Merge pull request #266 from HEXRD/Peak-Profile

whole powder pattern fitting update
HEXRD · Jun 8, 2021 · ab052ce · ab052ce
2 parents 3687f33 + 8087248
commit ab052ce
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Showing 13 changed files with 6,429 additions and 4,288 deletions.
diff --git a/hexrd/WPPF.py b/hexrd/WPPF.py
diff --git a/hexrd/imageutil.py b/hexrd/imageutil.py
@@ -117,7 +117,7 @@ def snip1d_quad(y, w=4, numiter=2):
         # quadratic kernel
         kern2 = np.zeros(N)
         kern2[0] = kern2[-1] = -1./6.
-        kern2[int(p/2)] = kern2[int(3*p/2)] = 4./6.
+        kern2[int(p/2.)] = kern2[int(3.*p/2.)] = 4./6.
         kernels.append([kern1, kern2])
 
     z = b = _scale_image_snip(y, min_val, invert=False)

diff --git a/hexrd/instrument.py b/hexrd/instrument.py
@@ -67,10 +67,11 @@
 from hexrd.utils.concurrent import distribute_tasks
 from hexrd.utils.decorators import memoize
 from hexrd.valunits import valWUnit
-from hexrd.WPPF import LeBail
+from hexrd.wppf import LeBail
 
 from skimage.draw import polygon
 from skimage.util import random_noise
+from hexrd.wppf import wppfsupport
 
 try:
     from fast_histogram import histogram1d
@@ -1142,14 +1143,16 @@ def simulate_powder_pattern(self,
         eta1, eta2, eta3 : Mixing parameters
         '''
         if(params is None):
-            params = {'zero_error': [0.0, -1., 1., True],
-                      'U': [2e-1, -1., 1., True],
-                      'V': [2e-2, -1., 1., True],
-                      'W': [2e-2, -1., 1., True],
-                      'X': [2e-1, -1., 1., True],
-                      'Y': [2e-1, -1., 1., True]
-                      }
-
+            # params = {'zero_error': [0.0, -1., 1., True],
+            #           'U': [2e-1, -1., 1., True],
+            #           'V': [2e-2, -1., 1., True],
+            #           'W': [2e-2, -1., 1., True],
+            #           'X': [2e-1, -1., 1., True],
+            #           'Y': [2e-1, -1., 1., True]
+            #           }
+            params = wppfsupport._generate_default_parameters_LeBail(
+                mat_list, 
+                1)
         '''
         use the material list to obtain the dictionary of initial intensities
         we need to make sure that the intensities are properly scaled by the
@@ -1220,7 +1223,8 @@ def simulate_powder_pattern(self,
                 'synchrotron': wavelength
             },
             'bkgmethod': bkgmethod,
-            'intensity_init': intensity
+            'intensity_init': intensity,
+            'peakshape': 'pvtch'
         }
 
         self.WPPFclass = LeBail(**kwargs)

diff --git a/hexrd/unitcell.py b/hexrd/unitcell.py
@@ -90,14 +90,14 @@ def CalcWavelength(self):
 
     def calcBetaij(self):
 
-        self.betaij = np.zeros([self.atom_ntype, 3, 3])
+        self.betaij = np.zeros([3, 3, self.atom_ntype])
         for i in range(self.U.shape[0]):
             U = self.U[i, :]
-            self.betaij[i, :, :] = np.array([[U[0], U[3], U[4]],
+            self.betaij[:, :, i] = np.array([[U[0], U[3], U[4]],
                                              [U[3], U[1], U[5]],
                                              [U[4], U[5], U[2]]])
 
-            self.betaij[i, :, :] *= 2. * np.pi**2 * self._aij
+            self.betaij[:, :, i] *= 2. * np.pi**2 * self._aij
 
     def calcmatrices(self):
 
@@ -761,7 +761,7 @@ def CalcXRSF(self, hkl):
             ff = self.CalcXRFormFactor(Z, charge, s)
 
             if(self.aniU):
-                T = np.exp(-np.dot(hkl, np.dot(self.betaij[i, :, :], hkl)))
+                T = np.exp(-np.dot(hkl, np.dot(self.betaij[:, :, i], hkl)))
             else:
                 T = np.exp(-8.0*np.pi**2 * self.U[i]*s)