Changeset 2043

Timestamp:

Nov 11, 2015 10:19:17 AM (8 years ago)

Author:

vondreele

Message:

some SS deriv work
trap G2frame.PatternId? = None (or 0) in PLotPatterns
put missing import numpy in G2img_1TIF.py

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIImath.py (modified) (2 diffs)
• GSASIIplot.py (modified) (4 diffs)
• imports/G2img_1TIF.py (modified) (3 diffs)

trunk/GSASII.py

@@ -1077 +1077 @@
             DataType = Iparm['INS   HTYPE '].strip()[:3]  # take 1st 3 chars
             # override inst values with values read from data file
+            Bank = rd.powderentry[2]    #should be used in multibank iparm files
             if rd.instdict.get('type'):
                 DataType = rd.instdict.get('type')

trunk/GSASIImath.py

@@ -1041 +1041 @@
     Xmod = np.swapaxes(Xmod,1,2)
     D = twopi*H[:,3][:,nxs]*glTau[nxs,:]              #m*e*tau; ops X 32
-    HdotX = twopi*np.inner(HP,Xmod)+D[:,nxs,:]        #ops x atoms X 32
+    HdotX = twopi*np.inner(HP,Xmod)        #ops x atoms X 32
     HdotXD = HdotX+D[:,nxs,:]
-    HdotXA = HP[:,nxs,nxs,nxs,:]*np.swapaxes(XmodA,-1,-2)[nxs,:,:,:,:]+D[:,nxs,nxs,:,nxs]  #ops x atoms x waves x 32 x xyz
-    HdotXB = HP[:,nxs,nxs,nxs,:]*np.swapaxes(XmodB,-1,-2)[nxs,:,:,:,:]+D[:,nxs,nxs,:,nxs]
+    HdotXA = twopi*HP[:,nxs,nxs,nxs,:]*np.swapaxes(XmodA,-1,-2)[nxs,:,:,:,:]+D[:,nxs,nxs,:,nxs]  #ops x atoms x waves x 32 x xyz
+    HdotXB = twopi*HP[:,nxs,nxs,nxs,:]*np.swapaxes(XmodB,-1,-2)[nxs,:,:,:,:]+D[:,nxs,nxs,:,nxs]
     if Af.shape[1]:
         tauF = np.arange(1.,Af.shape[1]+1-nf)[:,nxs]*glTau  #Fwaves x 32
@@ -1079 +1079 @@
     dHdXA = HP[:,nxs,nxs,nxs,:]*np.swapaxes(StauX,-1,-2)[nxs,:,:,:,:]    #ops x atoms x waves x 32 x xyz
     dHdXB = HP[:,nxs,nxs,nxs,:]*np.swapaxes(CtauX,-1,-2)[nxs,:,:,:,:]              #ditto
-    dGdMxCa = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(-twopi*dHdXA*np.sin(twopi*HdotXA))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
-    dGdMxCb = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(-twopi*dHdXB*np.sin(twopi*HdotXB))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
+    dGdMxCa = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(-dHdXA*np.sin(HdotXA))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
+    dGdMxCb = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(-dHdXB*np.sin(HdotXB))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
     dGdMxC = np.concatenate((dGdMxCa,dGdMxCb),axis=-1)
 # ops x atoms x waves x xyz - real part
-    dGdMxSa = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(twopi*dHdXA*np.cos(twopi*HdotXA))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)    
-    dGdMxSb = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(twopi*dHdXB*np.cos(twopi*HdotXB))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)    
+    dGdMxSa = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(dHdXA*np.cos(HdotXA))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)    
+    dGdMxSb = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(dHdXB*np.cos(HdotXB))*glWt[nxs,nxs,nxs,:,nxs],axis=-2)    
     dGdMxS = np.concatenate((dGdMxSa,dGdMxSb),axis=-1)
 # ops x atoms x waves x xyz - imaginary part

trunk/GSASIIplot.py

@@ -1042 +1042 @@
     global Ymax
     plottype = plotType
+    if not G2frame.PatternId:
+        return
 #patch
     data = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)
@@ -3116 +3118 @@
     Title += ' map for atom '+atom[0]+    \
         ' at %.4f %.4f %.4f'%(atxyz[0],atxyz[1],atxyz[2])
-    ix = -np.array(np.rint(rhoSize[:3]*atxyz),dtype='i')
+    ix = -np.array(np.rint(rhoSize[:3]*atxyz)+1,dtype='i')
     ix += (rhoSize[:3]/2)
     ix = ix%rhoSize[:3]
@@ -3122 +3124 @@
     ix = rhoSize[:3]/2
     ib = 4
+    hdx = [0,0,0]       #this needs to be something for an offset correction on atom positions
     if Ax == 'x':
+        Doff = (hdx[0]+Off)*.005
         slab = np.sum(np.sum(rho[:,ix[1]-ib:ix[1]+ib,ix[2]-ib:ix[2]+ib,:],axis=2),axis=1)
         Plot.plot(tau,wave[0])
     elif Ax == 'y':
+        Doff = (hdx[1]+Off)*.005
         slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,:,ix[2]-ib:ix[2]+ib,:],axis=2),axis=0)
         Plot.plot(tau,wave[1])
     elif Ax == 'z':
+        Doff = (hdx[2]+Off)*.005
         slab = np.sum(np.sum(rho[ix[0]-ib:ix[0]+ib,ix[1]-ib:ix[1]+ib,:,:],axis=1),axis=0)
         Plot.plot(tau,wave[2])
@@ -3137 +3143 @@
     acolor = mpl.cm.get_cmap('RdYlGn')
     if 'delt' in MapType:
-        Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Off*.005,.5+Off*.005),cmap=acolor)
+        Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Doff,.5+Doff),cmap=acolor)
     else:
-        Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Off*.005,.5+Off*.005))
+        Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Doff,.5+Doff))
     Page.canvas.draw()
    

trunk/imports/G2img_1TIF.py

@@ -21 +21 @@
 import GSASIIIO as G2IO
 import GSASIIpath
+import numpy as np
 GSASIIpath.SetVersionNumber("$Revision: $")
 class TIF_ReaderClass(G2IO.ImportImage):
@@ -197 +198 @@
                     print 'Read CHESS-detector tiff file: ',filename
                 image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
-            
+    elif 270 in IFD:
+        File.seek(IFD[270][2][0])
+        S = File.read(IFD[273][2][0]-IFD[270][2][0])
+        if 'ImageJ' in S:
+            tifType = 'ImageJ'
+            dataType = 0
+            pixy = [200,200]*IFD[277][2][0]
+            File.seek(IFD[273][2][0])
+            if not imageOnly:
+                print 'Read ImageJ tiff file: ',filename
+            image = ar.array('H',File.read(2*Npix))
+            if '>' in byteOrd:
+                image.byteswap()
+            image = np.array(np.asarray(image,dtype='H'),dtype=np.int32)            
     elif 262 in IFD and IFD[262][2][0] > 4:
         tifType = 'DND'
@@ -250 +264 @@
                 print 'Read 11-ID-C tiff file: ',filename
             image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
-        elif IFD[273][2][0] == 168:
-            tifType = 'ImageJ'
-            dataType = 0
-            pixy = [200,200]
-            File.seek(IFD[273][2][0])
-            if not imageOnly:
-                print 'Read ImageJ tiff file: ',filename
-            image = ar.array('H',File.read(2*Npix))
-            if '>' in byteOrd:
-                image.byteswap()
-            image = np.array(np.asarray(image,dtype='H'),dtype=np.int32)            
                     
     elif sizexy == [4096,4096]: