Changeset 108

Timestamp:

Jul 7, 2010 4:08:38 PM (13 years ago)

Author:

vondreel

Message:

fix to GenHlaue?; add Hx2Rh & Rh2Hx
mod to ReadPDBPhase to use np.inner instead of np.sum
mod to ImRelease?
mods to ImageIntegrate?

Location:

trunk

Files:

• GSASIIIO.py (modified) (1 diff)
• GSASIIimage.py (modified) (2 diffs)
• GSASIIlattice.py (modified) (7 diffs)
• GSASIIplot.py (modified) (2 diffs)

trunk/GSASIIIO.py

@@ -969 +969 @@
         elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
             XYZ = [float(S[31:39]),float(S[39:47]),float(S[47:55])]
-            XYZ = np.sum(AB*XYZ,axis=1)
+            XYZ = np.inner(AB,XYZ)
             SytSym,Mult = G2spc.SytSym(XYZ,SGData)
             Uiso = float(S[61:67])/EightPiSq

trunk/GSASIIimage.py

@@ -524 +524 @@
     t0 = time.time()
     NST = np.zeros(shape=(numAzms,numChans),dtype=np.int,order='F')
-    H0 = np.zeros(shape=(numAzms,numChans),order='F')
+    H0 = np.zeros(shape=(numAzms,numChans),order='F',dtype=np.float32)
     H1 = np.zeros(shape=(numAzms+1,))
     H2 = np.zeros(shape=(numChans+1,))    
+    HST = [H0,H1,H2]
     NST,H0,H1,H2 = h2d.histogram2d(len(tax),tax,tay,taz,numAzms,numChans,LRazm,LUtth,NST,H0,H1,H2)
-    HST = [H0,H1,H2]
-    print "Binning elapsed time:","%8.3f"%(time.time()-t0), "s"
     return NST,HST
 
@@ -549 +548 @@
         print 'Bin image by 2-theta/azimuth intervals'
         NST,HST = Bin2ThetaAzimuthMap(data,tax,tay,taz)
+        print 'Binning complete'
         del tax,tay,taz
         dlg.Update(3)
         print 'Form normalized 1D pattern(s)'
-        self.Integrate = [HST[0]/NST,HST[1],HST[2]]
-        del NST,HST
+        HST[0] = np.divide(HST[0],NST)
+        print 'Normalize done'
+        self.Integrate = HST
+        del NST
         dlg.Update(4)
         t1 = time.time()

trunk/GSASIIlattice.py

@@ -149 +149 @@
        
 def MaxIndex(dmin,A):
-    #finds maximum allowed hkl for given A within dmin
     Hmax = [0,0,0]
     try:
@@ -186 +185 @@
     else:
         return [H[2],H[0],H[1]]
+        
+def Rh2Hx(Rh):
+    Hx = [0,0,0]
+    Hx[0] = Rh[0]-Rh[1]
+    Hx[1] = Rh[1]-Rh[2]
+    Hx[2] = np.sum(Rh)
+    return Hx
+    
+def Hx2Rh(Hx):
+        Rh = [0,0,0]
+        itk = -Hx[0]+Hx[1]+Hx[2]
+        if itk%3 != 0:
+            return 0        #error - not rhombohedral reflection
+        else:
+            Rh[1] = itk/3
+            Rh[0] = Rh[1]+Hx[0]
+            Rh[2] = Rh[1]-Hx[1]
+            if Rh[0] < 0:
+                for i in range(3):
+                    Rh[i] = -Rh[i]
+            return Rh
         
 def CentCheck(Cent,H):
@@ -368 +388 @@
 # part of reciprocal space ignoring anomalous dispersion
     import math
-    Hmax = MaxIndex(dmin,A)
+    #finds maximum allowed hkl for given A within dmin
+    if Laue in ['3R','3mR']:        #Rhombohedral axes
+        Hmax = [0,0,0]
+        cell = A2cell(A)
+        aHx = cell[0]*math.sqrt(2.0*(1.0-cosd(cell[3])))
+        cHx = cell[0]*math.sqrt(3.0*(1.0+2.0*cosd(cell[3])))
+        Hmax[0] = Hmax[1] = int(round(aHx/dmin))
+        Hmax[2] = int(round(cHx/dmin))
+        print Hmax,aHx,cHx
+    else:                           # all others
+        Hmax = MaxIndex(dmin,A)
+        
     dminsq = 1./(dmin**2)
     HKL = []
@@ -427 +458 @@
                 if Laue in ['3R','3']:
                     kmax = h
-                    kmin = -int((h-1)/2.)
+#                    kmin = -int((h-1.)/2.)
+                    kmin = -(h-1)/2
                 else:
                     kmin = 0
@@ -436 +468 @@
                     H = []
                     if CentCheck(Cent,[h,k,l]): H=[h,k,l]
+                    if Laue in ['3R','3mR']:
+                        H = Hx2Rh(H)
                     if H:
                         rdsq = calc_rDsq(H,A)
                         if 0 < rdsq <= dminsq:
                             HKL.append([h,k,l,1/math.sqrt(rdsq)])
+                            print H,1/math.sqrt(rdsq)
     else:                                   #cubic
         for h in range(Hmax[0]+1):
@@ -581 +616 @@
             assert np.allclose(ortho,to), msg
             assert np.allclose(frac,tf), msg
+            to = np.sum(A*frac,axis=1)
+            tf = np.sum(B*to,axis=1)
+            assert np.allclose(ortho,to), msg
+            assert np.allclose(frac,tf), msg
 
 # test GetBraviasNum(...) and GenHBravais(...)
@@ -649 +688 @@
         elif system == 'trigonal':
             permlist = [(1,2,3),(2,1,3),(-1,-2,3),(-2,-1,3)]
+        elif system == 'rhombohedral':
+            permlist = [(1,2,3),(2,3,1),(3,1,2),(-1,-2,-3),(-2,-3,-1),(-3,-1,-2)]
         else:
             permlist = [(1,2,3)]

trunk/GSASIIplot.py

@@ -665 +665 @@
         scalex = 1000./pixelSize[0]
         scaley = 1000./pixelSize[1]
+        print self.itemPicked
         if self.itemPicked is None and PickName == 'Image Controls':
             size = len(self.ImageZ)
@@ -815 +816 @@
         interpolation='nearest',vmin=0,vmax=2,extent=[0,Xmax,Xmax,0])
     Img = Plot.imshow(A,aspect='equal',cmap=acolor,
-        interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Xmax,0],picker=True)
+        interpolation='nearest',vmin=Imin,vmax=Imax,extent=[0,Xmax,Xmax,0])
 
     Plot.plot(xcent,ycent,'x')