Changeset 824

Timestamp:

Jan 10, 2013 3:22:25 PM (9 years ago)

Author:

vondreele

Message:

added read of edf (European data file) image files
more work on texture restraints - no derivatives yet

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIIIO.py (modified) (4 diffs)
• GSASIImath.py (modified) (1 diff)
• GSASIIstruct.py (modified) (3 diffs)

trunk/GSASII.py

@@ -1182 +1182 @@
         dlg = wx.FileDialog(
             self, 'Choose image files', '.', '',
-            'Any image file (*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img)|'
-            '*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img;*.zip|'
+            'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img)|'
+            '*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img;*.zip|'
+            'European detector file (*.edf)|*.edf|'
             'Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|'
             'MAR file (*.mar*)|*.mar*|'

trunk/GSASIIIO.py

@@ -94 +94 @@
     if not ospath.exists(imagefile):
         dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
-        'Any image file (*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img)\
-        |*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img|\
+        'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img)\
+        |*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img|\
+        European detector file (*.edf)|*.edf|\
         Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|\
         MAR file (*.mar*)|*.mar*|\
@@ -116 +117 @@
     if ext == '.tif' or ext == '.tiff':
         Comments,Data,Npix,Image = GetTifData(imagefile)
+    elif ext == '.edf':
+        Comments,Data,Npix,Image = GetEdfData(imagefile)
     elif ext == '.img':
         Comments,Data,Npix,Image = GetImgData(imagefile)
@@ -142 +145 @@
     return Comments,Data,Npix,image
     
+def GetEdfData(filename,imageOnly=False):    
+    import struct as st
+    import array as ar
+    if not imageOnly:
+        print 'Read European detector data edf file: ',filename
+    File = open(filename,'rb')
+    head = File.read(3072)
+    lines = head.split('\n')
+    sizexy = [0,0]
+    pixSize = [0,0]
+    cent = [0,0]
+    head = ['European detector data',]
+    for line in lines:
+        fields = line.split()
+        if 'Dim_1' in line:
+            sizexy[0] = int(fields[2])
+        elif 'Dim_2' in line:
+            sizexy[1] = int(fields[2])
+        elif 'DataType' in line:
+            dType = fields[2]
+        elif 'refined_wavelength' in line:
+            wave = float(fields[2])
+        elif 'Size' in line:
+            imSize = int(fields[2])
+        elif 'DataType' in lines:
+            dType = fields[2]
+        elif 'pixel_size_x' in line:
+            pixSize[0] = float(fields[2])
+        elif 'pixel_size_y' in line:
+            pixSize[1] = float(fields[2])
+        elif 'beam_center_x' in line:
+            cent[0] = float(fields[2])
+        elif 'beam_center_y' in line:
+            cent[1] = float(fields[2])
+        elif 'refined_distance' in line:
+            dist = float(fields[2])
+        if line:
+            head.append(line)
+    if dType == 'UnsignedShort':        
+        image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
+    image = np.reshape(image,(sizexy[1],sizexy[0]))
+    data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
+    Npix = sizexy[0]*sizexy[1]
+    File.close()    
+    if imageOnly:
+        return image
+    else:
+        return head,data,Npix,image
+        
 def GetGEsumData(filename,imageOnly=False):
     import struct as st
@@ -285 +337 @@
     else:
         return head,data,Npix,image.T
-        
+
 def GetTifData(filename,imageOnly=False):
     import struct as st

trunk/GSASIImath.py

@@ -368 +368 @@
 def getRestPolefig(ODFln,SamSym,Grid):
     X,Y = np.meshgrid(np.linspace(1.,-1.,Grid),np.linspace(-1.,1.,Grid))
-    R,P = np.sqrt(X**2+Y**2).flatten(),atan2d(X,Y).flatten()
+    R,P = np.sqrt(X**2+Y**2).flatten(),atan2d(Y,X).flatten()
     R = np.where(R <= 1.,2.*atand(R),0.0)
     Z = np.zeros_like(R)

trunk/GSASIIstruct.py

@@ -2103 +2103 @@
                         ODFln = G2lat.Flnh(False,SHCoef,phi,beta,SGData)
                         R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid)
-                        Z = ma.masked_greater(Z,0.0)
-                    raise Exception
+                        Z1 = -ma.masked_greater(Z,0.0)
+                        IndZ1 = np.array(ma.nonzero(Z1))
+                        for ind in IndZ1.T:
+                            pNames.append('%d:%s:%d:%.2f:%.2f'%(pId,name,i,R[ind[0],ind[1]],P[ind[0],ind[1]]))
+                            pVals.append(Z1[ind[0]][ind[1]])
+                            pWt.append(wt/esd1**2)
+                        if ifesd2:
+                            Z2 = 1.-Z
+                            for ind in np.ndindex(grid,grid):
+                                pNames.append('%d:%s:%d:%.2f:%.2f'%(pId,name+'-unit',i,R[ind[0],ind[1]],P[ind[0],ind[1]]))
+                                pVals.append(Z1[ind[0]][ind[1]])
+                                pWt.append(wt/esd2**2)
          
     for item in varyList:
@@ -2127 +2137 @@
         SGData = General['SGData']
         AtLookup = G2mth.FillAtomLookUp(Phases[phase]['Atoms'])
-        Amat,Bmat = G2lat.cell2AB(General['Cell'][1:7])
+        cell = General['Cell'][1:7]
+        Amat,Bmat = G2lat.cell2AB(cell)
+        textureData = General['SH Texture']
+
+        SHCoef = textureData['SH Coeff'][1]
+        shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
+        SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
         phaseRest = restraintDict[phase]
         names = {'Bond':'Bonds','Angle':'Angles','Plane':'Planes',
             'Chiral':'Volumes','Torsion':'Torsions','Rama':'Ramas',
             'ChemComp':'Sites','Texture':'HKLs'}
+        lasthkl = np.array([0,0,0])
         for ip,pName in enumerate(pNames):
             pnames = pName.split(':')
@@ -2170 +2187 @@
                         mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cs+1))
                         deriv = mul*factors
-                elif name == 'Texture':
+                elif 'Texture' in name:
+                    hkl,grid,esd1,ifesd2,esd2 = itemRest[names[name]][id]
+                    if np.any(lasthkl-hkl):
+                        PH = np.array(hkl)
+                        phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData)
+                        ODFln = G2lat.Flnh(False,SHCoef,phi,beta,SGData)
+#                        R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid)
+                        lasthkl = copy.copy(hkl)                        
+                    if 'unit' in name:
+                        pass
+                    else:
+                        gam = float(pnames[3])
+                        phi = float(pnames[4])
+                        pass
+                    
                     raise Exception
                 for dName,drv in zip(dNames,deriv):