Repository: UXARRAY/uxarray
Issue category: Performance Issue

Issue:
Optimize Face Centroid Calculations
If `Grid.face_lon` does not exist, `_populate_face_centroids()`, actually `_construct_face_centroids()` in it, takes extremely long for large datasets. For instance, the benchmark/profiling below is for a ~4GB SCREAM dataset, around 5 mins:

@rajeeja FYI: I'm already working on this and have gotten optimized results, which will be good for "cartesian" parts of the face center calculations, but you may want to look into the `Welzl` parts as well, i.e. `_populate_face_centerpoints()`.

<img width="1065" alt="Image" src="https://github.com/user-attachments/assets/9aba545f-0fdb-4a4c-b2be-b8fb9ffe087e" />



Hints:

Patch:
diff --git a/uxarray/grid/connectivity.py b/uxarray/grid/connectivity.py
index 78e936117..54bd1017e 100644
--- a/uxarray/grid/connectivity.py
+++ b/uxarray/grid/connectivity.py
@@ -146,13 +146,14 @@ def _build_n_nodes_per_face(face_nodes, n_face, n_max_face_nodes):
     """Constructs ``n_nodes_per_face``, which contains the number of non-fill-
     value nodes for each face in ``face_node_connectivity``"""
 
-    # padding to shape [n_face, n_max_face_nodes + 1]
-    closed = np.ones((n_face, n_max_face_nodes + 1), dtype=INT_DTYPE) * INT_FILL_VALUE
-
-    closed[:, :-1] = face_nodes.copy()
-
-    n_nodes_per_face = np.argmax(closed == INT_FILL_VALUE, axis=1)
-
+    n_face, n_max_face_nodes = face_nodes.shape
+    n_nodes_per_face = np.empty(n_face, dtype=INT_DTYPE)
+    for i in range(n_face):
+        c = 0
+        for j in range(n_max_face_nodes):
+            if face_nodes[i, j] != INT_FILL_VALUE:
+                c += 1
+        n_nodes_per_face[i] = c
     return n_nodes_per_face
 
 
diff --git a/uxarray/grid/coordinates.py b/uxarray/grid/coordinates.py
index 45e00ba42..2d78b978a 100644
--- a/uxarray/grid/coordinates.py
+++ b/uxarray/grid/coordinates.py
@@ -328,23 +328,25 @@ def _construct_face_centroids(node_x, node_y, node_z, face_nodes, n_nodes_per_fa
     tuple
         The x, y, and z coordinates of the centroids.
     """
+
     centroid_x = np.zeros((face_nodes.shape[0]), dtype=np.float64)
     centroid_y = np.zeros((face_nodes.shape[0]), dtype=np.float64)
     centroid_z = np.zeros((face_nodes.shape[0]), dtype=np.float64)
-    n_face = n_nodes_per_face.shape[0]
-
-    for i_face in prange(n_face):
-        n_max_nodes = n_nodes_per_face[i_face]
 
-        x = np.mean(node_x[face_nodes[i_face, 0:n_max_nodes]])
-        y = np.mean(node_y[face_nodes[i_face, 0:n_max_nodes]])
-        z = np.mean(node_z[face_nodes[i_face, 0:n_max_nodes]])
+    for face_idx in prange(face_nodes.shape[0]):
+        n_max_nodes = n_nodes_per_face[face_idx]
+        # Compute Cartesian Average
+        x = np.mean(node_x[face_nodes[face_idx, 0:n_max_nodes]])
+        y = np.mean(node_y[face_nodes[face_idx, 0:n_max_nodes]])
+        z = np.mean(node_z[face_nodes[face_idx, 0:n_max_nodes]])
 
+        # Normalize coordinates
         x, y, z = _normalize_xyz_scalar(x, y, z)
+        # Store coordinates
+        centroid_x[face_idx] = x
+        centroid_y[face_idx] = y
+        centroid_z[face_idx] = z
 
-        centroid_x[i_face] = x
-        centroid_y[i_face] = y
-        centroid_z[i_face] = z
     return centroid_x, centroid_y, centroid_z
 
 


Test patch: