oops, forgot to pull before commits

Merge branch 'main' of github.com:AdvancedPhotonSource/GSAS-II

Author: briantoby

GSASII/GSASIIphsGUI2.py

@@ -332,7 +332,7 @@ def OnVvec(event):
                 Obj.SetValue(deformationData[-dId]['V'])
                 G2G.G2MessageBox(G2frame,'ERROR: V-vector zero or parallel to U','Invalid vector choice')
                 return
-            if nl.det(UVmat) < 0.:  #ensure right hand
+            if nl.det(UVmat) < 0.:  #insure right hand
                 UVmat *= -1.
             deformationData[-dId]['V'] =  Obj.GetValue()
             data['Deformations'][-dId]['UVmat'] = UVmat
@@ -343,7 +343,7 @@ def OnAtSel(event):
         wx.CallAfter(UpdateDeformation,G2frame,data,dId)
 
     def Kappa(deformation,orbSizer,dId,orb,kname,Indx):
-        orbSizer.Add(G2G.ValidatedTxtCtrl(deformation,orb[1][kname],0,nDig=(8,3),xmin=0.5,xmax=1.5))
+        orbSizer.Add(G2G.ValidatedTxtCtrl(deformation,orb[1][kname],0,nDig=(8,3),xmin=0.5,xmax=3.0))
         Tcheck = wx.CheckBox(deformation,-1,'Refine?')
         Tcheck.SetValue(orb[1][kname][1])
         Tcheck.Bind(wx.EVT_CHECKBOX,OnDeformRef)
@@ -618,6 +618,7 @@ def OnAtCol(event):
                                 for i in range(nB): orbSizer.Add((5,5),0)
                         Dsizer(deformation,orbSizer,Names,dId,orb,Indx)
         mainSizer.Add(orbSizer)    
+    G2frame.GetStatusBar().SetStatusText('On plot: RGB = XYZ',1)
 
     G2phsG.SetPhaseWindow(deformation,mainSizer)
 

GSASII/GSASIIplot.py

@@ -5,7 +5,6 @@
 # Note that documentation for GSASIIplot.py has been moved
 # to file docs/source/GSASIIplot.rst
 
-from __future__ import division, print_function
 import copy
 import math
 import sys
@@ -6747,6 +6746,34 @@ def RenderRBtriplet(orig,Q,Bmat,symAxis=None):
         GL.glDisable(GL.GL_COLOR_MATERIAL)
         GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[.2,.2,.2,1])
 
+    def RenderTriplet(orig,Rmat,Bmat):
+        '''draw an axes triplet located at the origin of a deformation atom
+        and with the x, y & z axes drawn as red, green and blue.
+        '''
+        GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[.7,.7,.7,1])
+        GL.glEnable(GL.GL_COLOR_MATERIAL)
+        GL.glLineWidth(3)
+        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(*orig)
+        GL.glBegin(GL.GL_LINES)
+        lines = np.inner(np.inner(np.eye(3),Rmat),Bmat)*.75
+        colors = [Rd,Gr,Bl]
+        # lines along axial directions
+        for line,color in zip(lines,colors):
+            GL.glColor3ubv(color)
+            GL.glVertex3fv(np.zeros(3))
+            GL.glVertex3fv(line)
+        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)
+        GL.glLightfv(GL.GL_LIGHT0,GL.GL_AMBIENT,[.2,.2,.2,1])
+
     def RenderPlane(plane,color):
         fade = list(color) + [.25,]
         GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_AMBIENT_AND_DIFFUSE,fade)
@@ -7351,11 +7378,13 @@ def Draw(caller='',Fade=[],NPkey=False):
                                 atcolor = atColor*255
                             defParms = deformationData[atom[ci]]
                             SytSym = G2spc.SytSym(atom[cx:cx+3],SGData)[0]
-                            SGM = np.array(G2spc.GetOpFromCode(atom[cs-1],SGData)[0])
                             SHC = defParms[0][1]
                             SHC = {item.replace('D','C'):SHC[item] for item in SHC if item not in ['Ne','kappa']}
+                            SGM = np.array(G2spc.GetOpFromCode(atom[cs-1],SGData)[0])
                             SGC = nl.inv(G2lat.CrysM2CartM(Amat,Bmat,SGM))
                             UVMat = np.inner(defCtrls['UVmat'],SGC.T)
+                            UVMat1 = np.inner(defCtrls['UVmat'].T,SGC.T).T
+                            RenderTriplet([x,y,z],UVMat1,Bmat)
                             Npsi,Ngam = 60,30 
                             PSI,GAM = np.mgrid[0:Npsi,0:Ngam]   #[azm,pol]
                             PSI = PSI.flatten()*360./Npsi  #azimuth 0-360 incl

