UGRID Conformance, Grid Construction from Minimal Grid Variables (#628)

* initial work * work on convetnions * topology reader * work on topo, getitem for grid * work on conventions * run pre-commit * fix from face vertices * add sizes, dims, coordinates, and connectivity properties * reader * work on ugrid reader * use ugrid conventions module in esmf reader * update scrip reader * add test for from topo * update topology reader * update mpas reader * update exodus reader * update ugrid reader * fix tests after refactor * fix tests * update connectivity.py with refactor * update connectivity.py with refactor * investigate failing test * investigate failing test * investigate failing test * fix failing connectivity tests * testing * update grid.py * update user api * update face areas and add grid.to_netcdf * update ValueError * update internall api * add docstring to __getitem__ * add edge dimension to grid topology * docstring for Grid.to_netcdf * remove Grid.to_netcdf in favor of Grid.to_xarray * update repr * fix failing test * update docstrings * update repr * coments * fix failing test * remove leftover method in api * specify Cartesiain in xyz coordinates * add cartesiain coordinate names * update docstrings * update docstrings * update conventions --------- Co-authored-by: Hongyu Chen <hyvchen@ucdavis.edu> Co-authored-by: Orhan Eroglu <32553057+erogluorhan@users.noreply.github.com>
UXARRAY · Apr 1, 2024 · 545a18d · 545a18d
1 parent 556cdc7
commit 545a18d
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diff --git a/docs/user_api/index.rst b/docs/user_api/index.rst
@@ -220,6 +220,11 @@ Dimensions
    Grid.n_face
    Grid.n_max_face_nodes
    Grid.n_max_face_edges
+   Grid.n_max_face_faces
+   Grid.n_max_edge_edges
+   Grid.n_max_node_faces
+   Grid.n_max_node_edges
+   Grid.n_max_node_nodes
    Grid.n_nodes_per_face
 
 Spherical Coordinates
@@ -255,13 +260,12 @@ Connectivity
    :toctree: generated/
 
    Grid.face_node_connectivity
-   Grid.edge_node_connectivity
-   Grid.node_node_connectivity
    Grid.face_edge_connectivity
-   Grid.edge_edge_connectivity
-   Grid.node_edge_connectivity
    Grid.face_face_connectivity
+   Grid.edge_node_connectivity
+   Grid.edge_edge_connectivity
    Grid.edge_face_connectivity
+   Grid.node_edge_connectivity
    Grid.node_face_connectivity
 
 Grid Descriptors
@@ -279,7 +283,7 @@ Attributes
    :toctree: generated/
 
    Grid.grid_spec
-   Grid.parsed_attrs
+   Grid.attrs
 
 
 Plotting

diff --git a/test/constants.py b/test/constants.py
@@ -5,7 +5,7 @@
 NNODES_outCSne8 = 386
 NNODES_outCSne30 = 5402
 NNODES_outRLL1deg = 64442
-DATAVARS_outCSne30 = 2
+DATAVARS_outCSne30 = 4
 TRI_AREA = 1.047
 # 4*Pi is 12.56
 MESH30_AREA = 12.566

diff --git a/test/test_api.py b/test/test_api.py
@@ -131,7 +131,7 @@ def test_open_dataset_grid_kwargs(self):
         """Drops ``Mesh2_face_nodes`` from the inputted grid file using
         ``grid_kwargs``"""
 
