Add option to fix HKLF when incorrectly import F^2 data as F. Converts "F^4" to "F^2"

fix Sph Harm texture bugs from newest python/numpy

Author: vondreele

GSASII/GSASIIdataGUI.py

@@ -6627,7 +6627,7 @@ def _makemenu():     # routine to create menu when first used
         self.PWDRMenu = _makemenu
 
         # HKLF - many wxIDs defined in PWDR & SASD above
-        G2G.Define_wxId('wxID_3DALLHKLPLOT','wxID_MERGEHKL')
+        G2G.Define_wxId('wxID_3DALLHKLPLOT','wxID_MERGEHKL','wxID_FIXFSQSQDATA')
         def _makemenu():     # routine to create menu when first used
             self.HKLFMenu = wx.MenuBar()
             self.PrefillDataMenu(self.HKLFMenu)
@@ -6638,6 +6638,7 @@ def _makemenu():     # routine to create menu when first used
             self.ErrorAnal.Append(G2G.wxID_1DHKLSTICKPLOT,'Plot 1D HKLs','Plot of HKLs from single crystal data in 1D')
             self.ErrorAnal.Append(G2G.wxID_PWD3DHKLPLOT,'Plot 3D HKLs','Plot HKLs from single crystal data in 3D')
             self.ErrorAnal.Append(G2G.wxID_3DALLHKLPLOT,'Plot all 3D HKLs','Plot HKLs from all single crystal data in 3D')
+            self.ErrorAnal.Append(G2G.wxID_FIXFSQSQDATA,'Fix (F^2)^2 data','Fix F^2 data imported as F')
     #        self.ErrorAnal.Append(G2G.wxID_PWDCOPY,'Copy params','Copy of HKLF parameters') #unused
             self.PostfillDataMenu()
             SetDataMenuBar(G2frame,self.HKLFMenu)
@@ -8135,6 +8136,47 @@ def OnMergeHKL(event):
         G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),Inst)
         G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection List'),{})  #dummy entry for GUI use
         G2frame.GPXtree.SetItemPyData(Id,newData)
+        
+    def OnFixFsqFsq(event):
+        ''' Fix HKLF data that had been misimported as F instead of F^2'''
+        Name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
+        Inst = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,
+            G2frame.PatternId,'Instrument Parameters'))
+        CId = GetGPXtreeItemId(G2frame,G2frame.PatternId,'Comments')
+        if CId:
+            Comments = G2frame.GPXtree.GetItemPyData(CId)
+        else:
+            Comments = []
+        Super = data[1]['Super']
+        refList = np.copy(data[1]['RefList'])
+        Comments.append(' Changing %d reflection F^2^2 to F^2 from %s'%(len(refList),Name))
+        for ih,hkl in enumerate(refList):       #undo F--> F^2
+            hkl[5+Super] = np.sqrt(hkl[5+Super])
+            hkl[6+Super] = hkl[6+Super]/(2.0*hkl[5+Super])
+            hkl[7+Super] = np.sqrt(hkl[7+Super])
+        HKLFlist = []
+        if G2frame.GPXtree.GetCount():
+            item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
+            while item:
+                name = G2frame.GPXtree.GetItemText(item)
+                if name.startswith('HKLF ') and name not in HKLFlist:
+                    HKLFlist.append(name)
+                item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
+        newName = G2obj.MakeUniqueLabel(Name,HKLFlist)
+        newData = copy.deepcopy(data)
+        newData[0]['ranId'] = ran.randint(0,sys.maxsize)
+        newData[1]['RefList'] = refList
+        newData[0]['Nobs'] = refList.shape[0]
+        newData[0]['wR'] = 0.0
+        keys = list(newData[0].keys())
+        for item in keys:
+            if ':' in item:
+                del newData[0][item]
+        Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=newName)
+        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
+        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),Inst)
+        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection List'),{})  #dummy entry for GUI use
+        G2frame.GPXtree.SetItemPyData(Id,newData)
 
     def OnErrorAnalysis(event):
         '''Plots an "Abrams" plot - sorted delta/sig across data set.
@@ -8207,6 +8249,7 @@ def OnEditMag(**args):
         G2frame.Bind(wx.EVT_MENU, OnPlot1DHKL, id=G2G.wxID_1DHKLSTICKPLOT)
         G2frame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=G2G.wxID_PWD3DHKLPLOT)
         G2frame.Bind(wx.EVT_MENU, OnPlotAll3DHKL, id=G2G.wxID_3DALLHKLPLOT)
+        G2frame.Bind(wx.EVT_MENU, OnFixFsqFsq, id=G2G.wxID_FIXFSQSQDATA)
     if kind == 'PWDR':
         lbl = 'Powder'
     elif kind == 'SASD':

GSASII/GSASIIlattice.py

@@ -2662,7 +2662,7 @@ def CrsAng(H,cell,SGData):
         DR = np.inner(H3,np.inner(G,H3))
         DHR = np.inner(H,np.inner(G,H3))
     DHR /= np.sqrt(DR*DH)
-    phi = acosd(max(-1,min(DHR,1.)))
+    phi = acosd(DHR)
     if Laue == '-1':
         BA = H.T[1]*a/(b-H.T[0]*cosd(ga))
         BB = H.T[0]*sind(ga)**2

GSASII/GSASIIplot.py

@@ -7252,14 +7252,13 @@ def Draw(caller='',Fade=[],NPkey=False):
                         defCtrls = deformationData[-atom[ci]]
                         defParms = deformationData[atom[ci]]
                         SytSym = G2spc.SytSym(atom[cx:cx+3],SGData)[0]
-                        if defCtrls.get('showDef',False):
+                        if defCtrls.get('showDef',False) and defCtrls['Radial'] == 'Slater':
                             useAtColor = defCtrls.get('atColor',True) 
                             atcolor = None
                             if useAtColor:
                                 atcolor = atColor*255
-                            if defCtrls['Radial'] == 'Slater':
-                                SHC = defParms[0][1]
-                                SHC = {item.replace('D','C'):SHC[item] for item in SHC if item not in ['Ne','kappa']}
+                            SHC = defParms[0][1]
+                            SHC = {item.replace('D','C'):SHC[item] for item in SHC if item not in ['Ne','kappa']}
                             UVMat = defCtrls['UVmat']
                             Npsi,Ngam = 90,45 
                             PSI,GAM = np.mgrid[0:Npsi,0:Ngam]   #[azm,pol]

GSASII/GSASIIpwdGUI.py

@@ -7186,7 +7186,7 @@ def setBackgroundColors(im,it):
     def OnToggleExt(event):
         G2frame.Hide = not G2frame.Hide
         UpdateReflectionGrid(G2frame,data,HKLF=True,Name=Name)
-
+        
     def OnPageChanged(event):
         '''Respond to a press on a phase tab by displaying the reflections. This
         routine is needed because the reflection table may not have been created yet.