Merge latest changes in branch 'origin/main' into logging

Author: briantoby

GSASII/GSASIIctrlGUI.py

@@ -7691,6 +7691,15 @@ def ShowHelp(helpType,frame,helpMode=None):
         helplink = os.path.join(path2GSAS2,'help',helplink)
         pfx = "file://"
         if sys.platform.lower().startswith('win'):
+            # really don't understand what urlunsplit is doing, but this seems
+            # to prevent windows from encoding the # for the anchor
+            # (suggested by Google's AI!) 
+            from urllib.parse import urlunsplit
+            f = helplink.split('#')[0]
+            a = ''
+            if '#' in helplink:
+                a = helplink.split('#')[1]
+            helplink = urlunsplit(['file','',f,'',a])
             pfx = ''
         #if GSASIIpath.GetConfigValue('debug'): print 'DBG_Help link=',pfx+helplink
         if htmlFirstUse:
@@ -8436,7 +8445,7 @@ def ChooseOrigin(G2frame,rd):
     for atom in O2atoms:
         for i in [0,1,2]:
             atom[cx+i] += T[i]
-            atom[cs:cs+2] = G2spc.SytSym(atom[cx:cx+3],SGData)[0:2] # update symmetry & mult
+        atom[cs:cs+2] = G2spc.SytSym(atom[cx:cx+3],SGData)[0:2] # update symmetry & mult
     #get density & distances
     DisAglData = {}
     DisAglData['SGData'] = rd.Phase['General']['SGData']
@@ -8563,7 +8572,7 @@ def OnSlider(event):
             G2frame.Cmax = val
         else:
             G2frame.Cmin = val
-        obj.txt.SetValue(int(Ymax*val))
+        obj.txt.ChangeValue(int(Ymax*val))
         updatePlot()
     def OnNewVal(*args,**kwargs):
         'respond when a value is placed in the min or max text box'

GSASII/GSASIIdataGUI.py

@@ -83,7 +83,7 @@ def new_util_find_library( name ):
 WACV = wx.ALIGN_CENTER_VERTICAL
 VERY_LIGHT_GREY = wx.Colour(240,240,240)
 DULL_YELLOW = (230,230,190)
-
+GkDelta = chr(0x0394)
 # transformation matrices
 commonTrans = {'abc':np.eye(3),'a-cb':np.array([[1.,0.,0.],[0.,0.,-1.],[0.,1.,0.]]),
     'ba-c':np.array([[0.,1.,0.],[1.,0.,0.],[0.,0.,-1.]]),'-cba':np.array([[0.,0.,-1.],[0.,1.,0.],[1.,0.,0.]]),
@@ -129,10 +129,12 @@ def __init__(self,parent,data):
             self.Trans = np.eye(4)
         else:
             self.Trans = np.eye(3)
+        self.Type = data[0]['Type']
         self.Cent = 'noncentrosymmetric'
         self.Laue = '1'
         self.Class = 'triclinic'
         self.Common = 'abc'
+        self.Smart = False
         self.Draw()
 
     def Draw(self):
@@ -159,6 +161,9 @@ def OnCommon(event):
             self.Common = Obj.GetValue()
             self.Trans = commonTrans[self.Common]
             wx.CallAfter(self.Draw)
+            
+        def OnSmart(event):
+            self.Smart = not self.Smart
 
         self.panel.Destroy()
         self.panel = wx.Panel(self)
@@ -215,6 +220,10 @@ def OnCommon(event):
         Laue.Bind(wx.EVT_COMBOBOX,OnLaue)
         mergeSizer.Add(Laue,0,WACV)
         mainSizer.Add(mergeSizer)
+        if self.Type == 'SEC':
+            Smart = wx.CheckBox(self.panel,label=' Do smart merge for microED?')
+            Smart.Bind(wx.EVT_CHECKBOX,OnSmart)
+        mainSizer.Add(Smart,0)    
 
         OkBtn = wx.Button(self.panel,-1,"Ok")
         OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
@@ -234,7 +243,7 @@ def OnCommon(event):
         self.Fit()
 
     def GetSelection(self):
-        return self.Trans,self.Cent,self.Laue
+        return self.Trans,self.Cent,self.Laue,self.Smart
 
     def OnOk(self,event):
         parent = self.GetParent()
@@ -1180,7 +1189,7 @@ def _Add_ImportMenu_Phase(self,parent):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu,'Phase','Import phase data')
         for reader in self.ImportPhaseReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
         item = submenu.Append(wx.ID_ANY,'guess format from file','Import phase data, use file to try to determine format')
@@ -1367,7 +1376,7 @@ def _Add_ImportMenu_Image(self,parent):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu, 'Image','Import image file')
         for reader in self.ImportImageReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportImage, id=item.GetId())
         item = submenu.Append(wx.ID_ANY,'guess format from file','Import image data, use file to try to determine format')
@@ -1397,7 +1406,7 @@ def _Add_ImportMenu_Sfact(self,parent):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu,'Structure Factor','Import Structure Factor data')
         for reader in self.ImportSfactReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
         item = submenu.Append(wx.ID_ANY,'guess format from file','Import Structure Factor, use file to try to determine format')
@@ -1513,7 +1522,7 @@ def OnAutoImport(event):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu,'Powder Data','Import Powder data')
         for reader in self.ImportPowderReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
         item = submenu.Append(wx.ID_ANY,'guess format from file','Import powder data, use file to try to determine format')
@@ -2447,7 +2456,7 @@ def _Add_ImportMenu_smallangle(self,parent):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu,'Small Angle Data','Import small angle data')
         for reader in self.ImportSmallAngleReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId())
         # item = submenu.Append(wx.ID_ANY,
@@ -2540,7 +2549,7 @@ def _Add_ImportMenu_reflectometry(self,parent):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu,'Reflectometry Data','Import reflectometry data')
         for reader in self.ImportReflectometryReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId())
         # item = submenu.Append(wx.ID_ANY,
@@ -2635,7 +2644,7 @@ def _Add_ImportMenu_PDF(self,parent):
         submenu = wx.Menu()
         item = parent.AppendSubMenu(submenu,'PDF G(R) Data','Import PDF G(R) data')
         for reader in self.ImportPDFReaderlist:
-            item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName)
+            item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
             self.ImportMenuId[item.GetId()] = reader
             self.Bind(wx.EVT_MENU, self.OnImportPDF, id=item.GetId())
         submenu.AppendSeparator()
@@ -6725,13 +6734,19 @@ def _makemenu():     # routine to create menu when first used
                     if  lbl == 'Project':
                         submenu.Append(G2G.wxID_XPORTSEQFCIF,'... as full CIF',
                                 'Save all sequential refinement results as a CIF file')
+                        G2G.Define_wxId('wxID_XPORTCINEMA')
+                        submenu.Append(G2G.wxID_XPORTCINEMA,'... to CINEMA: Debye-Scherrer',
+                                'Pass sequential refinement results for plotting in CINEMA: Debye-Scherrer')                        
                     for obj in objlist:
                         item = submenu.Append(wx.ID_ANY,obj.formatName,obj.longFormatName)
                         self.SeqExportLookup[item.GetId()] = (obj,lbl) # lookup table for submenu item
                         # Bind is in UpdateSeqResults
 
             self.SequentialEx.Append(G2G.wxID_XPORTSEQCSV,'Save table as CSV',
                 'Save all sequential refinement results as a CSV spreadsheet file')
+            G2G.Define_wxId('wxID_XPORTSEQIMG')
+            self.SequentialEx.Append(G2G.wxID_XPORTSEQIMG,'Save histogram images',
+                'Save all sequential refinements as a series of images')
             self.PostfillDataMenu()
             SetDataMenuBar(G2frame,self.SequentialMenu)
         self.SequentialMenu = _makemenu
@@ -7585,6 +7600,14 @@ def _makemenu():     # routine to create menu when first used
         self.DataGeneral = _makemenu
     # end of GSAS-II menu definitions
 
+def readFromFile(reader):
+    '''Define a caption for a file import menu item'''
+    nam = reader.formatName
+    if nam.startswith('(user'):
+        return nam.replace('(user)','(user) from')+' file'
+    else:
+        return f'from {reader.formatName} file'
+
 ####  Notebook Tree Item editor ##############################################
 NBinfo = {}
 def UpdateNotebook(G2frame,data):
@@ -8307,7 +8330,7 @@ def OnMergeHKL(event):
         dlg = MergeDialog(G2frame,data)
         try:
             if dlg.ShowModal() == wx.ID_OK:
-                Trans,Cent,Laue = dlg.GetSelection()
+                Trans,Cent,Laue,Smart = dlg.GetSelection()
             else:
                 return
         finally:
@@ -8338,15 +8361,31 @@ def OnMergeHKL(event):
             style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
         sumDf = 0.
         sumFo = 0.
+        Nmerge = {1:[0,0],}
+        MaxN = 1
         for ih,hkl in enumerate(HKLdict):
             HKL = HKLdict[hkl]
+            Nhkl = len(HKL[1])
+            if Nhkl not in Nmerge:
+                Nmerge.update({Nhkl:[1,0],})
+                MaxN = max(MaxN,Nhkl)
+                
+            else:
+                Nmerge[Nhkl][0] += 1
             newHKL = list(HKL[0])+list(HKL[1][0])
             if len(HKL[1]) > 1:
                 fos = np.array(HKL[1])
                 wFo = 1/fos[:,3]**2
                 Fo = np.average(fos[:,2],weights=wFo)
                 std = np.std(fos[:,2])
                 sig = np.sqrt(np.mean(fos[:,3])**2+std**2)
+                if Smart:
+                    test = np.abs(fos[:,2]-Fo)/std
+                    Nmerge[Nhkl][1] += len(fos[:,2][test >2.0])
+                    fos[:,2] = np.where(test > 2.0,Fo,fos[:,2])
+                    Fo = np.average(fos[:,2],weights=wFo)
+                    std = np.std(fos[:,2])
+                    sig = np.sqrt(np.mean(fos[:,3])**2+std**2)
                 sumFo += np.sum(fos[:,2])
                 sumDf += np.sum(np.abs(fos[:,2]-Fo))
                 dlg.Update(ih)
@@ -8356,6 +8395,12 @@ def OnMergeHKL(event):
             if newHKL[5+Super] > 0.:
                 mergeRef.append(list(newHKL))
         dlg.Destroy()
+        print(' Duplicate reflection statistics:')
+        for ihkl in range(MaxN):
+            try:
+                print('Ndup hkl:',ihkl+1,' Number: ',Nmerge[ihkl+1][0],' Rej:',Nmerge[ihkl+1][1])
+            except KeyError:
+                print('Ndup hkl:',ihkl+1,' Number: ',0)
         if Super:
             mergeRef = G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(mergeRef,3),2),1),0)
         else:
@@ -8436,19 +8481,25 @@ def OnFixFsqFsq(event):
     def OnErrorAnalysis(event):
         '''Plots an "Abrams" plot - sorted delta/sig across data set.
         Should be straight line of slope 1 - never is'''
-        def OnPlotFoFcVsFc(kind):
+        def OnPlotFoFcVsFc():
             ''' Extinction check, plots Fo-Fc & 1/ExtC vs Fo for single crystal data '''
-            iFo,iFc,iExt = 5,7,11
+            test = lambda xy:(xy[iFlg+Super]>0 and xy[iFo+Super]>0)
+            iFlg,iFo,iSig,iFc,iFcT,iExt = 3,5,6,7,9,11
             refList = data[1]['RefList']
-            XY = np.array([[xy[iFo+Super],xy[iFo+Super]-xy[iFc+Super]] for xy in refList if xy[3+Super]>0])
-            XY = np.sqrt(np.abs(XY)).T
-            XE = [[xy[iFo+Super],xy[iExt+Super]] for xy in refList if xy[3+Super]>0]
-            XE = np.array([[np.sqrt(xe[0]),1./xe[1]] for xe in XE]).T
-            G2plt.PlotXY(G2frame,[[XY[0],XY[0]-XY[1]],],XY2=[XE,],labelX='|Fo|',labelY='|Fo|-|Fc|, 1/ExtC',newPlot=False,
-               Title='Extinction check',lines=False,points2=True,names=['|Fo|-|Fc|',],names2=['1/ExtC',])
+            wtFctr = data[0]['wtFactor']
+            Fo = np.sqrt(np.array([xy[iFo+Super] for xy in refList if test(xy)]))
+            Fc = np.sqrt(np.array([xy[iFc+Super] for xy in refList if test(xy)]))
+            FcT = np.sqrt(np.array([xy[iFcT+Super] for xy in refList if test(xy)]))
+            Sig = np.array([xy[iSig+Super] for xy in refList if test(xy)])/wtFctr      #sig(fo^2)/wtFactor (1/GOF)
+            XE = [[xy[iFcT+Super],xy[iExt+Super]] for xy in refList if test(xy)]
+            XE = np.array([[np.sqrt(xe[0]),xe[1]] for xe in XE]).T
+            XE[1] = np.where(XE[1]>0.,XE[1],1.0)
+            G2plt.PlotXY(G2frame,[[FcT,2.*Fo*(Fo-Fc)/Sig],],XY2=[XE,],labelX='Fc',labelY=GkDelta+'F/sig, ExtC',newPlot=False,
+               Title='Extinction check',lines=False,points2=True,names=[GkDelta+'F/sig',],names2=['ExtC',])
+            
         G2plt.PlotDeltSig(G2frame,kind)
         if kind in ['HKLF',]:
-            OnPlotFoFcVsFc(kind)
+            OnPlotFoFcVsFc()
 
 #    def OnCompression(event):
 #        data[0] = int(comp.GetValue())

GSASII/GSASIIddataGUI.py

@@ -562,7 +562,7 @@ def OnHKLList(event):
         shPenalty.Add(shToler,0,WACV)
         return shPenalty
 
-    def ExtSizer(Type):
+    def ExtSizer(Type,Htype):
 
         def OnSCExtType(event):
             Obj = event.GetEventObject()
@@ -595,21 +595,30 @@ def ExtVal(Ekey,valSizer,fmt,lim):
             extSizer = wx.BoxSizer(wx.VERTICAL)
             typeSizer = wx.BoxSizer(wx.HORIZONTAL)
             typeSizer.Add(wx.StaticText(DData,wx.ID_ANY,' Extinction type: '),0,WACV)
-            Choices = ['None','Primary','Secondary Type I','Secondary Type II',]    # remove 'Secondary Type I & II'
+            Choices = ['None','Primary','Secondary Type I','Secondary Type II','microED']    # remove 'Secondary Type I & II'
+            if Htype == 'SEC':
+                Choices = ['None','microED']
             typeTxt = wx.ComboBox(DData,wx.ID_ANY,choices=Choices,value=UseList[G2frame.hist]['Extinction'][1],
                 style=wx.CB_READONLY|wx.CB_DROPDOWN)
             Indx[typeTxt.GetId()] = [G2frame.hist,1]
             typeTxt.Bind(wx.EVT_COMBOBOX,OnSCExtType)
             typeSizer.Add(typeTxt)
-            typeSizer.Add(wx.StaticText(DData,wx.ID_ANY,' Approx: '),0,WACV)
-            Choices=['Lorentzian','Gaussian']
-            approxTxT = wx.ComboBox(DData,wx.ID_ANY,choices=Choices,value=UseList[G2frame.hist]['Extinction'][0],
-                style=wx.CB_READONLY|wx.CB_DROPDOWN)
-            Indx[approxTxT.GetId()] = [G2frame.hist,0]
-            approxTxT.Bind(wx.EVT_COMBOBOX,OnSCExtType)
-            typeSizer.Add(approxTxT)
+            if Htype != 'SEC':
+                typeSizer.Add(wx.StaticText(DData,wx.ID_ANY,' Approx: '),0,WACV)
+                Choices=['Lorentzian','Gaussian']
+                approxTxT = wx.ComboBox(DData,wx.ID_ANY,choices=Choices,value=UseList[G2frame.hist]['Extinction'][0],
+                    style=wx.CB_READONLY|wx.CB_DROPDOWN)
+                Indx[approxTxT.GetId()] = [G2frame.hist,0]
+                approxTxT.Bind(wx.EVT_COMBOBOX,OnSCExtType)
+                typeSizer.Add(approxTxT)
             if UseList[G2frame.hist]['Extinction'][1] == 'None':
                 extSizer.Add(typeSizer,0)
+            elif UseList[G2frame.hist]['Extinction'][1] == 'microED':
+                extSizer.Add(typeSizer,0)
+                extSizer.Add(wx.StaticText(DData,label=' Small F microED dynamical scattering correction:'))
+                val3Sizer =wx.BoxSizer(wx.HORIZONTAL)
+                Ekey = ['Ma','Mb','Mc']
+                extSizer.Add(ExtVal(Ekey,val3Sizer,'g',[-1.,10.]),0,)
             else:
                 extSizer.Add(typeSizer,0,wx.BOTTOM,5)
                 if 'Tbar' in UseList[G2frame.hist]['Extinction'][2]:       #skipped for TOF
@@ -633,11 +642,6 @@ def ExtVal(Ekey,valSizer,fmt,lim):
                 else:
                     Ekey = ['Eg','Es']
                 extSizer.Add(ExtVal(Ekey,val2Sizer,'g',[0.,100.]),0)
-                # extSizer.Add(wx.StaticText(DData,label=' Small F dynamical scattering correction:'))
-                # val3Sizer =wx.BoxSizer(wx.HORIZONTAL)
-                # if 'Primary' in UseList[G2frame.hist]['Extinction'][1]:
-                #     Ekey = ['Ma','Mb',]
-                #     extSizer.Add(ExtVal(Ekey,val3Sizer,'f',[-1.,10.]),0,)
         else:   #PWDR
             extSizer = wx.BoxSizer(wx.HORIZONTAL)
             extRef = wx.CheckBox(DData,wx.ID_ANY,label=' Extinction: ')
@@ -935,6 +939,8 @@ def OnFixVals(event):
             if 'Ma' not in UseList[G2frame.hist]['Extinction'][2]:
                 UseList[G2frame.hist]['Extinction'][2].update({'Ma':[1.0,False]})
                 UseList[G2frame.hist]['Extinction'][2].update({'Mb':[0.0,False]})
+            if 'Mc' not in UseList[G2frame.hist]['Extinction'][2]:
+                UseList[G2frame.hist]['Extinction'][2].update({'Mc':[1.0,False]})
         elif 'PWDR' in UseList[G2frame.hist]['Histogram']:
             if 'LeBail' not in UseList[G2frame.hist]:
                 UseList[G2frame.hist]['LeBail'] = False
@@ -949,6 +955,8 @@ def OnFixVals(event):
         useData.Bind(wx.EVT_CHECKBOX, OnUseData)
         useData.SetValue(UseList[G2frame.hist]['Use'])
         useBox.Add(useData,0,WACV)
+        Htype = UseList[G2frame.hist].get('Type','SXC')
+        useBox.Add(wx.StaticText(DData,label=' Histogram type: '+Htype))
         if not generalData['doPawley'] and 'PWDR' in G2frame.hist[:4]:
             lbLabel = 'Start Le Bail extraction?   '
             if UseList[G2frame.hist]['LeBail']:
@@ -984,7 +992,7 @@ def OnFixVals(event):
                     fixBox.Add(wx.StaticText(DData,label=' (currently {} fixed)'.format(len(fixedVars))),0,WACV)
                 bottomSizer.Add(fixBox)
 