-        with self.assertRaises(KeyError):
+        with self.assertRaises(ValueError):
             # attempt to open a dataset after dropping face nodes should raise a KeyError
             uxds = ux.open_dataset(
                 self.gridfile_ne30,

diff --git a/test/test_from_topology.py b/test/test_from_topology.py
@@ -0,0 +1,87 @@
+import uxarray as ux
+
+from uxarray.constants import INT_FILL_VALUE
+import numpy.testing as nt
+import os
+
+import pytest
+
+from pathlib import Path
+
+current_path = Path(os.path.dirname(os.path.realpath(__file__)))
+
+GRID_PATHS = [
+    current_path / 'meshfiles' / "mpas" / "QU" / 'oQU480.231010.nc',
+    current_path / "meshfiles" / "ugrid" / "geoflow-small" / "grid.nc",
+    current_path / "meshfiles" / "ugrid" / "outCSne30" / "outCSne30.ug"
+]
+
+
+
+
+def test_minimal_class_method():
+    """Tests the minimal required variables for constructing a grid using the
+    from topology class method."""
+
+    for grid_path in GRID_PATHS:
+        uxgrid = ux.open_grid(grid_path)
+
+        uxgrid_ft = ux.Grid.from_topology(node_lon=uxgrid.node_lon.values,
+                                          node_lat=uxgrid.node_lat.values,
+                                          face_node_connectivity=uxgrid.face_node_connectivity.values,
+                                          fill_value=INT_FILL_VALUE,
+                                          start_index=0)
+
+        nt.assert_array_equal(uxgrid.node_lon.values, uxgrid_ft.node_lon.values)
+        nt.assert_array_equal(uxgrid.node_lat.values, uxgrid_ft.node_lat.values)
+        nt.assert_array_equal(uxgrid.face_node_connectivity.values, uxgrid_ft.face_node_connectivity.values)
+
+
+def test_minimal_api():
+    """Tests the minimal required variables for constructing a grid using the
+    ``ux.open_dataset`` method."""
+
+    for grid_path in GRID_PATHS:
+        uxgrid = ux.open_grid(grid_path)
+
+        uxgrid_ft = ux.Grid.from_topology(node_lon=uxgrid.node_lon.values,
+                                          node_lat=uxgrid.node_lat.values,
+                                          face_node_connectivity=uxgrid.face_node_connectivity.values,
+                                          fill_value=INT_FILL_VALUE,
+                                          start_index=0)
+
+        grid_topology = {'node_lon': uxgrid.node_lon.values,
+                         'node_lat': uxgrid.node_lat.values,
+                         'face_node_connectivity': uxgrid.face_node_connectivity.values,
+                         'fill_value': INT_FILL_VALUE,
+                         'start_index': 0}
+
+        uxgrid_ft = ux.open_grid(grid_topology)
+
+        nt.assert_array_equal(uxgrid.node_lon.values, uxgrid_ft.node_lon.values)
+        nt.assert_array_equal(uxgrid.node_lat.values, uxgrid_ft.node_lat.values)
+        nt.assert_array_equal(uxgrid.face_node_connectivity.values, uxgrid_ft.face_node_connectivity.values)
+
+
+def test_dataset():
+    uxds = ux.open_dataset(GRID_PATHS[0], GRID_PATHS[0])
+
+    grid_topology = {'node_lon': uxds.uxgrid.node_lon.values,
+                     'node_lat': uxds.uxgrid.node_lat.values,
+                     'face_node_connectivity': uxds.uxgrid.face_node_connectivity.values,
+                     'fill_value': INT_FILL_VALUE,
+                     'start_index': 0,
+                     "dims_dict" : {"nVertices": "n_node"}}
+
+
+    uxds_ft = ux.open_grid(grid_topology, GRID_PATHS[1])
+
+    uxgrid = uxds.uxgrid
+    uxgrid_ft = uxds_ft
+
+
+    nt.assert_array_equal(uxgrid.node_lon.values, uxgrid_ft.node_lon.values)
+    nt.assert_array_equal(uxgrid.node_lat.values, uxgrid_ft.node_lat.values)
+    nt.assert_array_equal(uxgrid.face_node_connectivity.values, uxgrid_ft.face_node_connectivity.values)
+
+    assert uxds_ft.dims == {'n_face', 'n_node', 'n_max_face_nodes'}
diff --git a/test/test_grid.py b/test/test_grid.py
@@ -643,6 +643,8 @@ def test_build_face_edges_connectivity_mpas(self):
         """Tests the construction of (``Mesh2_edge_nodes``) on an MPAS grid
         with known edge nodes."""
 
+        from uxarray.grid.connectivity import _build_edge_node_connectivity
+
         # grid with known edge node connectivity
         mpas_grid_ux = ux.open_grid(self.mpas_filepath)
         edge_nodes_expected = mpas_grid_ux._ds['edge_node_connectivity'].values
@@ -652,8 +654,12 @@ def test_build_face_edges_connectivity_mpas(self):
         edge_nodes_expected = np.unique(edge_nodes_expected, axis=0)
 
         # construct edge nodes
-        _build_edge_node_connectivity(mpas_grid_ux, repopulate=True)
-        edge_nodes_output = mpas_grid_ux._ds['edge_node_connectivity'].values
+        edge_nodes_output, _, _ = _build_edge_node_connectivity(mpas_grid_ux.face_node_connectivity.values,
+                                                          mpas_grid_ux.n_face,
+                                                          mpas_grid_ux.n_max_face_nodes)
+
+        # _populate_face_edge_connectivity(mpas_grid_ux)
+        # edge_nodes_output = mpas_grid_ux._ds['edge_node_connectivity'].values
 
         self.assertTrue(np.array_equal(edge_nodes_expected, edge_nodes_output))
 
@@ -705,28 +711,6 @@ def test_build_face_edges_connectivity(self):
                     np.array_equal(reverted_mesh2_edge_nodes[i],
                                    original_face_nodes_connectivity[i]))
 
-    def test_build_face_edges_connectivity_mpas(self):
-        tgrid = ux.open_grid(self.mpas_filepath)
-
-        face_node_connectivity = tgrid._ds["face_node_connectivity"]
-
-        _populate_face_edge_connectivity(tgrid)
-        mesh2_face_edges = tgrid._ds.face_edge_connectivity
-        mesh2_edge_nodes = tgrid._ds.edge_node_connectivity
-
-        # Assert if the mesh2_face_edges sizes are correct.
-        self.assertEqual(mesh2_face_edges.sizes["n_face"],
-                         face_node_connectivity.sizes["n_face"])
-        self.assertEqual(mesh2_face_edges.sizes["n_max_face_edges"],
-                         face_node_connectivity.sizes["n_max_face_nodes"])
-
-        # Assert if the mesh2_edge_nodes sizes are correct.
-        # Euler formular for determining the edge numbers: n_face = n_edges - n_nodes + 2
-        num_edges = mesh2_face_edges.sizes["n_face"] + tgrid._ds[
-            "node_lon"].sizes["n_node"] - 2
-        size = mesh2_edge_nodes.sizes["n_edge"]
-        self.assertEqual(mesh2_edge_nodes.sizes["n_edge"], num_edges)
-
     def test_build_face_edges_connectivity_fillvalues(self):
         verts = [
             self.f0_deg, self.f1_deg, self.f2_deg, self.f3_deg, self.f4_deg,

diff --git a/uxarray/conventions/__init__.py b/uxarray/conventions/__init__.py
diff --git a/uxarray/conventions/descriptors.py b/uxarray/conventions/descriptors.py
@@ -0,0 +1,18 @@
+DESCRIPTOR_NAMES = ["face_areas", "edge_face_distances", "edge_node_distances"]
+
+
+FACE_AREAS_DIMS = ["n_face"]
+
+FACE_AREAS_ATTRS = {"cf_role": "face_areas"}
+
+EDGE_FACE_DISTANCES_DIMS = ["n_edge"]
+EDGE_FACE_DISTANCES_ATTRS = {
+    "cf_role": "edge_face_distances",
+    "long_name": "Distances between the face centers that " "saddle each edge",
+}
+
+EDGE_NODE_DISTANCES_DIMS = ["n_edge"]
+EDGE_NODE_DISTANCES_ATTRS = {
+    "cf_role": "edge_node_distances",
+    "long_name": "Distances between the nodes that make up " "each edge.",
+}