Enhance cell index retrieval in get_cell_indices_by_name function

- Improved handling of cell indices in the get_cell_indices_by_name function to accommodate cases where cell names may match multiple entries or be represented as slices or arrays.
- Updated test cases to utilize variables for initial and target cell names, enhancing code readability and maintainability.

Author: Starlitnightly

dynamo/prediction/least_action_path.py

@@ -1751,8 +1751,20 @@ def get_cell_indices_by_name(adata, cell_names):
     indices = []
     for name in cell_names:
         if name in adata.obs_names:
+            # get_loc with string is safe
             idx = adata.obs_names.get_loc(name)
-            indices.append(idx)
+            if isinstance(idx, slice):
+                # if name matches multiple cells (rare but possible with non-unique index)
+                # we'll take the first one to match original logic which appended single idx
+                start = idx.start if idx.start is not None else 0
+                indices.append(start)
+            elif isinstance(idx, np.ndarray):
+                 # mask
+                 where = np.where(idx)[0]
+                 if len(where) > 0:
+                     indices.append(where[0])
+            else:
+                indices.append(idx)
         else:
             print(f"Warning: Cell name '{name}' not found in adata.obs_names")
 

tests/test_pl.py

@@ -185,10 +185,12 @@ def test_lap_plots():
 
     HSC_cells_indices = nearest_neighbors(fixed_points[0], adata.obsm["X_umap"])
     Meg_cells_indices = nearest_neighbors(fixed_points[1], adata.obsm["X_umap"])
+    init_cells = [adata.obs_names[HSC_cells_indices[0]][0]]
+    target_cells = [adata.obs_names[Meg_cells_indices[0]][0]]
     dyn.pd.least_action(
         adata,
-        [adata.obs_names[HSC_cells_indices[0]][0]],
-        [adata.obs_names[Meg_cells_indices[0]][0]],
+        init_cells,
+        target_cells,
         basis="umap",
         adj_key="X_umap_distances",
         min_lap_t=True,