape).T,order=1,mode='wrap'),(npts,npts)) Z = np.where(Zslice<=Rmax,Zslice,Rmax) plt.rcParams['figure.facecolor'] = (1.,1.,1.,.5) oldSize = plt.rcParams['figure.figsize'] plt.rcParams['figure.figsize'] = [6.0,6.0] plt.cla() contourSet = plt.contour(Z,colors='k',linewidths=1) plt.axis("off") plt.subplots_adjust(bottom=0.,top=1.,left=0.,right=1.,wspace=0.,hspace=0.) canvas = plt.get_current_fig_manager().canvas agg = canvas.switch_backends(hcCanvas) agg.draw() img, (width, height) = agg.print_to_buffer() Zimg = np.frombuffer(img, np.uint8).reshape((height, width, 4)) plt.rcParams['figure.facecolor'] = (1.,1.,1.,1.) plt.rcParams['figure.figsize'] = oldSize # agg = canvas.switch_backends(Canvas) RenderViewPlane(msize*eplane,Zimg,width,height) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Page.canvas.SwapBuffers() def OnSize(event): Draw('size') def OnFocus(event): Draw('focus') # PlotStructure starts here global mcsaXYZ,mcsaTypes,mcsaBonds,txID,contourSet,Zslice global cell, Vol, Amat, Bmat, A4mat, B4mat txID = 0 ForthirdPI = 4.0*math.pi/3.0 generalData = data['General'] cell = generalData['Cell'][1:7] ABC = np.array(cell[0:3]) Vol = generalData['Cell'][7:8][0] Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse Gmat,gmat = G2lat.cell2Gmat(cell) A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) SGData = generalData['SGData'] SpnFlp = SGData.get('SpnFlp',[1,]) atomData = data['Atoms'] mapPeaks = [] contourSet = 0 if generalData.get('DisAglCtrls',{}): BondRadii = generalData['DisAglCtrls']['BondRadii'] else: BondRadii = generalData['BondRadii'] drawingData = data['Drawing'] if not drawingData: return #nothing setup, nothing to draw G2phG.SetDrawingDefaults(drawingData) if 'Map Peaks' in data: mapPeaks = np.array(data['Map Peaks']) peakMax = 100. if len(mapPeaks): peakMax = np.max(mapPeaks.T[0]) if 'Plane' not in drawingData: drawingData['Plane'] = [[0,0,1],False,False,0.0,[255,255,0]] resRBData = data['RBModels'].get('Residue',[]) vecRBData = data['RBModels'].get('Vector',[]) rbAtmDict = {} for rbObj in resRBData+vecRBData: exclList = ['X' for i in range(len(rbObj['Ids']))] rbAtmDict.update(dict(zip(rbObj['Ids'],exclList))) testRBObj = data.get('testRBObj',{}) rbObj = testRBObj.get('rbObj',{}) MCSA = data.get('MCSA',{}) mcsaModels = MCSA.get('Models',[]) if len(mcsaModels) > 1: XYZs,Types = G2mth.UpdateMCSAxyz(Bmat,MCSA) mcsaXYZ = [] mcsaTypes = [] neqv = 0 for xyz,atyp in zip(XYZs,Types): equiv = list(G2spc.GenAtom(xyz,SGData,All=True,Move=False)) neqv = max(neqv,len(equiv)) for item in equiv: mcsaXYZ.append(item[0]) mcsaTypes.append(atyp) mcsaXYZ = np.array(mcsaXYZ) mcsaTypes = np.array(mcsaTypes) nuniq = mcsaXYZ.shape[0]//neqv mcsaXYZ = np.reshape(mcsaXYZ,(nuniq,neqv,3)) mcsaTypes = np.reshape(mcsaTypes,(nuniq,neqv)) cent = np.fix(np.sum(mcsaXYZ+2.,axis=0)/nuniq)-2 cent[0] = [0,0,0] #make sure 1st one isn't moved mcsaXYZ = np.swapaxes(mcsaXYZ,0,1)-cent[:,np.newaxis,:] mcsaTypes = np.swapaxes(mcsaTypes,0,1) mcsaXYZ = np.reshape(mcsaXYZ,(nuniq*neqv,3)) mcsaTypes = np.reshape(mcsaTypes,(nuniq*neqv)) mcsaBonds = FindPeaksBonds(mcsaXYZ) drawAtoms = drawingData.get('Atoms',[]) mapData = {'MapType':False, 'rho':[]} showBonds = False if 'Map' in generalData: mapData = generalData['Map'] showBonds = mapData.get('Show bonds',False) Wt = np.array([255,255,255]) Rd = np.array([255,0,0]) Gr = np.array([0,255,0]) wxGreen = wx.Colour(0,255,0) Bl = np.array([0,0,255]) Or = np.array([255,128,0]) wxOrange = wx.Colour(255,128,0) 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]]) eBox = np.array([[0,1],[0,0],[1,0],[1,1],]) eplane = np.array([[-1,-1,0],[-1,1,0],[1,1,0],[1,-1,0]]) uEdges = np.array([ [uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]], [uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]], [uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]]) mD = 0.1 mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]]) mapPeakVecs = np.inner(mV,Bmat) backColor = np.array(list(drawingData['backColor'])+[0,]) Bc = np.array(list(drawingData['backColor'])) uColors = [Rd,Gr,Bl,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc] G2frame.tau = 0. G2frame.seq = 0 new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(generalData['Name'],'ogl') if new: Page.views = False Font = Page.GetFont() Page.Choice = None choice = [' save as/key:','jpeg','tiff','bmp','c: center on 1/2,1/2,1/2'] if mapData['MapType']: choice += ['k: toggle contour plot',] if mapData.get('Flip',False): choice += ['u: roll up','d: roll down','l: roll left','r: roll right'] else: choice += ['n: next','p: previous'] if generalData['Modulated'] and len(drawAtoms): choice += ['+: increase tau','-: decrease tau','0: set tau = 0'] Tx,Ty,Tz = drawingData['viewPoint'][0] rho = G2mth.getRho([Tx,Ty,Tz],mapData) G2frame.G2plotNB.status.SetStatusText('View point: %.4f, %.4f, %.4f; density: %.4f'%(Tx,Ty,Tz,rho),1) cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice) cb.Bind(wx.EVT_COMBOBOX, OnKeyBox) cb.SetValue(' save as/key:') Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_KEY_UP, OnKey) Page.canvas.Bind(wx.EVT_KEY_DOWN,OnKeyPressed) Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove) Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel) Page.canvas.Bind(wx.EVT_SIZE, OnSize) Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus) Page.camera['position'] = drawingData['cameraPos'] Page.camera['viewPoint'] = np.inner(Amat,drawingData['viewPoint'][0]) Page.camera['backColor'] = backColor/255. try: Page.canvas.SetCurrent() except: pass wx.CallAfter(Draw,'main') # on Mac (& Linux?) the structure must be drawn twice the first time that graphics are displayed if firstCall: Draw('main') # redraw return Draw,['main'] ################################################################################ #### Plot Bead Model ################################################################################ def PlotBeadModel(G2frame,Atoms,defaults,PDBtext): '''Bead modelplotting package. For bead models from SHAPES ''' def OnMouseDown(event): xy = event.GetPosition() defaults['oldxy'] = list(xy) def OnMouseMove(event): newxy = event.GetPosition() if event.Dragging(): if event.LeftIsDown(): SetRotation(newxy) Q = defaults['Quaternion'] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) # elif event.RightIsDown(): # SetRBOrigin(newxy) elif event.MiddleIsDown(): SetRotationZ(newxy) Q = defaults['Quaternion'] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) Draw('move') def OnMouseWheel(event): defaults['cameraPos'] += event.GetWheelRotation()/24 defaults['cameraPos'] = max(10,min(500,defaults['cameraPos'])) G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1) Draw('wheel') def SetBackground(): R,G,B,A = Page.camera['backColor'] GL.glClearColor(R,G,B,A) GL.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT) def SetLights(): GL.glEnable(GL.GL_DEPTH_TEST) GL.glShadeModel(GL.GL_FLAT) GL.glEnable(GL.GL_LIGHTING) GL.glEnable(GL.GL_LIGHT0) GL.glLightModeli(GL.GL_LIGHT_MODEL_TWO_SIDE,0) GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[1,1,1,.8]) GL.glLightfv(GL.GL_LIGHT0,GL.GL_DIFFUSE,[1,1,1,1]) def SetRotation(newxy): #first get rotation vector in screen coords. & angle increment oldxy = defaults['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! defaults['oldxy'] = list(newxy) V = np.array([dxy[1],dxy[0],0.]) A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) # next transform vector back to xtal coordinates via inverse quaternion # & make new quaternion Q = defaults['Quaternion'] V = G2mth.prodQVQ(G2mth.invQ(Q),V) DQ = G2mth.AVdeg2Q(A,V) Q = G2mth.prodQQ(Q,DQ) defaults['Quaternion'] = Q # finally get new view vector - last row of rotation matrix VD = G2mth.Q2Mat(Q)[2] VD /= np.sqrt(np.sum(VD**2)) defaults['viewDir'] = VD def SetRotationZ(newxy): #first get rotation vector (= view vector) in screen coords. & angle increment View = GL.glGetIntegerv(GL.GL_VIEWPORT) cent = [View[2]/2,View[3]/2] oldxy = defaults['oldxy'] if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy defaults['oldxy'] = list(newxy) V = defaults['viewDir'] A = [0,0] A[0] = dxy[1]*.25 A[1] = dxy[0]*.25 if newxy[0] > cent[0]: A[0] *= -1 if newxy[1] < cent[1]: A[1] *= -1 # next transform vector back to xtal coordinates & make new quaternion Q = defaults['Quaternion'] Qx = G2mth.AVdeg2Q(A[0],V) Qy = G2mth.AVdeg2Q(A[1],V) Q = G2mth.prodQQ(Q,Qx) Q = G2mth.prodQQ(Q,Qy) defaults['Quaternion'] = Q def RenderUnitVectors(x,y,z): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(1) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glBegin(GL.GL_LINES) for line,color in zip(uEdges,uColors): GL.glColor3ubv(color) GL.glVertex3fv(-line[1]) GL.glVertex3fv(line[1]) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderSphere(x,y,z,radius,color): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) q = GLU.gluNewQuadric() GLU.gluSphere(q,radius,40,20) GL.glPopMatrix() def Draw(caller=''): #useful debug? # if caller: # print caller # end of useful debug cPos = defaults['cameraPos'] VS = np.array(Page.canvas.GetSize()) aspect = float(VS[0])/float(VS[1]) Q = defaults['Quaternion'] SetBackground() GL.glInitNames() GL.glPushName(0) GL.glMatrixMode(GL.GL_PROJECTION) GL.glLoadIdentity() GL.glViewport(0,0,VS[0],VS[1]) GLU.gluPerspective(50.,aspect,1.,500.) GLU.gluLookAt(0,0,cPos,0,0,0,0,1,0) SetLights() GL.glMatrixMode(GL.GL_MODELVIEW) GL.glLoadIdentity() matRot = G2mth.Q2Mat(Q) matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) GL.glMultMatrixf(matRot.T) RenderUnitVectors(0.,0.,0.) radius = 2.0 for iat,atom in enumerate(XYZ): x,y,z = atom color = np.array([144,144,144])/255. RenderSphere(x,y,z,radius,color) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Page.canvas.SwapBuffers() def OnSize(event): Draw('size') def OnFocus(event): Draw('focus') def OnKeyBox(event): mode = cb.GetValue() if mode in ['jpeg','bmp','tiff',]: try: import Image as Im except ImportError: try: from PIL import Image as Im except ImportError: print ("PIL/pillow Image module not present. Cannot save images without this") raise Exception("PIL/pillow Image module not found") Fname = os.path.join(Mydir,Page.name+'.'+mode) print (Fname+' saved') size = Page.canvas.GetSize() GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1) Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB, GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) try: im.frombytes(Pix) except AttributeError: im.fromstring(Pix) im = im.transpose(Im.FLIP_TOP_BOTTOM) im.save(Fname,mode) cb.SetValue(' save as/key:') G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1) elif mode == 'pdb': Fname = os.path.join(Mydir,Page.name+'.'+mode) PDB = open(Fname,'w') PDB.write('REMARK '+PDBtext+'\n') for iatm,xyz in enumerate(XYZ): PDB.write('ATOM %4d CA ALA A%4d %8.3f%8.3f%8.3f 1.00 0.00\n'%(iatm+1,iatm+1,xyz[0],xyz[1],xyz[2])) PDB.close() G2frame.G2plotNB.status.SetStatusText('PDB model saved to: '+Fname,1) # PlotBeadModel execution starts here Mydir = G2frame.dirname Rd = np.array([255,0,0]) Gr = np.array([0,255,0]) Bl = np.array([0,0,255]) uBox = np.array([[0,0,0],[50,0,0],[0,50,0],[0,0,50]]) uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]]) uColors = [Rd,Gr,Bl] XYZ = np.array(Atoms[1:]).T #don't mess with original! new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Bead model','ogl') if new: Page.views = False Page.name = Atoms[0] Page.Choice = None choice = [' save as:','jpeg','tiff','bmp','pdb',] cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice) cb.Bind(wx.EVT_COMBOBOX, OnKeyBox) cb.SetValue(' save as/key:') Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel) Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove) Page.canvas.Bind(wx.EVT_SIZE, OnSize) Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus) Page.camera['position'] = defaults['cameraPos'] Page.camera['backColor'] = np.array([0,0,0,0]) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Draw('main') Draw('main') #to fill both buffers so save works ################################################################################ #### Plot Rigid Body ################################################################################ def PlotRigidBody(G2frame,rbType,AtInfo,rbData,defaults): '''RB plotting package. Can show rigid body structures as balls & sticks ''' def FindBonds(XYZ): rbTypes = rbData['rbTypes'] Radii = [] for Atype in rbTypes: Radii.append(AtInfo[Atype][0]) if Atype == 'H': Radii[-1] = 0.5 Radii = np.array(Radii) Bonds = [[] for i in range(len(Radii))] for i,xyz in enumerate(XYZ): Dx = XYZ-xyz dist = np.sqrt(np.sum(Dx**2,axis=1)) sumR = Radii[i]+Radii IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.)) for j in IndB[0]: Bonds[i].append(Dx[j]*Radii[i]/sumR[j]) Bonds[j].append(-Dx[j]*Radii[j]/sumR[j]) return Bonds # def SetRBOrigin(): # page = getSelection() # if page: # if G2frame.GetPageText(page) == 'Rigid bodies': # G2frame.MapPeaksTable.SetData(mapPeaks) # panel = G2frame.GetPage(page).GetChildren() # names = [child.GetName() for child in panel] # panel[names.index('grid window')].Refresh() def OnMouseDown(event): xy = event.GetPosition() defaults['oldxy'] = list(xy) def OnMouseMove(event): newxy = event.GetPosition() if event.Dragging(): if event.LeftIsDown(): SetRotation(newxy) Q = defaults['Quaternion'] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) # elif event.RightIsDown(): # SetRBOrigin(newxy) elif event.MiddleIsDown(): SetRotationZ(newxy) Q = defaults['Quaternion'] G2frame.G2plotNB.status.SetStatusText('New quaternion: %.2f+, %.2fi+ ,%.2fj+, %.2fk'%(Q[0],Q[1],Q[2],Q[3]),1) Draw('move') def OnMouseWheel(event): defaults['cameraPos'] += event.GetWheelRotation()/24 defaults['cameraPos'] = max(10,min(500,defaults['cameraPos'])) G2frame.G2plotNB.status.SetStatusText('New camera distance: %.2f'%(defaults['cameraPos']),1) Draw('wheel') def SetBackground(): R,G,B,A = Page.camera['backColor'] GL.glClearColor(R,G,B,A) GL.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT) def SetLights(): GL.glEnable(GL.GL_DEPTH_TEST) GL.glShadeModel(GL.GL_FLAT) GL.glEnable(GL.GL_LIGHTING) GL.glEnable(GL.GL_LIGHT0) GL.glLightModeli(GL.GL_LIGHT_MODEL_TWO_SIDE,0) GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[1,1,1,.8]) GL.glLightfv(GL.GL_LIGHT0,GL.GL_DIFFUSE,[1,1,1,1]) def SetRotation(newxy): #first get rotation vector in screen coords. & angle increment oldxy = defaults['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! defaults['oldxy'] = list(newxy) V = np.array([dxy[1],dxy[0],0.]) A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) # next transform vector back to xtal coordinates via inverse quaternion # & make new quaternion Q = defaults['Quaternion'] V = G2mth.prodQVQ(G2mth.invQ(Q),V) DQ = G2mth.AVdeg2Q(A,V) Q = G2mth.prodQQ(Q,DQ) defaults['Quaternion'] = Q # finally get new view vector - last row of rotation matrix VD = G2mth.Q2Mat(Q)[2] VD /= np.sqrt(np.sum(VD**2)) defaults['viewDir'] = VD def SetRotationZ(newxy): #first get rotation vector (= view vector) in screen coords. & angle increment View = GL.glGetIntegerv(GL.GL_VIEWPORT) cent = [View[2]/2,View[3]/2] oldxy = defaults['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! defaults['oldxy'] = list(newxy) V = defaults['viewDir'] A = [0,0] A[0] = dxy[1]*.25 A[1] = dxy[0]*.25 if newxy[0] > cent[0]: A[0] *= -1 if newxy[1] < cent[1]: A[1] *= -1 # next transform vector back to xtal coordinates & make new quaternion Q = defaults['Quaternion'] Qx = G2mth.AVdeg2Q(A[0],V) Qy = G2mth.AVdeg2Q(A[1],V) Q = G2mth.prodQQ(Q,Qx) Q = G2mth.prodQQ(Q,Qy) defaults['Quaternion'] = Q def RenderUnitVectors(x,y,z): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(1) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glBegin(GL.GL_LINES) for line,color in zip(uEdges,uColors): GL.glColor3ubv(color) GL.glVertex3fv(-line[1]) GL.glVertex3fv(line[1]) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderSphere(x,y,z,radius,color): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) q = GLU.gluNewQuadric() GLU.gluSphere(q,radius,20,10) GL.glPopMatrix() def RenderBonds(x,y,z,Bonds,radius,color,slice=20): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) for Dx in Bonds: GL.glPushMatrix() Z = np.sqrt(np.sum(Dx**2)) if Z: azm = atan2d(-Dx[1],-Dx[0]) phi = acosd(Dx[2]/Z) GL.glRotate(-azm,0,0,1) GL.glRotate(phi,1,0,0) q = GLU.gluNewQuadric() GLU.gluCylinder(q,radius,radius,Z,slice,2) GL.glPopMatrix() GL.glPopMatrix() def RenderLabel(x,y,z,label,matRot): GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glDisable(GL.GL_LIGHTING) GL.glRasterPos3f(0,0,0) GL.glMultMatrixf(matRot) GL.glRotate(180,1,0,0) #fix to flip about x-axis text = gltext.TextElement(text=label,font=Font,foreground=wx.WHITE) text.draw_text(scale=0.025) GL.glEnable(GL.GL_LIGHTING) GL.glPopMatrix() def Draw(caller=''): #useful debug? # if caller: # print caller # end of useful debug cPos = defaults['cameraPos'] VS = np.array(Page.canvas.GetSize()) aspect = float(VS[0])/float(VS[1]) Q = defaults['Quaternion'] SetBackground() GL.glInitNames() GL.glPushName(0) GL.glMatrixMode(GL.GL_PROJECTION) GL.glLoadIdentity() GL.glViewport(0,0,VS[0],VS[1]) GLU.gluPerspective(20.,aspect,1.,500.) GLU.gluLookAt(0,0,cPos,0,0,0,0,1,0) SetLights() GL.glMatrixMode(GL.GL_MODELVIEW) GL.glLoadIdentity() matRot = G2mth.Q2Mat(Q) matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) GL.glMultMatrixf(matRot.T) RenderUnitVectors(0.,0.,0.) radius = 0.2 s = 1 selected = rbData.get('Selection') if len(XYZ) != len(rbData['rbTypes']): # H atoms have been removed return for iat,atom in enumerate(XYZ): if selected: if selected[iat]: s = 1 else: s = 3 x,y,z = atom CL = AtInfo[rbData['rbTypes'][iat]][1] color = np.array(CL)/(s*255.) RenderSphere(x,y,z,radius,color) RenderBonds(x,y,z,Bonds[iat],0.05,color) RenderLabel(x,y,z,' '+atNames[iat],matRot) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Page.canvas.SwapBuffers() def OnSize(event): Draw('size') def OnFocus(event): Draw('focus') def OnKeyBox(event): mode = cb.GetValue() if mode in ['jpeg','bmp','tiff',]: try: import Image as Im except ImportError: try: from PIL import Image as Im except ImportError: print ("PIL/pillow Image module not present. Cannot save images without this") raise Exception("PIL/pillow Image module not found") Fname = os.path.join(Mydir,Page.name+'.'+mode) print (Fname+' saved') size = Page.canvas.GetSize() GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1) Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB, GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) try: im.frombytes(Pix) except AttributeError: im.fromstring(Pix) im = im.transpose(Im.FLIP_TOP_BOTTOM) im.save(Fname,mode) cb.SetValue(' save as/key:') G2frame.G2plotNB.status.SetStatusText('Drawing saved to: '+Fname,1) def UpdateDraw(): '''This updates the drawing arrays in place''' for i,Ty in enumerate(rbData['rbTypes']): atNames[i] = str(i)+':'+Ty for i in range(len(XYZ)): XYZ[i].fill(0) for imag,mag in enumerate(rbData['VectMag']): XYZ[i] += mag*rbData['rbVect'][imag][i] # number of bonds should not change (=# of atoms) newBonds = FindBonds(XYZ) for i in range(len(Bonds)): Bonds[i] = newBonds[i] Draw() # drawing twice seems needed sometimes at least on mac Draw() # PlotRigidBody execution starts here Mydir = G2frame.dirname Rd = np.array([255,0,0]) Gr = np.array([0,255,0]) Bl = np.array([0,80,255]) # blue on black is hard to see uBox = np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1]]) uEdges = np.array([[uBox[0],uBox[1]],[uBox[0],uBox[2]],[uBox[0],uBox[3]]]) uColors = [Rd,Gr,Bl] if rbType == 'Vector': atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['rbTypes'])] XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']]) for imag,mag in enumerate(rbData['VectMag']): XYZ += mag*rbData['rbVect'][imag] Bonds = FindBonds(XYZ) elif rbType == 'Residue': # atNames = [str(i)+':'+Ty for i,Ty in enumerate(rbData['atNames'])] atNames = rbData['atNames'] XYZ = np.copy(rbData['rbXYZ']) #don't mess with original! Seq = rbData['rbSeq'] for ia,ib,ang,mv in Seq: va = XYZ[ia]-XYZ[ib] Q = G2mth.AVdeg2Q(ang,va) for im in mv: vb = XYZ[im]-XYZ[ib] vb = G2mth.prodQVQ(Q,vb) XYZ[im] = XYZ[ib]+vb Bonds = FindBonds(XYZ) elif rbType == 'Z-matrix': pass else: print('rbType=', rbType) if GSASIIpath.GetConfigValue('debug'): raise Exception('Should not happen') new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Rigid body','ogl') if new: Page.views = False Page.name = rbData['RBname'] Page.Choice = None choice = [' save as:','jpeg','tiff','bmp',] cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice) cb.Bind(wx.EVT_COMBOBOX, OnKeyBox) cb.SetValue(' save