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DRAFT: MPAS Reader Updates #1310

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15 changes: 13 additions & 2 deletions test/test_mpas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,9 +18,20 @@
# Fill value
fv = INT_FILL_VALUE

def test_read_mpas():
"""Tests execution of _read_mpas()"""


def test_read_prima():
mpas_primal_ugrid, _ = _read_mpas(mpas_xr_ds, use_dual=False)

assert "face_edge_connectivity" in mpas_primal_ugrid
assert "face_node_connectivity" in mpas_primal_ugrid
assert "node_edge_connectivity" in mpas_primal_ugrid
assert "edge_face_connectivity" in mpas_primal_ugrid
assert "node_face_connectivity" in mpas_primal_ugrid
assert "edge_node_connectivity" in mpas_primal_ugrid
assert "face_face_connectivity" in mpas_primal_ugrid

def test_read_dual():
mpas_dual_ugrid, _ = _read_mpas(mpas_xr_ds, use_dual=True)

def test_mpas_to_grid():
Expand Down
150 changes: 59 additions & 91 deletions uxarray/io/_mpas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,9 @@ def _primal_to_ugrid(in_ds, out_ds):
_parse_face_nodes(in_ds, out_ds, mesh_type="primal")
_parse_node_faces(in_ds, out_ds, mesh_type="primal")

if "edgesOnVertex" in in_ds:
_parse_node_edges(in_ds, out_ds, mesh_type="primal")

if "verticesOnEdge" in in_ds:
_parse_edge_nodes(in_ds, out_ds, "primal")
source_dims_dict[in_ds["verticesOnEdge"].dims[0]] = "n_edge"
Expand Down Expand Up @@ -112,6 +115,9 @@ def _dual_to_ugrid(in_ds, out_ds):
_parse_face_nodes(in_ds, out_ds, mesh_type="dual")
_parse_node_faces(in_ds, out_ds, mesh_type="dual")

if "edgesOnCell" in in_ds:
_parse_node_edges(in_ds, out_ds, mesh_type="dual")

if "cellsOnEdge" in in_ds:
_parse_edge_nodes(in_ds, out_ds, mesh_type="dual")
source_dims_dict[in_ds["cellsOnEdge"].dims[0]] = "n_edge"
Expand Down Expand Up @@ -266,136 +272,96 @@ def _parse_edge_xyz_coords(in_ds, out_ds, mesh_type):


def _parse_face_nodes(in_ds, out_ds, mesh_type):
"""Parses face node connectivity for either the Primal or Dual Mesh."""
if mesh_type == "primal":
verticesOnCell = in_ds["verticesOnCell"].astype(INT_DTYPE)
nEdgesOnCell = in_ds["nEdgesOnCell"].astype(INT_DTYPE)

# Replace padded values with fill values
verticesOnCell = _replace_padding(verticesOnCell, nEdgesOnCell)

# Replace missing/zero values with fill values
verticesOnCell = _replace_zeros(verticesOnCell)

# Convert to zero-indexed
face_nodes = _to_zero_index(verticesOnCell)

else:
cellsOnVertex = in_ds["cellsOnVertex"].astype(INT_DTYPE)
"""Parses face to node connectivity for either the primal or dual mesh."""
key = "verticesOnCell" if mesh_type == "primal" else "cellsOnVertex"
arr = in_ds[key].astype(INT_DTYPE)

# Replace missing/zero values with fill values
cellsOnVertex = _replace_zeros(cellsOnVertex)
if mesh_type == "primal":
count = in_ds["nEdgesOnCell"].astype(INT_DTYPE)
arr = _replace_padding(arr, count)

# Convert to zero-indexed
face_nodes = _to_zero_index(cellsOnVertex)
arr = _replace_zeros(arr)
face_nodes = _to_zero_index(arr)

out_ds["face_node_connectivity"] = face_nodes.assign_attrs(
ugrid.FACE_NODE_CONNECTIVITY_ATTRS
).rename(dict(zip(face_nodes.dims, ugrid.FACE_NODE_CONNECTIVITY_DIMS)))


def _parse_edge_nodes(in_ds, out_ds, mesh_type):
"""Parses edge node connectivity for either the Primal or Dual Mesh."""
if mesh_type == "primal":
verticesOnEdge = in_ds["verticesOnEdge"].astype(INT_DTYPE)
"""Parses edge to node connectivity for either the primal or dual mesh."""
key = "verticesOnEdge" if mesh_type == "primal" else "cellsOnEdge"
arr = in_ds[key].astype(INT_DTYPE)

# Replace missing/zero values with fill values
verticesOnEdge = _replace_zeros(verticesOnEdge)

# Convert to zero-indexed
edge_nodes = _to_zero_index(verticesOnEdge)

else:
cellsOnEdge = in_ds["cellsOnEdge"].astype(INT_DTYPE)

# Replace missing/zero values with fill values
cellsOnEdge = _replace_zeros(cellsOnEdge)

# Convert to zero-indexed
edge_nodes = _to_zero_index(cellsOnEdge)
arr = _replace_zeros(arr)
edge_nodes = _to_zero_index(arr)

out_ds["edge_node_connectivity"] = edge_nodes.assign_attrs(
ugrid.EDGE_NODE_CONNECTIVITY_ATTRS
).rename(dict(zip(edge_nodes.dims, ugrid.EDGE_NODE_CONNECTIVITY_DIMS)))


def _parse_node_faces(in_ds, out_ds, mesh_type):
"""Parses node face connectivity for either the Primal or Dual Mesh."""
if mesh_type == "primal":
cellsOnVertex = in_ds["cellsOnVertex"].astype(INT_DTYPE)
"""Parses node to face connectivity for either the primal or dual mesh."""
key = "cellsOnVertex" if mesh_type == "primal" else "verticesOnCell"
arr = in_ds[key].astype(INT_DTYPE)

