Changeset 292

Timestamp:

May 17, 2011 4:45:20 PM (11 years ago)

Author:

vondreele

Message:

allow more than one phase for calibration
fix temperature reading from 11BM header

Location:

trunk

Files:

• GSASII.py (modified) (2 diffs)
• GSASIIIO.py (modified) (1 diff)
• GSASIIimage.py (modified) (3 diffs)
• GSASIIpwd.py (modified) (6 diffs)
• ImageCalibrants.py (modified) (1 diff)

trunk/GSASII.py

@@ -452 +452 @@
                             Data['cutoff'] = 10
                             Data['pixLimit'] = 20
+                            Data['edgemin'] = 100000000
                             Data['calibdmin'] = 0.5
                             Data['calibskip'] = 0
@@ -468 +469 @@
                             Data['calibdmin'] = 0.5
                             Data['calibskip'] = 0
+                            Data['edgemin'] = 100000000
                             Data['ellipses'] = []
                             Data['calibrant'] = ''

trunk/GSASIIIO.py

@@ -80 +80 @@
             else:
                 Comments.append(S[:-1])
-                if 'Temp' in S:
-                    Temperature = float(S[:-1].split()[-1])
+                if 'Temp' in S.split('=')[0]:
+                    Temperature = float(S.split('=')[1])
         File.close()
     finally:

trunk/GSASIIimage.py

@@ -170 +170 @@
         return xpix,ypix,np.ravel(Z)[Zmax],np.ravel(Z)[Zmin]
     else:
-        return 0,0,0,0
+        return 0,0,0,0      
     
 def makeRing(dsp,ellipse,pix,reject,scalex,scaley,image):
@@ -326 +326 @@
     return abs(avg-curr)/avg < .02
 
+def EdgeFinder(image,data):          #this makes list of all x,y where I>edgeMin suitable for an ellipse search?
+    import numpy.ma as ma
+    Nx,Ny = data['size']
+    pixelSize = data['pixelSize']
+    edgemin = data['edgemin']
+    scalex = pixelSize[0]/1000.
+    scaley = pixelSize[1]/1000.    
+    tay,tax = np.mgrid[0:Nx,0:Ny]
+    tax = np.asfarray(tax*scalex,dtype=np.float32)
+    tay = np.asfarray(tay*scaley,dtype=np.float32)
+    tam = ma.getmask(ma.masked_less(image.flatten(),edgemin))
+    tax = ma.compressed(ma.array(tax.flatten(),mask=tam))
+    tay = ma.compressed(ma.array(tay.flatten(),mask=tam))
+    return zip(tax,tay)
+            
 def ImageCalibrate(self,data):
     import copy
@@ -373 +388 @@
     skip = data['calibskip']
     dmin = data['calibdmin']
-    Bravais,cell = calFile.Calibrants[data['calibrant']][:2]
-    A = G2lat.cell2A(cell)
+    Bravais,Cells = calFile.Calibrants[data['calibrant']][:2]
+    HKL = []
+    for bravais,cell in zip(Bravais,Cells):
+        A = G2lat.cell2A(cell)
+        hkl = G2lat.GenHBravais(dmin,bravais,A)[skip:]
+        HKL += hkl
+    HKL = G2lat.sortHKLd(HKL,True,False)
     wave = data['wavelength']
     cent = data['center']
     elcent,phi,radii = ellipse
-    HKL = G2lat.GenHBravais(dmin,Bravais,A)[skip:]
     dsp = HKL[0][3]
     tth = 2.0*asind(wave/(2.*dsp))

trunk/GSASIIpwd.py

@@ -55 +55 @@
     Parameters
     -----------------------------------------
-    x: array like 2-theta positions
+    x: array like 2-theta steps (-1 to 1)
     t: 2-theta position of peak
     s: sum(S/L,H/L); S: sample height, H: detector opening, 
         L: sample to detector opening distance
+    dx: 2-theta step size in deg
     Result for fcj.pdf
     -----------------------------------------
-    if x < t & s = S/L+H/L: 
-        fcj.pdf = [1/sqrt({cos(x)**2/cos(t)**2}-1) - 1/s]/cos(x)    
-    if x >= t:
+    if t < 90:
+        X = dx*x+t
+    else:
+        X = 180.-dx*x-t
+    if X < t & s = S/L+H/L: 
+        fcj.pdf = [1/sqrt({cos(x)**2/cos(t)**2}-1) - 1/s]/|cos(X)|    
+    if X >= t:
         fcj.pdf = 0    
     """
-    def _pdf(self,x,t,s):
-        ax = npcosd(x)**2
+    def _pdf(self,x,t,s,dx):
+        T = np.where(t<=90.,dx*x+t,180.-dx*x-t)
+        ax = npcosd(T)**2
         bx = npcosd(t)**2
         bx = np.where(ax>bx,bx,ax)
-        fx = np.where(ax>bx,(1./np.sqrt((ax/bx)-1.)-1./s)/npcosd(x),0.0)
-        return np.where(((x < t) & (fx > 0)),fx,0.0)
+        fx = np.where(ax>bx,(np.sqrt(bx/(ax-bx))-1./s)/np.sqrt(ax),0.0)
+        fx = np.where(fx > 0,fx,0.0)
+        return fx
 #    def _cdf(self, x):
 #    def _ppf(self, q):
@@ -90 +97 @@
     Parameters
     -----------------------------------------
-    x: array like 2-theta positions
+    x: array like 2-theta step numbers (-1 to 1)
     t: 2-theta position of peak
     h: detector opening height/sample to detector opening distance
     s: sample height/sample to detector opening distance
+    dx: 2-theta step size in deg
     Result for fcj2.pdf
     -----------------------------------------
+    if t < 90:
+        X = dx*x+t
+    else:
+        X = 180.-dx*x-t
     infl = acos(cos(t)*sqrt((h-s)**2+1))
-    if x < infl:    
-        fcj.pdf = [1/sqrt({cos(x)**2/cos(t)**2}-1) - 1/shl]/cos(2phi)
-    
-    for 2phi < 2tth & shl = S/L+H/L
-    
-    fcj.pdf(x,tth,shl) = 0
-    
+    if X < infl:    
+        fcj.pdf = [1/sqrt({cos(X)**2/cos(t)**2}-1) - 1/shl]/cos(X)    
+    for X < t & s = S/L+H/L    
+    fcj.pdf(x,t,s) = 0    
     for 2phi >= 2th
     """
-    def _pdf(self,x,t,h,s):
-        a = npcosd(t)*(np.sqrt((h-s)**2+1.))
-        infl = np.where((a <= 1.),npacosd(a),t)
-        ax = npcosd(x)**2
+    def _pdf(self,x,t,h,s,dx):
+        T = np.where(t<=90.,dx*x+t,180.-dx*x-t)
+        a = np.abs(npcosd(t))*(np.sqrt((h-s)**2+1.))
+        infl = np.where((a <= 1.),np.abs(npacosd(a)),T)
+        ax = npcosd(T)**2
         bx = npcosd(t)**2
         bx = np.where(ax>bx,bx,ax)
@@ -115 +125 @@
         W1 = h+s-H
         W2 = np.where ((h > s),2.*s,2.*h)
-        fx = 2.*h*np.sqrt((ax/bx)-1.)*npcosd(x)
+        fx = 2.*h*np.sqrt((ax/bx)-1.)*np.sqrt(ax)
         fx = np.where(fx>0.0,1./fx,0.0)
-        fx = np.where((x < infl),fx*W1,fx*W2)
+        fx = np.where((T < infl),fx*W1,fx*W2)
         return np.where((fx > 0.),fx,0.0)
 #    def _cdf(self, x):
@@ -133 +143 @@
     """
     Finger-Cox-Jephcoat D(2phi,2th) function for S/L != H/L using sum & difference
-    
-    fcj.pdf(x,tth,shl) = [1/sqrt({cos(2phi)**2/cos(2th)**2}-1) - 1/shl]/cos(2phi)
+    Ref: J. Appl. Cryst. (1994) 27, 892-900.
+    Parameters
+    -----------------------------------------
+    x: array like 2-theta positions
+    t: 2-theta position of peak
+    s: sum(S/L,H/L); S: sample height, H: detector opening, 
+        L: sample to detector opening distance
+    d: difference(S/L,H/L)
+    dx: 2-theta step size in deg
+    Result for fcj2.pdf
+    -----------------------------------------
+    if t < 90:
+        X = dx*x+t
+    else:
+        X = 180.-dx*x-t
+    
+    fcj.pdf(x,t,s,d) = [1/sqrt({cos(X)**2/cos(t)**2}-1) - 1/shl]/cos(2phi)
     
     for 2phi < 2tth & shl = S/L+H/L
@@ -142 +167 @@
     for 2phi >= 2th
     """
-    def _argcheck(self,t,s,d):
+    def _argcheck(self,t,s,d,dx):
         return (t > 0)&(s > 0)&(abs(d) < s)
-    def _pdf(self,x,t,s,d):
-        a = npcosd(t)*np.sqrt(d**2+1.)
-        infl = np.where((a < 1.),npacosd(a),t)
-        ax = npcosd(x)**2
+    def _pdf(self,x,t,s,d,dx):
+        T = np.where(t<=90.,dx*x+t,180.-dx*x-t)
+        a = np.abs(npcosd(t))*np.sqrt(d**2+1.)
+        infl = np.where((a < 1.),np.abs(npacosd(a)),T)
+        ax = npcosd(T)**2
         bx = npcosd(t)**2
         bx = np.where(ax>bx,bx,ax)
@@ -153 +179 @@
         W1 = s-H
         W2 = np.where ((d > 0),s-d,s+d)
-        fx = np.where(ax>bx,1./((s+d)*np.sqrt((ax/bx)-1.)*npcosd(x)),0.0)
-        fx = np.where((x < infl),fx*W1,fx*W2)
+        fx = np.where(ax>bx,1./((s+d)*np.sqrt((ax/bx)-1.)*np.sqrt(ax)),0.0)
+        fx = np.where((T < infl),fx*W1,fx*W2)
         return np.where((fx > 0.),fx,0.0)
 #    def _cdf(self, x):

trunk/ImageCalibrants.py

@@ -4 +4 @@
 #Useful Bravais nos.: F-cubic=0,I-cubic=1,P-cubic=2,R3/m(hex)=3, P6=4, P4mmm=6
 Calibrants={
-'':(0,(0,0,0,0,0,0),0,(0,0,0)),
-'LaB6  SRM660a':(2,(4.1569162,4.1569162,4.1569162,90,90,90),0,(0.5,20,10)),
-'LaB6  SRM660a skip 1':(2,(4.1569162,4.1569162,4.1569162,90,90,90),1,(0.5,20,10)),
-'LaB6  SRM660': (2,(4.15695,4.15695,4.15695,90,90,90),0,(0.5,20,10)),
-'Si    SRM640c':(0,(5.4311946,5.4311946,5.4311946,90,90,90),0,(0.5,20,10)),
-'CeO2  SRM674b':(0,(5.411651,5.411651,5.411651,90,90,90),0,(0.5,2,1)),
-'Al2O3 SRM676a':(3,(4.759091,4.759091,12.991779,90,90,120),0,(0.75,5,5)),
-'Ni   @ 298K':(0,(3.52475,3.52475,3.52475,90,90,90),0,(0.5,20,10)),
-'NaCl @ 298K':(0,(5.6402,5.6402,5.6402,90,90,90),0,(0.5,20,10)),
-'NaCl even hkl only':(2,(2.8201,2.8201,2.8201,90,90,90),0,(0.5,20,10)),
-'Ag behenate':(6,(1.0,1.0,58.380,90,90,90),0,(7.0,5,1)),
-'Spun Si grating':(6,(1.0,1.0,2777.78,90,90,90),2,(200.,5,1)),
-'Pt   @ 298K':(0,(3.9231,3.9231,3.9231,90,90,90),0,(0.5,5,1)),
-    }
+'':([0,],[(0,0,0,0,0,0),],0,(0,0,0)),
+'LaB6  SRM660a':([2,],[(4.1569162,4.1569162,4.1569162,90,90,90),],0,(0.5,20,10)),
+'LaB6  SRM660a skip 1':([2,],[(4.1569162,4.1569162,4.1569162,90,90,90),],1,(0.5,20,10)),
+'LaB6  SRM660': ([2,],[(4.15695,4.15695,4.15695,90,90,90),],0,(0.5,20,10)),
+'Si    SRM640c':([0,],[(5.4311946,5.4311946,5.4311946,90,90,90),],0,(0.5,20,10)),
+'CeO2  SRM674b':([0,],[(5.411651,5.411651,5.411651,90,90,90),],0,(0.5,2,1)),
+'Al2O3 SRM676a':([3,],[(4.759091,4.759091,12.991779,90,90,120),],0,(0.75,5,5)),
+'Ni   @ 298K':([0,],[(3.52475,3.52475,3.52475,90,90,90),],0,(0.5,20,10)),
+'NaCl @ 298K':([0,],[(5.6402,5.6402,5.6402,90,90,90),],0,(0.5,20,10)),
+'NaCl even hkl only':([2,],[(2.8201,2.8201,2.8201,90,90,90),],0,(0.5,20,10)),
+'Ag behenate':([6,],[(1.0,1.0,58.380,90,90,90),],0,(7.0,5,1)),
+'Spun Si grating':([6,],[(1.0,1.0,2777.78,90,90,90),],2,(200.,5,1)),
+'Pt   @ 298K':([0,],[(3.9231,3.9231,3.9231,90,90,90),],0,(0.5,5,1)),
+'LaB6 & CeO2':([2,0],[(4.1569162,4.1569162,4.1569162,90,90,90),(5.411651,5.411651,5.411651,90,90,90)],0,(0.5,2,1)),
+}
+