GSASII/GSASIIpwdGUI.py

@@ -7431,6 +7431,9 @@ def MakeReflectionTable(phaseName):
             if 'T' in Inst['Type'][0]:
                 colLabels = ['H','K','L','flag','d','Fosq','sig','Fcsq','FoTsq','FcTsq','phase','ExtC','wave','tbar']
                 Types += 2*[wg.GRID_VALUE_FLOAT+':10,3',]
+            elif 'E' in Inst['Type'][0]:                
+                colLabels = ['H','K','L','flag','d','Fosq','sig','Fcsq','FoTsq','FcTsq','phase','ExtC','Nexp','Zpos']
+                Types += [wg.GRID_VALUE_LONG,wg.GRID_VALUE_FLOAT+':10,3',]
             if Super:
                 colLabels.insert(3,'M')
         else:

GSASII/imports/G2sfact.py

@@ -361,6 +361,66 @@ def Reader(self,filename, ParentFrame=None, **unused):
         except:
             return False
 
+class SHELX4ED_ReaderClass(G2obj.ImportStructFactor):
+    'Routines to import F**2, sig(F**2), exp# & Z-pos reflections from a Shelx HKLF 4 microED file'
+    def __init__(self):
+        if 'linux' in sys.platform:  # wx 3.0.0.0 on gtk does not like Unicode in menus
+            formatName = 'HKLF 4ed'
+            longFormatName = 'Shelx HKLF 4ed [hkl, Fo2, sig(Fo2), exp#, Z-pos] Structure factor text file'
+        else:
+            formatName = u'Shelx HKLF 4ed F\u00b2'
+            longFormatName = u'Shelx HKLF 4ed [hkl, Fo\u00b2, sig(Fo\u00b2), exp#, Z-pos] Structure factor text file'
+        super(self.__class__,self).__init__( # fancy way to self-reference
+            extensionlist=('.hkl','.HKL'),
+            strictExtension=False,
+            formatName=formatName,
+            longFormatName=longFormatName)
+
+    def ContentsValidator(self, filename):
+        'Make sure file contains the expected columns on numbers'
+        return True
+#        return ColumnValidator(self, filepointer)
+
+    def Reader(self,filename, ParentFrame=None, **unused):
+        'Read the file'
+        try:
+            fp = open(filename,'r')
+            for line,S in enumerate(fp):
+                self.errors = '  Error reading line '+str(line+1)
+                if S[0] == '#': continue       #ignore comments, if any
+                try:   # use a simple split if possible
+                    items = S.split()
+                    if len(items) > 5:
+                        h,k,l,Fo,sigFo,Nexp,Zpos = items[:7]
+                    else:
+                        h,k,l,Fo,sigFo = items[:5]
+                        Nexp = '0'
+                        Zpos = '0.'
+                    h,k,l = [int(h),int(k),int(l)]
+                except: # but sometimes if no space between k & F
+                        # need to use some fixed formatting
+                    h,k,l = S[:12].split()
+                    h,k,l = [int(h),int(k),int(l)]
+                    Fo,sigFo = S[12:].split()[:2]
+                if not any([h,k,l]):
+                    break
+                Fo = float(Fo)
+                sigFo = float(sigFo)
+                Nexp = int(Nexp)
+                Zpos = float(Zpos)
+                # h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
+                self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,1,Nexp,Zpos])
+                #self.RefDict['FF'].append({}) # now done in OnImportSfact
+            fp.close()
+            self.errors = 'Error after reading reflections (unexpected!)'
+            self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
+            self.RefDict['Type'] = 'SEC'
+            self.RefDict['Super'] = 0
+            self.UpdateParameters(Type='SEC',Wave=0.02851) # histogram type
+            return True
+        except:
+            return False
+            
 class M90_ReaderClass(G2obj.ImportStructFactor):
     'Routines to import F**2, sig(F**2) reflections from a JANA M90/M91 file'
     def __init__(self):