Add scan_positions

OpenChemistry · Sep 16, 2024 · 62b9478 · 62b9478
1 parent 7c8a771
commit 62b9478
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/python/stempy/io/sparse_array.py b/python/stempy/io/sparse_array.py
@@ -207,7 +207,9 @@ def from_hdf5(cls, filepath, keep_flyback=True, **init_kwargs):
                     end2 = (ii+1)*new_num_cols*num + num*ii
                     data[start:end] = frames[start2:end2]
                 scan_shape = (scan_shape[0]-1, scan_shape[1]) # update scan shape
-
+                # Create the proper scan_positions without the flyback column
+                scan_positions = np.ravel_multi_index([ii.ravel() for ii in np.indices(scan_shape)], scan_shape)
+
             # Load any metadata
             metadata = {}
             if 'metadata' in f: