Merge f800053 into accb829

diffsims/generators/diffraction_generator.py

@@ -270,7 +270,7 @@ def calculate_profile_data(
                 # Use Miller-Bravais indices for hexagonal lattices.
                 hkl = (hkl[0], hkl[1], -hkl[0] - hkl[1], hkl[2])
 
-            peaks[g_hkl] = [i_hkl, [tuple(hkl)], d_hkl]
+            peaks[tuple(hkl)] = [i_hkl, g_hkl, d_hkl]
 
         # Scale intensities so that the max intensity is 100.
         max_intensity = max([v[0] for v in peaks.values()])
@@ -280,9 +280,9 @@ def calculate_profile_data(
         d_hkls = []
         for k in sorted(peaks.keys()):
             v = peaks[k]
-            fam = get_unique_families(v[1])
+            fam = get_unique_families([k])
             if v[0] / max_intensity * 100 > minimum_intensity:
-                x.append(k)
+                x.append(v[1])
                 y.append(v[0])
                 hkls.append(fam)
                 d_hkls.append(v[2])

diffsims/sims/diffraction_simulation.py

@@ -20,6 +20,8 @@
 import numpy as np
 from scipy import ndimage as ndi
 
+from diffsims.utils.sim_utils import get_unique_families
+
 
 class DiffractionSimulation:
     """Holds the result of a kinematic diffraction pattern simulation.
@@ -148,16 +150,17 @@ def get_diffraction_pattern(self, size=512, sigma=10):
         the order of 0.5nm and a the default size and sigma are used.
         """
         side_length = np.min(np.multiply((size / 2), self.calibration))
-        mask_for_sides = np.all((np.abs(self.coordinates[:, 0:2]) < side_length), axis=1)
-
+        mask_for_sides = np.all(
+            (np.abs(self.coordinates[:, 0:2]) < side_length), axis=1
+        )
 
         spot_coords = np.add(
             self.calibrated_coordinates[mask_for_sides], size / 2
         ).astype(int)
         spot_intens = self.intensities[mask_for_sides]
         pattern = np.zeros([size, size])
-        #checks that we have some spots
-        if spot_intens.shape[0]==0:
+        # checks that we have some spots
+        if spot_intens.shape[0] == 0:
             return pattern
         else:
             pattern[spot_coords[:, 0], spot_coords[:, 1]] = spot_intens
@@ -200,10 +203,13 @@ def get_plot(self, g_max, annotate_peaks=True, with_labels=True, fontsize=12):
         fontsize : integer
             Fontsize for peak labels.
         """
+
+        label_hkl = get_unique_families(self.hkls.keys())
+
         ax = plt.gca()
         for g, i, hkls in zip(self.magnitudes, self.intensities, self.hkls):
             if g <= g_max:
-                label = ", ".join([str(hkl) for hkl in hkls.keys()])
+                label = ", ".join([str(hkl) for hkl in label_hkl.keys()])
                 ax.plot([g, g], [0, i], color="k", linewidth=3, label=label)
                 if annotate_peaks:
                     ax.annotate(label, xy=[g, i], xytext=[g, i], fontsize=fontsize)