# Replace missing/zero values with fill values
cellsOnVertex = _replace_zeros(cellsOnVertex)
if mesh_type != "primal":
count = in_ds["nEdgesOnCell"].astype(INT_DTYPE)
arr = _replace_padding(arr, count)

# Convert to zero-indexed
node_faces = _to_zero_index(cellsOnVertex)
else:
verticesOnCell = in_ds["verticesOnCell"].astype(INT_DTYPE)
nEdgesOnCell = in_ds["nEdgesOnCell"].astype(INT_DTYPE)

# Replace padded values with fill values
verticesOnCell = _replace_padding(verticesOnCell, nEdgesOnCell)

# Replace missing/zero values with fill values
verticesOnCell = _replace_zeros(verticesOnCell)

# Convert to zero-indexed
node_faces = _to_zero_index(verticesOnCell)
arr = _replace_zeros(arr)
node_faces = _to_zero_index(arr)

out_ds["node_face_connectivity"] = node_faces.assign_attrs(
ugrid.NODE_FACE_CONNECTIVITY_ATTRS
).rename(dict(zip(node_faces.dims, ugrid.NODE_FACE_CONNECTIVITY_DIMS)))


def _parse_face_edges(in_ds, out_ds, mesh_type):
"""Parses face edge connectivity for either the Primal or Dual Mesh."""
if mesh_type == "primal":
edgesOnCell = in_ds["edgesOnCell"].astype(INT_DTYPE)
nEdgesOnCell = in_ds["nEdgesOnCell"].astype(INT_DTYPE)

# Replace padded values with fill values
edgesOnCell = _replace_padding(edgesOnCell, nEdgesOnCell)
def _parse_node_edges(in_ds, out_ds, mesh_type):
"""Parses node to edge connectivity for either the Primal or Dual Mesh."""
key = "edgesOnVertex" if mesh_type == "primal" else "edgesOnCell"
arr = in_ds[key].astype(INT_DTYPE)
arr = _replace_zeros(arr)
node_edges = _to_zero_index(arr)

# Replace missing/zero values with fill values
edgesOnCell = _replace_zeros(edgesOnCell)
out_ds["node_edge_connectivity"] = node_edges.assign_attrs(
ugrid.NODE_EDGE_CONNECTIVITY_ATTRS
).rename(dict(zip(node_edges.dims, ugrid.NODE_EDGE_CONNECTIVITY_DIMS)))

# Convert to zero-indexed
face_edges = _to_zero_index(edgesOnCell)

else:
edgesOnVertex = in_ds["edgesOnVertex"].astype(INT_DTYPE)
def _parse_face_edges(in_ds, out_ds, mesh_type):
"""Parses face to edge connectivity for either the primal or dual mesh."""
# choose the right source array
key = "edgesOnCell" if mesh_type == "primal" else "edgesOnVertex"
arr = in_ds[key].astype(INT_DTYPE)

# Replace missing/zero values with fill values
edgesOnVertex = _replace_zeros(edgesOnVertex)
# for the primal mesh, pad entries by the number of edges per cell
if mesh_type == "primal":
count = in_ds["nEdgesOnCell"].astype(INT_DTYPE)
arr = _replace_padding(arr, count)

# Convert to zero-indexed
face_edges = _to_zero_index(edgesOnVertex)
# replace zeros with the fill value, then convert to zero-based indexing
arr = _replace_zeros(arr)
face_edges = _to_zero_index(arr)

# write out with standard UGRID attrs and dims
out_ds["face_edge_connectivity"] = face_edges.assign_attrs(
ugrid.FACE_EDGE_CONNECTIVITY_ATTRS
).rename(dict(zip(face_edges.dims, ugrid.FACE_EDGE_CONNECTIVITY_DIMS)))


def _parse_edge_faces(in_ds, out_ds, mesh_type):
"""Parses edge face connectivity for either the Primal or Dual Mesh."""
if mesh_type == "primal":
cellsOnEdge = in_ds["cellsOnEdge"].astype(INT_DTYPE)

# Replace missing/zero values with fill values
cellsOnEdge = _replace_zeros(cellsOnEdge)

# Convert to zero-indexed
edge_faces = _to_zero_index(cellsOnEdge)
"""Parses edge to face connectivity for either the primal or dual mesh."""
# choose the right source array
key = "cellsOnEdge" if mesh_type == "primal" else "verticesOnEdge"
arr = in_ds[key].astype(INT_DTYPE)

else:
verticesOnEdge = in_ds["verticesOnEdge"].astype(INT_DTYPE)

# Replace missing/zero values with fill values
verticesOnEdge = _replace_zeros(verticesOnEdge)

# Convert to zero-indexed
edge_faces = _to_zero_index(verticesOnEdge)
# replace zeros with the fill value, then convert to zero-based indexing
arr = _replace_zeros(arr)
edge_faces = _to_zero_index(arr)

# write out with standard UGRID attrs and dims
out_ds["edge_face_connectivity"] = edge_faces.assign_attrs(
ugrid.EDGE_FACE_CONNECTIVITY_ATTRS
).rename(dict(zip(edge_faces.dims, ugrid.EDGE_FACE_CONNECTIVITY_DIMS)))
Expand Down Expand Up @@ -457,6 +423,8 @@ def _parse_face_areas(in_ds, out_ds, mesh_type):

def _parse_boundary_node_indices(in_ds, out_ds, mesh_type):
"""Parses the boundary node indices."""

# TODO:
boundary_node_mask = in_ds["boundaryVertex"]
boundary_node_indices = boundary_node_mask.where(boundary_node_mask).dropna(
dim=boundary_node_mask.dims[0]
Expand Down
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