Added new function for finding maxima of occupation

src/mdevaluate/extra/free_energy_landscape.py

@@ -44,7 +44,7 @@ def occupation_matrix(trajectory, edge_length=0.05, segments=1000, skip=0.1, nod
     occupation_df = pd.DataFrame(
         {"x": coords[0], "y": coords[1], "z": coords[2], "occupation": matbin_new}
     )
-    occupation_df = occupation_df.query("occupation != 0")
+    occupation_df = occupation_df.query("occupation != 0").reset_index(drop=True)
     return occupation_df
 
 
@@ -64,6 +64,32 @@ def _calc_histogram(numberlist, trajectory, bins):
     return matbin
 
 
+def find_maxima(occupation_df, box, edge_length=0.05):
+    maxima_df = occupation_df.copy()
+    maxima_df["maxima"] = None
+    points = np.array(maxima_df[["x", "y", "z"]])
+    tree = KDTree(points, boxsize=box)
+    all_neighbors = tree.query_ball_point(
+        points, edge_length * 3 ** (1 / 2) + edge_length / 100
+    )
+    for i in range(len(maxima_df)):
+        if maxima_df.loc[i, "maxima"] is not None:
+            continue
+        neighbors = np.array(all_neighbors[i])
+        neighbors = neighbors[neighbors != i]
+        if len(neighbors) == 0:
+            maxima_df.loc[i, "maxima"] = True
+        elif (
+                maxima_df.loc[neighbors, "occupation"].max()
+                < maxima_df.loc[i, "occupation"]
+        ):
+            maxima_df.loc[neighbors, "maxima"] = False
+            maxima_df.loc[i, "maxima"] = True
+        else:
+            maxima_df.loc[i, "maxima"] = False
+    return maxima_df
+
+
 def get_fel(
     traj,
     path,