Merge remote-tracking branch 'origin/main' into MAXIV-HDF5

Author: briantoby

GSASII/GSASIIctrlGUI.py

@@ -44,9 +44,6 @@
 #from . import GSASIIstrMain as G2stMn
 from . import GSASIImiscGUI as G2IO
 from .tutorialIndex import tutorialIndex
-if sys.version_info[0] >= 3:
-    unicode = str
-    basestring = str
 
 # Define a short names for convenience
 DULL_YELLOW = (230,230,190)
@@ -406,7 +403,7 @@ def __init__(self,parent,loc,key,nDig=None,notBlank=True,xmin=None,xmax=None,
             self.type = int
         elif 'float' in str(type(val)):
             self.type = float
-        elif isinstance(val,str) or isinstance(val,unicode):
+        elif isinstance(val,str):
             self.type = str
         elif val is None:
             raise Exception("ValidatedTxtCtrl error: value of "+str(key)+
@@ -4762,11 +4759,7 @@ def __init__(self,G2frame,title,parmDict,varyList,fullVaryList,
             self.frozenList = []
         # make lists of variables of different types along with lists of parameter names, histogram #s, phase #s,...
         self.parmNames = sorted(list(parmDict.keys()))
-        if '2' in platform.python_version_tuple()[0]:
-            basestr = basestring
-        else:
-            basestr = str
-        splitNames = [item.split(':') for item in self.parmNames if len(item) > 3 and not isinstance(self.parmDict[item],basestr)]
+        splitNames = [item.split(':') for item in self.parmNames if len(item) > 3 and not isinstance(self.parmDict[item],str)]
         globNames = [':'.join(item) for item in splitNames if not item[0] and not item[1]]
         if len(globNames):
             self.choiceDict['Global'] = G2obj.SortVariables(globNames)
@@ -5022,11 +5015,7 @@ def __init__(self, parent):
     def SetContents(self,parent):
         self.varList = []
         for name in parent.choiceDict[parent.parmChoice]:
-            if '2' in platform.python_version_tuple()[0]:
-                basestr = basestring
-            else:
-                basestr = str
-            if isinstance(parent.parmDict[name],basestr): continue
+            if isinstance(parent.parmDict[name],str): continue
             if 'Refined' in parent.listSel and (name not in parent.fullVaryList
                                               ) and (name not in parent.varyList):
                 continue
@@ -5281,19 +5270,24 @@ def SetWildAfter(d,name,wname,mode):
     # Callbacks to display info in table
     def OnGetItemText(self, item, col):
         name = self.varList[item]
+        atmParNam  = None
+        if name.split(':')[2].startswith('dA'):
+            atmParNam = name.replace(':dA',':A')
         if col == 0:
             return str(item)
         elif col == 1:
+            if atmParNam: return atmParNam
             return name
         elif col == 2:
             if name in self.parmWin.fullVaryList and name in self.parmWin.frozenList:
-                    return "F"
+                return "F"
             elif name in self.parmWin.varyList:
                 return "R"
             elif name in self.parmWin.fullVaryList:
                 return "C"
             return ""
         elif col == 3:
+            if atmParNam: name = atmParNam
             try:
                 value = G2fil.FormatSigFigs(self.parmWin.parmDict[name])
             except ValueError:

GSASII/GSASIIdataGUI.py

@@ -3340,11 +3340,9 @@ class SumDialog(wx.Dialog):
         '''Used to sum images or powder patterns. Allows user to supply 
         scale factor(s) when summing data.
 
-        TODO: clean up the scrolling & resize on this dialog
-              Can we use the copy down button from CIF?
-        TODO: move it to GSASIIctrlGUI?
-        BHT: this class should not be in the middle of the (already too complex)
-        GSASIImain class. 
+        TODO: clean up the scrolling & resize on this dialog. Can we use the copy down button from CIF?
+        TODO: move it to GSASIIctrlGUI? (BHT) this class should not be in 
+        the middle of the (already too complex) GSASIImain class. 
         '''
         def __init__(self,parent,title,text,dataType,data,dataList,Limits=None):
             wx.Dialog.__init__(self,parent,-1,title,size=(400,250),
@@ -3736,8 +3734,8 @@ def OnImageSum(self,event):
                             newimagefile = dlg.GetPath()
                             newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile)
                             G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage)
-                            Imax = np.amax(newImage)
-                            Imin = np.amin(newImage)
+                            Imax = int(np.amax(newImage))
+                            Imin = int(np.amin(newImage))
                             newImage = []
                             self.GPXtree.SetItemPyData(Id,[imSize,newimagefile])
                             self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),Comments)

GSASII/GSASIIfiles.py

@@ -13,10 +13,12 @@
 import os
 import sys
 import glob
+import copy
 #import inspect
 import re
 
 import numpy as np
+import numpy.ma as ma
 
 from . import GSASIIpath
 from . import GSASIIlattice as G2lat
@@ -2165,7 +2167,8 @@ def loadTree(self):
                     # the main info goes into Data, but the 0th
                     # element contains refinement results, carry
                     # that over too now.
-                    self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
+                    # make coopy so we can shift TOF
+                    self.Histograms[name]['Data'] = copy.deepcopy(self.G2frame.GPXtree.GetItemPyData(item)[1])
                     self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
                     item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
                     while item2:
@@ -2177,6 +2180,18 @@ def loadTree(self):
             for hist in self.Histograms:
                 if hist.startswith("PWDR"):
                     d = self.powderDict
+                    # shift TOF from midpoint to bin start
+                    if 'T' in self.Histograms[hist]['Instrument Parameters'][0]['Type'][0]:
+                        if hasattr(self.Histograms[hist]['Data'][0],'mask'):
+                            m = self.Histograms[hist]['Data'][0].mask
+                            x = self.Histograms[hist]['Data'][0].data
+                            # one half the averaged bin widths -- ~backs out the previous shift
+                            halfbin = (np.append(x[1]-x[0],np.diff(x)) + np.append(np.diff(x),x[-1]-x[-2]))/4
+                            self.Histograms[hist]['Data'][0] = ma.array(x-halfbin,mask=m)
+                        else:
+                            x = self.Histograms[hist]['Data'][0]
+                            halfbin = (np.append(x[1]-x[0],np.diff(x)) + np.append(np.diff(x),x[-1]-x[-2]))/4
+                            self.Histograms[hist]['Data'][0] -= halfbin
                 elif hist.startswith("HKLF"):
                     d = self.xtalDict
                 elif hist.startswith("SASD"):

GSASII/GSASIIimage.py

@@ -46,15 +46,18 @@
 
 def peneCorr(tth,dep,dist):
     ''' Compute empirical position correction due to detector absorption
+
     :param float/array tth: angle between detector normal & scattered ray vector
     :param float dep: coefficient
     :param float dist: sample to detector surface in mm
-    :returns: float/array distance: correction for penetration'''
+    :returns: float/array distance: correction for penetration
+    '''
 
     return dep*(1.-npcosd(tth))*dist**2/1000.         #best one
 
 def GetTthP(x,y,parmDict):
     ''' Compute angle between detector normal & sample scattering ray vector
+
     :param float/array x: detector x-position in mm
     :param float/array y: detector y-position in mm
     :param dict parmDict: dictionary of detector orientation parameters in fitting routine

GSASII/GSASIIimgGUI.py

@@ -2044,10 +2044,12 @@ def OnLoadPixelMask(event):
                                              # was loaded rather than a search
         data['SpotMask']['spotMask'] = maskImage > 0
         nmasked = sum(data['SpotMask']['spotMask'].flatten())
-        frac = nmasked/data['SpotMask']['spotMask'].size
+        frac = 100*nmasked/data['SpotMask']['spotMask'].size
         G2G.G2MessageBox(G2frame,
                              f'Mask removes {nmasked} pixels ({frac:.3f}%)',
                              'Mask loaded')
+        wx.CallAfter(UpdateMasks,G2frame,data)
+        wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event)
 
     def OnFindPixelMask(event):
         '''Do auto search for pixels to mask

GSASII/GSASIImiscGUI.py

@@ -266,7 +266,7 @@ def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
     TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
     Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
     G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
-    Imax = np.amax(Image)
+    Imax = int(np.amax(Image))
     if G2frame.imageDefault:
         Data.update(copy.deepcopy(G2frame.imageDefault))
         Data['showLines'] = True

GSASII/GSASIIpath.py

@@ -1781,24 +1781,6 @@ def makeScriptShortcut():
         return
     return newfil
 
-# see if a directory for local modifications is defined. If so, stick that in the path
-if os.path.exists(os.path.expanduser('~/.G2local/')):
-    sys.path.insert(0,os.path.expanduser('~/.G2local/'))
-    fl = glob.glob(os.path.expanduser('~/.G2local/GSASII*.py*'))
-    files = ""
-    prev = None
-    for f in sorted(fl): # make a list of files, dropping .pyc files where a .py exists
-        f = os.path.split(f)[1]
-        if os.path.splitext(f)[0] == prev: continue
-        prev = os.path.splitext(f)[0]
-        if files: files += ", "
-        files += f
-    if files:
-        print("*"*75)
-        print("Warning: the following source files are locally overridden in "+os.path.expanduser('~/.G2local/'))
-        print("  "+files)
-        print("*"*75)
-
 BinaryPathFailed = False
 BinaryPathLoaded = False
 binaryPath = ''

GSASII/GSASIIphsGUI.py

@@ -13377,10 +13377,9 @@ def rbKeyPress(event):
         G2frame.phaseDisplay.AddPage(G2frame.MCSA,'MC/SA')
         Pages.append('MC/SA')
 
-    if nhist:   
-        G2frame.FRMC = wx.ScrolledWindow(G2frame.phaseDisplay)
-        G2frame.phaseDisplay.AddPage(G2frame.FRMC,'RMC')
-        Pages.append('RMC')
+    G2frame.FRMC = wx.ScrolledWindow(G2frame.phaseDisplay)
+    G2frame.phaseDisplay.AddPage(G2frame.FRMC,'RMC')
+    Pages.append('RMC')
 
     if dataGeneral['Type'] == 'nuclear':
         G2frame.ISODIST = wx.ScrolledWindow(G2frame.phaseDisplay)

GSASII/GSASIIphsGUI2.py

@@ -1,8 +1,7 @@
 # -*- coding: utf-8 -*-
 #GSASII - phase data display routines
 '''
-
-Routines for Phase dataframes follow. Only Update routines are here
+Routines for Phase dataframes follow. Only a few Update routines are here
 all others are in GSASIIphsGUI.py
 '''
 import os

GSASII/GSASIIplot.py

@@ -215,6 +215,7 @@ def __init__(self,parent,id=-1,dpi=None,publish=None,**kwargs):
         _tabPlotWin.__init__(self,parent,id=id,**kwargs)
         mpl.rcParams['legend.fontsize'] = 12
         mpl.rcParams['axes.grid'] = False
+        #TODO: set dpi here via config var: this changes the size of the labeling font 72-100 is normal
         self.figure = mplfig.Figure(dpi=dpi,figsize=(5,6))
         self.canvas = Canvas(self,-1,self.figure)
         self.toolbar = GSASIItoolbar(self.canvas,publish=publish)
@@ -634,6 +635,11 @@ def set_message(self,s):
         '''
         pass
 
+# TODO: perhaps someday we could pull out the bitmaps and rescale there here    
+#    def AddTool(self,*args,**kwargs):
+#        print('AddTool',args,kwargs)
+#        return Toolbar.AddTool(self,*args,**kwargs)
+
     def AddToolBarTool(self,label,title,filename,callback):
         bmpFilename = GSASIIpath.getIconFile(filename)
         if bmpFilename is None:
@@ -642,10 +648,7 @@ def AddToolBarTool(self,label,title,filename,callback):
         else:
             bmp = wx.Bitmap(bmpFilename)
 #            bmp = wx.Bitmap(bmpFilename,type=wx.BITMAP_TYPE_ANY) # probably better
-        if 'phoenix' in wx.version():
-            button = self.AddTool(wx.ID_ANY, label, bmp, title)
-        else:
-            button = self.AddSimpleTool(wx.ID_ANY, bmp, label, title)
+        button = self.AddTool(wx.ID_ANY, label, bmp, title)
         wx.EVT_TOOL.Bind(self, button.GetId(), button.GetId(), callback)
         return button.GetId()
 
@@ -732,6 +735,20 @@ def OnArrow(self,event):
     def OnHelp(self,event):
         'Respond to press of help button on plot toolbar'
         bookmark = self.Parent.helpKey  # get help category used to create plot
+        G2frame = wx.GetApp().GetMainTopWindow()
+        if bookmark != G2frame.dataWindow.helpKey:
+            # plot window and data window are different
+            try:
+                selText = '/'.join(G2frame.PickIdText)
+            except:
+                selText = G2frame.GPXtree.GetItemText(G2frame.GPXtree.GetSelection())
+            G2G.G2MessageBox(G2frame,
+                 'Displaying help on plot window, but you have moved to a '
+                 f'different data tree item ({selText}) where plot menu items '
+                 'and key commands are not available. '
+                 'Return to the appropriate data tree '
+                 'item for full plot functionality',
+                 'Wrong data tree selection')
         #if GSASIIpath.GetConfigValue('debug'): print 'plot help: key=',bookmark
         G2G.ShowHelp(bookmark,self.TopLevelParent)
 
@@ -3275,24 +3292,26 @@ def OnKeyPress(event):
         sGp = []
         Wp = []
         Qp = []
+        sQp = []
         for ip,peak in enumerate(peaks):
             Qp.append(2.*np.pi*difC/peak[0])
+            sQp.append(2.*np.pi*difC*peakEsds.get('pos%d'%ip,0.0)/peak[0]**2)
             Ap.append(peak[4])
             sAp.append(peakEsds.get('alp%d'%ip,0.0))
             Bp.append(peak[6])
             sBp.append(peakEsds.get('bet%d'%ip,0.0))
-            sp = 1.17741*np.sqrt(peak[8])/peak[0]
+            sp = 0.5*sq8ln2*np.sqrt(peak[8])/peak[0]
             Sp.append(sp)     #sqrt(8ln2)/2
-            sSp.append(0.5*sp*peakEsds.get('sig%d'%ip,0.0)/peak[8])
+            sSp.append(0.25*sq8ln2*peakEsds.get('sig%d'%ip,0.0)/(np.sqrt(peak[8])*peak[0]))
             Gp.append(peak[10]/peak[0])
             sGp.append(peakEsds.get('gam%d'%ip,0.0)/peak[0])
 
         if Qp:
             if G2frame.ErrorBars:
-                Plot.errorbar(Qp,Ap,yerr=sAp,fmt='r+',capsize=2,label='A peak')
-                Plot.errorbar(Qp,Bp,yerr=sBp,fmt='+',color='orange',capsize=2,label='B peak')
-                Plot.errorbar(Qp,Sp,yerr=sSp,fmt='b+',capsize=2,label='G peak')
-                Plot.errorbar(Qp,Gp,yerr=sGp,fmt='m+',capsize=2,label='L peak')                
+                Plot.errorbar(Qp,Ap,xerr=sQp,yerr=sAp,fmt='r+',capsize=2,label='A peak')
+                Plot.errorbar(Qp,Bp,xerr=sQp,yerr=sBp,fmt='+',color='orange',capsize=2,label='B peak')
+                Plot.errorbar(Qp,Sp,xerr=sQp,yerr=sSp,fmt='b+',capsize=2,label='G peak')
+                Plot.errorbar(Qp,Gp,xerr=sQp,yerr=sGp,fmt='m+',capsize=2,label='L peak')                
             else:
                 Plot.plot(Qp,Ap,'+',color='r',label='A peak')
                 Plot.plot(Qp,Bp,'+',color='orange',label='B peak')
@@ -3394,6 +3413,7 @@ def OnKeyPress(event):
         Plot.plot(Q,Wf,color='b',dashes=(5,5),label='G+L fit')
 
         Xp = []
+        sXp = []
         Yp = []
         sYp = []
         Zp = []
@@ -3402,6 +3422,7 @@ def OnKeyPress(event):
         for ip,peak in enumerate(peaks):
             tpd = tand(peak[0]/2.)
             Xp.append(4.0*math.pi*sind(peak[0]/2.0)/lam)
+            sXp.append(2.0*math.pi*cosd(peak[0]/2.0)*peakEsds.get('pos%d'%ip,0.0)/lam)
             try:
                 s = math.sqrt(peak[isig])*math.pi/18000.
             except ValueError:
@@ -3410,14 +3431,14 @@ def OnKeyPress(event):
             G = G2pwd.getgamFW(g,s)         #/2.
             yp = sq8ln2*s
             Yp.append(yp/tpd)
-            sYp.append((math.pi/36000.)*peakEsds.get('sig%d'%ip,0.0)/yp)
+            sYp.append(0.5*sq8ln2*(math.pi/18000.)**2*peakEsds.get('sig%d'%ip,0.0)/(s*tpd))
             Zp.append(g/tpd)
             sZp.append((math.pi/18000.)*peakEsds.get('gam%d'%ip,0.0)/tpd)
             Wp.append(G/tpd)
         if len(peaks):
             if G2frame.ErrorBars:
-                Plot.errorbar(Xp,Yp,yerr=sYp,fmt='r+',capsize=2,label='G peak')
-                Plot.errorbar(Xp,Zp,yerr=sZp,fmt='g+',capsize=2,label='L peak')                                
+                Plot.errorbar(Xp,Yp,xerr=sXp,yerr=sYp,fmt='r+',capsize=2,label='G peak')
+                Plot.errorbar(Xp,Zp,xerr=sXp,yerr=sZp,fmt='g+',capsize=2,label='L peak')                                
             else:
                 Plot.plot(Xp,Yp,'+',color='r',label='G peak')
                 Plot.plot(Xp,Zp,'+',color='g',label='L peak')