as/key:') Font = Page.GetFont() Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel) Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove) Page.canvas.Bind(wx.EVT_SIZE, OnSize) Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus) Page.camera['position'] = defaults['cameraPos'] Page.camera['backColor'] = np.array([0,0,0,0]) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Draw('main') Draw('main') #to fill both buffers so save works if rbType == 'Vector': return UpdateDraw ################################################################################ #### Plot Layers ################################################################################ def PlotLayers(G2frame,Layers,laySeq,defaults): '''Layer plotting package. Can show layer structures as balls & sticks ''' global AtNames,AtTypes,XYZ,Bonds,Faces def FindBonds(atTypes,XYZ): Radii = [] for Atype in atTypes: Radii.append(AtInfo[Atype[0]]['Drad']) if Atype[0] == 'H': Radii[-1] = 0.5 Radii = np.array(Radii) Bonds = [[] for i in range(len(Radii))] for i,xyz in enumerate(XYZ): Dx = np.inner(Amat,(XYZ-xyz)).T dist = np.sqrt(np.sum(Dx**2,axis=1)) sumR = Radii[i]+Radii IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.)) for j in IndB[0]: Bonds[i].append(Dx[j]*Radii[i]/sumR[j]) Bonds[j].append(-Dx[j]*Radii[j]/sumR[j]) return Bonds def FindFaces(Bonds): Faces = [] for bonds in Bonds: faces = [] if len(bonds) > 2: FaceGen = G2lat.uniqueCombinations(bonds,3) #N.B. this is a generator for face in FaceGen: vol = nl.det(face) if abs(vol) > .5 or len(bonds) == 3: if vol < 0.: face = [face[0],face[2],face[1]] face = 1.8*np.array(face) if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in bonds]).any(): norm = np.cross(face[1]-face[0],face[2]-face[0]) norm /= np.sqrt(np.sum(norm**2)) faces.append([face,norm]) Faces.append(faces) return Faces def getAtoms(): global AtNames,AtTypes,XYZ,Bonds,Faces AtNames = [] AtTypes = [] newXYZ = np.zeros((0,3)) TX = np.zeros(3) for il in range(len(laySeq)): layer = laySeq[il] if Layers['Layers'][layer]['SameAs']: layer = Names.index(Layers['Layers'][layer]['SameAs']) atNames = [atom[0] for atom in Layers['Layers'][layer]['Atoms']] atTypes = [[atom[1],il] for atom in Layers['Layers'][layer]['Atoms']] XYZ = np.array([atom[2:5] for atom in Layers['Layers'][layer]['Atoms']]) if '-1' in Layers['Layers'][layer]['Symm']: atNames += atNames atTypes += atTypes XYZ = np.concatenate((XYZ,-XYZ)) if il: TX += np.array(Trans[laySeq[il-1]][laySeq[il]][1:4]) # TX[0] %= 1. # TX[1] %= 1. XYZ += TX AtNames += atNames AtTypes += atTypes newXYZ = np.concatenate((newXYZ,XYZ)) XYZ = newXYZ na = max(int(8./cell[0]),1) nb = max(int(8./cell[1]),1) indA = range(-na,na) indB = range(-nb,nb) Units = np.array([[h,k,0] for h in indA for k in indB]) newXYZ = np.zeros((0,3)) for unit in Units: newXYZ = np.concatenate((newXYZ,unit+XYZ)) if len(Units): AtNames *= len(Units) AtTypes *= len(Units) XYZ = newXYZ # GSASIIpath.IPyBreak() Bonds = FindBonds(AtTypes,XYZ) Faces = FindFaces(Bonds) def OnKeyBox(event): mode = cb.GetValue() if mode in ['jpeg','bmp','tiff',]: try: import Image as Im except ImportError: try: from PIL import Image as Im except ImportError: print ("PIL/pillow Image module not present. Cannot save images without this") raise Exception("PIL/pillow Image module not found") projFile = G2frame.GSASprojectfile Fname = (os.path.splitext(projFile)[0]+'.'+mode).replace('*','+') size = Page.canvas.GetSize() GL.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1) Pix = GL.glReadPixels(0,0,size[0],size[1],GL.GL_RGB, GL.GL_UNSIGNED_BYTE) im = Im.new("RGB", (size[0],size[1])) try: im.frombytes(Pix) except AttributeError: im.fromstring(Pix) im = im.transpose(Im.FLIP_TOP_BOTTOM) im.save(Fname,mode) print (' Drawing saved to: '+Fname) elif mode[0] in ['L','F','P']: event.key = cb.GetValue()[0] wx.CallAfter(OnPlotKeyPress,event) Page.canvas.SetFocus() # redirect the Focus from the button back to the plot def OnPlotKeyPress(event): global AtNames,AtTypes,XYZ,Bonds try: key = event.GetKeyCode() if key > 255: key = 0 keyCode = chr(key) except AttributeError: #if from OnKeyBox above keyCode = str(event.key).upper() dx = 0. dy = 0. dz = 0. if keyCode == 'L': Page.labels = not Page.labels Draw('labels') return elif keyCode =='F' and len(laySeq) == 2: Page.fade = not Page.fade elif keyCode == 'P': Page.poly = not Page.poly if len(laySeq) != 2: return Trans = Layers['Transitions'] Yi,Xi = laySeq dxyz = 0.01 if keyCode == 'X': dx = dxyz if event.shiftDown: dx *= -1. Trans[Yi][Xi][1] += dx SetTransText(Yi,Xi,Trans[Yi][Xi],1) elif keyCode == 'Y': dy = dxyz if event.shiftDown: dy *= -1. Trans[Yi][Xi][2] += dy SetTransText(Yi,Xi,Trans[Yi][Xi],2) elif keyCode == 'Z': dz = dxyz if event.shiftDown: dz *= -1. Trans[Yi][Xi][3] += dz SetTransText(Yi,Xi,Trans[Yi][Xi],3) getAtoms() Draw('shift') def SetTransText(Yi,Xi,XYZ,id): page = G2frame.phaseDisplay.GetSelection() if page: if G2frame.phaseDisplay.GetPageText(page) == 'Layers': G2frame.phaseDisplay.GetPage(page).transGrids[Yi].Refresh() def OnMouseDown(event): xy = event.GetPosition() defaults['oldxy'] = list(xy) def OnMouseMove(event): newxy = event.GetPosition() if event.Dragging(): if event.LeftIsDown(): SetRotation(newxy) elif event.RightIsDown(): SetTranslation(newxy) Tx,Ty,Tz = defaults['viewPoint'][0] elif event.MiddleIsDown(): SetRotationZ(newxy) Draw('move') def OnMouseWheel(event): defaults['cameraPos'] += event.GetWheelRotation()/24 defaults['cameraPos'] = max(10,min(500,defaults['cameraPos'])) Draw('wheel') def SetBackground(): R,G,B,A = Page.camera['backColor'] GL.glClearColor(R,G,B,A) GL.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT) def SetLights(): GL.glEnable(GL.GL_DEPTH_TEST) GL.glShadeModel(GL.GL_FLAT) GL.glEnable(GL.GL_LIGHTING) GL.glEnable(GL.GL_LIGHT0) GL.glLightModeli(GL.GL_LIGHT_MODEL_TWO_SIDE,0) GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[1,1,1,.8]) GL.glLightfv(GL.GL_LIGHT0,GL.GL_DIFFUSE,[1,1,1,1]) def SetTranslation(newxy): #first get translation vector in screen coords. oldxy = defaults['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy defaults['oldxy'] = list(newxy) V = np.array([-dxy[0],dxy[1],0.]) #then transform to rotated crystal coordinates & apply to view point Q = defaults['Quaternion'] V = np.inner(Bmat,G2mth.prodQVQ(G2mth.invQ(Q),V)) Tx,Ty,Tz = defaults['viewPoint'][0] delt = 0.01 Tx += V[0]*delt Ty += V[1]*delt Tz += V[2]*delt defaults['viewPoint'][0] = np.array([Tx,Ty,Tz]) def SetRotation(newxy): #first get rotation vector in screen coords. & angle increment oldxy = defaults['oldxy'] if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! defaults['oldxy'] = list(newxy) V = np.array([dxy[1],dxy[0],0.]) A = 0.25*np.sqrt(dxy[0]**2+dxy[1]**2) # next transform vector back to xtal coordinates via inverse quaternion # & make new quaternion Q = defaults['Quaternion'] V = G2mth.prodQVQ(G2mth.invQ(Q),V) DQ = G2mth.AVdeg2Q(A,V) Q = G2mth.prodQQ(Q,DQ) defaults['Quaternion'] = Q # finally get new view vector - last row of rotation matrix VD = G2mth.Q2Mat(Q)[2] VD /= np.sqrt(np.sum(VD**2)) defaults['viewDir'] = VD def SetRotationZ(newxy): #first get rotation vector (= view vector) in screen coords. & angle increment View = GL.glGetIntegerv(GL.GL_VIEWPORT) cent = [View[2]/2,View[3]/2] oldxy = defaults['oldxy'] if dxy[0] == dxy[1] == 0: return # on Mac motion can be less than a full pixel! if not len(oldxy): oldxy = list(newxy) dxy = newxy-oldxy defaults['oldxy'] = list(newxy) V = defaults['viewDir'] A = [0,0] A[0] = dxy[1]*.25 A[1] = dxy[0]*.25 if newxy[0] > cent[0]: A[0] *= -1 if newxy[1] < cent[1]: A[1] *= -1 # next transform vector back to xtal coordinates & make new quaternion Q = defaults['Quaternion'] Qx = G2mth.AVdeg2Q(A[0],V) Qy = G2mth.AVdeg2Q(A[1],V) Q = G2mth.prodQQ(Q,Qx) Q = G2mth.prodQQ(Q,Qy) defaults['Quaternion'] = Q def RenderUnitVectors(x,y,z): GL.glEnable(GL.GL_COLOR_MATERIAL) GL.glLineWidth(1) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glBegin(GL.GL_LINES) for line,color in zip(uEdges,uColors): GL.glColor3ubv(color) GL.glVertex3fv(line[0]) GL.glVertex3fv(line[1]) GL.glEnd() GL.glPopMatrix() GL.glColor4ubv([0,0,0,0]) GL.glDisable(GL.GL_COLOR_MATERIAL) def RenderSphere(x,y,z,radius,color): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) q = GLU.gluNewQuadric() GLU.gluSphere(q,radius,20,10) GL.glPopMatrix() def RenderBonds(x,y,z,Bonds,radius,color,slice=20): GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) for Dx in Bonds: GL.glPushMatrix() Z = np.sqrt(np.sum(Dx**2)) if Z: azm = atan2d(-Dx[1],-Dx[0]) phi = acosd(Dx[2]/Z) GL.glRotate(-azm,0,0,1) GL.glRotate(phi,1,0,0) q = GLU.gluNewQuadric() GLU.gluCylinder(q,radius,radius,Z,slice,2) GL.glPopMatrix() GL.glPopMatrix() def RenderPolyhedra(x,y,z,Faces,color): GL.glShadeModel(GL.GL_FLAT) GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color) GL.glShadeModel(GL.GL_SMOOTH) GL.glMultMatrixf(B4mat.T) for face,norm in Faces: GL.glPolygonMode(GL.GL_FRONT_AND_BACK,GL.GL_FILL) GL.glFrontFace(GL.GL_CW) GL.glNormal3fv(norm) GL.glBegin(GL.GL_TRIANGLES) for vert in face: GL.glVertex3fv(vert) GL.glEnd() GL.glPopMatrix() GL.glShadeModel(GL.GL_SMOOTH) def RenderLabel(x,y,z,label,matRot): GL.glPushMatrix() GL.glTranslate(x,y,z) GL.glMultMatrixf(B4mat.T) GL.glDisable(GL.GL_LIGHTING) GL.glRasterPos3f(0,0,0) GL.glMultMatrixf(matRot) GL.glRotate(180,1,0,0) #fix to flip about x-axis text = gltext.TextElement(text=label,font=Font,foreground=wx.WHITE) text.draw_text(scale=0.025) GL.glEnable(GL.GL_LIGHTING) GL.glPopMatrix() def Draw(caller=''): #useful debug? # if caller: # print caller # end of useful debug global AtNames,AtTypes,XYZ,Bonds,Faces cPos = defaults['cameraPos'] VS = np.array(Page.canvas.GetSize()) aspect = float(VS[0])/float(VS[1]) Tx,Ty,Tz = defaults['viewPoint'][0] Q = defaults['Quaternion'] SetBackground() GL.glInitNames() GL.glPushName(0) GL.glMatrixMode(GL.GL_PROJECTION) GL.glLoadIdentity() GL.glViewport(0,0,VS[0],VS[1]) GLU.gluPerspective(20.,aspect,1.,500.) GLU.gluLookAt(0,0,cPos,0,0,0,0,1,0) SetLights() GL.glMatrixMode(GL.GL_MODELVIEW) GL.glLoadIdentity() matRot = G2mth.Q2Mat(Q) matRot = np.concatenate((np.concatenate((matRot,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) GL.glMultMatrixf(matRot.T) GL.glMultMatrixf(A4mat.T) GL.glTranslate(-Tx,-Ty,-Tz) RenderUnitVectors(0.,0.,0.) bondRad = 0.1 atomRad = 0.5 if Page.labels: bondRad = 0.05 atomRad = 0.2 GL.glShadeModel(GL.GL_SMOOTH) for iat,atom in enumerate(XYZ): x,y,z = atom CL = AtInfo[AtTypes[iat][0]]['Color'] color = np.array(CL)/255. if len(laySeq) == 2 and AtTypes[iat][1] and Page.fade: color *= .5 if Page.poly: if len(Faces[iat])>16: #allows tetrahedra but not stray triangles RenderPolyhedra(x,y,z,Faces[iat],color) else: RenderSphere(x,y,z,atomRad,color) RenderBonds(x,y,z,Bonds[iat],bondRad,color) if Page.labels: RenderLabel(x,y,z,' '+AtNames[iat],matRot) try: if Page.context: Page.canvas.SetCurrent(Page.context) except: pass Page.canvas.SwapBuffers() def OnSize(event): Draw('size') def OnFocus(event): Draw('focus') # PlotLayers execution starts here cell = Layers['Cell'][1:7] Amat,Bmat = G2lat.cell2AB(cell) #Amat - crystal to cartesian, Bmat - inverse A4mat = np.concatenate((np.concatenate((Amat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) B4mat = np.concatenate((np.concatenate((Bmat,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0) Trans = Layers['Transitions'] Wt = np.array([255,255,255]) Rd = np.array([255,0,0]) Gr = np.array([0,255,0]) Bl = np.array([0,0,255]) Bc = np.array([0,0,0]) 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]]) uEdges = np.array([ [uBox[0],uBox[1]],[uBox[0],uBox[3]],[uBox[0],uBox[4]],[uBox[1],uBox[2]], [uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]], [uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]]) uColors = [Rd,Gr,Bl,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc, Wt-Bc,Wt-Bc,Wt-Bc,Wt-Bc] uEdges[2][1][2] = len(laySeq) AtInfo = Layers['AtInfo'] Names = [layer['Name'] for layer in Layers['Layers']] getAtoms() new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('Layer','ogl') if new: Page.views = False Page.labels = False Page.fade = False Page.poly = False choice = [' save as:','jpeg','tiff','bmp','use keys for:','L - toggle labels', 'F - fade 2nd layer','P - polyhedra'] if len(laySeq) == 2: choice += ['F - toggle fade','X/shift-X move Dx','Y/shift-Y move Dy','Z/shift-Z move Dz'] Page.keyPress = OnPlotKeyPress Font = Page.GetFont() cb = wx.ComboBox(G2frame.G2plotNB.status,style=wx.CB_DROPDOWN|wx.CB_READONLY,choices=choice) cb.Bind(wx.EVT_COMBOBOX, OnKeyBox) text = [str(Layers['Layers'][seq]['Name']) for seq in laySeq] G2frame.G2plotNB.status.SetStatusText(' Layers plotted: '+str(text).replace("'",'')[1:-1],1) Page.canvas.Bind(wx.EVT_MOUSEWHEEL, OnMouseWheel) Page.canvas.Bind(wx.EVT_LEFT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_RIGHT_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MIDDLE_DOWN, OnMouseDown) Page.canvas.Bind(wx.EVT_MOTION, OnMouseMove) Page.canvas.Bind(wx.EVT_KEY_UP, OnPlotKeyPress) Page.canvas.Bind(wx.EVT_SIZE, OnSize) Page.canvas.Bind(wx.EVT_SET_FOCUS, OnFocus) Page.camera['position'] = defaults['cameraPos'] Page.camera['backColor'] = np.array([0,0,0,0]) Page.context = wx.glcanvas.GLContext(Page.canvas) Page.canvas.SetCurrent(Page.context) wx.CallAfter(Draw,'main') def PlotFPAconvolutors(G2frame,NISTpk): '''Plot the convolutions used for the current peak computed with :func:GSASIIfpaGUI.doFPAcalc ''' import NIST_profile as FP new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('FPA convolutors','mpl') Page.SetToolTipString('') cntr = NISTpk.twotheta_window_center_deg Plot.set_title('Peak convolution functions @ 2theta={:.3f}'.format(cntr)) Plot.set_xlabel(r'$\Delta 2\theta, deg$',fontsize=14) Plot.set_ylabel(r'Intensity (arbitrary)',fontsize=14) # refColors=['b','r','c','g','m','k'] refColors = ['xkcd:blue','xkcd:red','xkcd:green','xkcd:cyan','xkcd:magenta','xkcd:black', 'xkcd:pink','xkcd:brown','xkcd:teal','xkcd:orange','xkcd:grey','xkcd:violet',] ttmin = ttmax = 0 #GSASIIpath.IPyBreak() i = -1 for conv in NISTpk.convolvers: if 'smoother' in conv: continue if 'crystallite_size' in conv: continue f = NISTpk.convolver_funcs[conv]() if f is None: continue i += 1 FFT = FP.best_irfft(f) if f[1].real > 0: FFT = np.roll(FFT,int(len(FFT)/2.)) FFT /= FFT.max() ttArr = np.linspace(-NISTpk.twotheta_window_fullwidth_deg/2, NISTpk.twotheta_window_fullwidth_deg/2,len(FFT)) ttmin = min(ttmin,ttArr[np.argmax(FFT>.005)]) ttmax = max(ttmax,ttArr[::-1][np.argmax(FFT[::-1]>.005)]) color = refColors[i%len(refColors)] Plot.plot(ttArr,FFT,color,label=conv[5:]) legend = Plot.legend(loc='best') SetupLegendPick(legend,new) Page.toolbar.push_current() Plot.set_xlim((ttmin,ttmax)) Page.toolbar.push_current() Page.toolbar.draw() Page.canvas.draw() def SetupLegendPick(legend,new,delay=5): legend.delay = delay*1000 # Hold time in ms for clear; 0 == forever for line in legend.get_lines(): line.set_picker(4) # bug: legend items with single markers don't seem to respond to a "pick" #GSASIIpath.IPyBreak() for txt in legend.get_texts(): txt.set_picker(4) if new: legend.figure.canvas.mpl_connect('pick_event',onLegendPick) def onLegendPick(event): '''When a line in the legend is selected, find the matching line in the plot and then highlight it by adding/enlarging markers. Set up a timer to make