-        if not UseList[G2frame.hist]['LeBail'] or 'HKLF' in G2frame.hist[:4]:
+        if  'HKLF' in G2frame.hist[:4] or not UseList[G2frame.hist]['LeBail']:
             bottomSizer.Add(ScaleSizer(),0,wx.BOTTOM,5)
         else:
             # if phase fraction/scale is hidden, turn off flag
@@ -1071,7 +1079,7 @@ def OnFixVals(event):
                         except:
                             print('SHPenalty error occurred')
                 bottomSizer.Add(poSizer)    #,0,wx.TOP|wx.BOTTOM,5)
-                bottomSizer.Add(ExtSizer('PWDR'),0,wx.TOP|wx.BOTTOM,5)
+                bottomSizer.Add(ExtSizer('PWDR',Htype),0,wx.TOP|wx.BOTTOM,5)
                 if generalData['Type'] != 'magnetic':
                     bottomSizer.Add(BabSizer(),0,wx.BOTTOM,5)
             else:
@@ -1082,7 +1090,7 @@ def OnFixVals(event):
                 # TODO: should turn off all Extinction refinement flags
                 UseList[G2frame.hist]['Extinction'][1] = False
         elif G2frame.hist[:4] == 'HKLF':
-            bottomSizer.Add(ExtSizer('HKLF'))  #,0,wx.BOTTOM,5)
+            bottomSizer.Add(ExtSizer('HKLF',Htype))  #,0,wx.BOTTOM,5)
             bottomSizer.Add(BabSizer())  #,0,wx.BOTTOM,5)
             if not SGData['SGInv'] and len(UseList[G2frame.hist]['Twins']) < 2:
                 bottomSizer.Add(FlackSizer())  #,0,wx.BOTTOM,5)