a reset after delay selected in SetupLegendPick ''' def clearHighlight(event): if not canvas.timer: return l,lm,lms,lmw = canvas.timer.lineinfo l.set_marker(lm) l.set_markersize(lms) l.set_markeredgewidth(lmw) canvas.draw() canvas.timer = None canvas = event.artist.get_figure().canvas if not hasattr(canvas,'timer'): canvas.timer = None plot = event.artist.get_figure().get_axes()[0] if hasattr(plot.get_legend(),'delay'): delay = plot.get_legend().delay if canvas.timer: # clear previous highlight if delay > 0: canvas.timer.Stop() clearHighlight(None) #if delay <= 0: return # use this in place of return # so that the next selected item is automatically highlighted (except when delay is 0) return if event.artist in plot.get_legend().get_lines(): # is this an artist item in the legend? lbl = event.artist.get_label() elif event.artist in plot.get_legend().get_texts(): # is this a text item in the legend? lbl = event.artist.get_text() else: #GSASIIpath.IPyBreak() return for l in plot.get_lines(): if lbl == l.get_label(): canvas.timer = wx.Timer() canvas.timer.Bind(wx.EVT_TIMER, clearHighlight) #GSASIIpath.IPyBreak() canvas.timer.lineinfo = (l,l.get_marker(),l.get_markersize(),l.get_markeredgewidth()) # highlight the selected item if l.get_marker() == 'None': l.set_marker('o') else: l.set_markersize(2*l.get_markersize()) l.set_markeredgewidth(2*l.get_markeredgewidth()) canvas.draw() if delay > 0: canvas.timer.Start(delay,oneShot=True) break else: print('Warning: artist matching ',lbl,' not found') def changePlotSettings(G2frame,Plot): '''Code in development to allow changes to plot settings prior to export of plot with "floppy disk" button ''' def RefreshPlot(*args,**kwargs): '''Apply settings to the plot ''' Plot.figure.subplots_adjust(left=int(plotOpt['labelSize'])/100., bottom=int(plotOpt['labelSize'])/150., right=.98, top=1.-int(plotOpt['labelSize'])/200., hspace=0.0) for P in Plot.figure.axes: P.get_xaxis().get_label().set_fontsize(plotOpt['labelSize']) P.get_yaxis().get_label().set_fontsize(plotOpt['labelSize']) for l in P.get_xaxis().get_ticklabels(): l.set_fontsize(plotOpt['labelSize']) for l in P.get_yaxis().get_ticklabels(): l.set_fontsize(plotOpt['labelSize']) for l in P.lines: l.set_linewidth(plotOpt['lineWid']) P.get_xaxis().set_tick_params(width=plotOpt['lineWid']) P.get_yaxis().set_tick_params(width=plotOpt['lineWid']) for l in P.spines.values(): l.set_linewidth(plotOpt['lineWid']) Plot.set_title(plotOpt['title'],fontsize=plotOpt['labelSize']) for i,P in enumerate(Plot.figure.axes): if not P.get_visible(): continue if i == 0: lbl = '' else: lbl = str(i) P.get_xaxis().set_label_text(plotOpt['xtitle'+lbl]) P.get_yaxis().set_label_text(plotOpt['ytitle'+lbl]) Plot.figure.canvas.draw() txtChoices = [str(i) for i in range (8,26)] lwidChoices = ('0.5','0.7','1','1.5','2','2.5','3','4') dlg = wx.Dialog(G2frame.plotFrame, style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER) vbox = wx.BoxSizer(wx.VERTICAL) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add(wx.StaticText(dlg,wx.ID_ANY,'Text size'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,txtChoices,None,None,plotOpt,'labelSize',RefreshPlot, size=(50,-1)) hbox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) vbox.Add(hbox,0,wx.ALL|wx.EXPAND) vbox.Add((1,5)) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add(wx.StaticText(dlg,wx.ID_ANY,' Line widths'),0,wx.ALL) w = G2G.G2ChoiceButton(dlg,lwidChoices,None,None,plotOpt,'lineWid',RefreshPlot, size=(50,-1)) hbox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) vbox.Add(hbox,0,wx.ALL|wx.EXPAND) vbox.Add((1,5)) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add(wx.StaticText(dlg,wx.ID_ANY,' Title'),0,wx.ALL) plotOpt['title'] = Plot.get_title() w = G2G.ValidatedTxtCtrl(dlg,plotOpt,'title',OnLeave=RefreshPlot, size=(200,-1),notBlank=False) hbox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) vbox.Add(hbox,0,wx.ALL|wx.EXPAND) for i,P in enumerate(Plot.figure.axes): if not P.get_visible(): continue if i == 0: lbl = '' else: lbl = str(i) vbox.Add((1,5)) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add(wx.StaticText(dlg,wx.ID_ANY,' x label '+lbl),0,wx.ALL) plotOpt['xtitle'+lbl] = P.get_xaxis().get_label_text() w = G2G.ValidatedTxtCtrl(dlg,plotOpt,'xtitle'+lbl,OnLeave=RefreshPlot, size=(200,-1),notBlank=False) hbox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) vbox.Add(hbox,0,wx.ALL|wx.EXPAND) vbox.Add((1,5)) hbox = wx.BoxSizer(wx.HORIZONTAL) hbox.Add(wx.StaticText(dlg,wx.ID_ANY,' y label '+lbl),0,wx.ALL) plotOpt['ytitle'+lbl] = P.get_yaxis().get_label_text() w = G2G.ValidatedTxtCtrl(dlg,plotOpt,'ytitle'+lbl,OnLeave=RefreshPlot, size=(200,-1),notBlank=False) hbox.Add(w,0,wx.ALL|wx.ALIGN_CENTER) vbox.Add(hbox,0,wx.ALL|wx.EXPAND) vbox.Add((1,10),1,wx.ALL|wx.EXPAND,1) hbox = wx.BoxSizer(wx.HORIZONTAL) OKbtn = wx.Button(dlg, wx.ID_OK) OKbtn.Bind(wx.EVT_BUTTON,lambda event:dlg.EndModal(wx.ID_OK)) hbox.Add((-1,-1),1,wx.ALL|wx.EXPAND,1) hbox.Add(OKbtn) hbox.Add((-1,-1),1,wx.ALL|wx.EXPAND,1) vbox.Add(hbox,1,wx.ALL|wx.EXPAND,1) dlg.SetSizer(vbox) vbox.Fit(dlg) #dlg.Show() RefreshPlot() dlg.ShowModal()