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fix 369 #370

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abae83d
fix 369
briochemc Aug 23, 2024
222a552
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 23, 2024
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92 changes: 46 additions & 46 deletions docs/postprocessing.ipynb
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10 changes: 5 additions & 5 deletions docs/tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -5253,7 +5253,7 @@
"<a id=\"units\"></a>\n",
"## Consistent CF bounds\n",
"Many of the CMIP6 models come with 'bound' dataarrays, that describe the extent of the finite grid cells.\n",
"For the longitude and latitude there are two conventions: 2-element 'bounds' (describing the width of a cell along the center) and 4 element 'verticies' (describing the 4 corner coordinates of the cell).\n",
"For the longitude and latitude there are two conventions: 2-element 'bounds' (describing the width of a cell along the center) and 4 element 'vertices' (describing the 4 corner coordinates of the cell).\n",
"`xmip` automatically renames these variables consistently and converts them so that every dataset has both conventions available.\n"
]
},
Expand Down Expand Up @@ -5376,11 +5376,11 @@
"Dimensions: (bnds: 2, lev: 60, member_id: 1, time: 1980, vertex: 4, x: 320, y: 384)\n",
"Coordinates:\n",
" lat (y, x) float64 dask.array<chunksize=(384, 320), meta=np.ndarray>\n",
" lat_verticies (y, x, vertex) float32 dask.array<chunksize=(384, 320, 4), meta=np.ndarray>\n",
" lat_vertices (y, x, vertex) float32 dask.array<chunksize=(384, 320, 4), meta=np.ndarray>\n",
" * lev (lev) float64 500.0 1.5e+03 2.5e+03 ... 5.125e+05 5.375e+05\n",
" lev_bounds (lev, bnds) float32 dask.array<chunksize=(60, 2), meta=np.ndarray>\n",
" lon (y, x) float64 dask.array<chunksize=(384, 320), meta=np.ndarray>\n",
" lon_verticies (y, x, vertex) float32 dask.array<chunksize=(384, 320, 4), meta=np.ndarray>\n",
" lon_vertices (y, x, vertex) float32 dask.array<chunksize=(384, 320, 4), meta=np.ndarray>\n",
" * y (y) float64 -79.22 -78.69 -78.15 -77.62 ... 89.11 89.66 89.71\n",
" * x (x) float64 1.062 2.187 3.312 4.437 ... 357.7 358.8 359.9\n",
" * time (time) float64 6.749e+05 6.749e+05 ... 7.351e+05 7.351e+05\n",
Expand Down Expand Up @@ -5454,8 +5454,8 @@
" lon (y, x) float32 dask.array<chunksize=(291, 360), meta=np.ndarray>\n",
" * time (time) int64 0 708 1416 2148 ... 1443192 1443924 1444656\n",
" time_bounds (time, bnds) float64 dask.array<chunksize=(1980, 2), meta=np.ndarray>\n",
" lat_verticies (y, x, vertex) float32 dask.array<chunksize=(291, 360, 4), meta=np.ndarray>\n",
" lon_verticies (y, x, vertex) float32 dask.array<chunksize=(291, 360, 4), meta=np.ndarray>\n",
" lat_vertices (y, x, vertex) float32 dask.array<chunksize=(291, 360, 4), meta=np.ndarray>\n",
" lon_vertices (y, x, vertex) float32 dask.array<chunksize=(291, 360, 4), meta=np.ndarray>\n",
" * bnds (bnds) int64 0 1\n",
" * vertex (vertex) int64 0 1 2 3\n",
" lon_bounds (bnds, y, x) float32 dask.array<chunksize=(1, 291, 360), meta=np.ndarray>\n",
Expand Down
34 changes: 17 additions & 17 deletions tests/test_grids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ def _test_data(grid_label="gn", z_axis=True):
[_add_small_rand(lev - 0.5), _add_small_rand(lev + 0.5)], dim="bnds"
)

lon_verticies = xr.concat(
lon_vertices = xr.concat(
[
_add_small_rand(lon_bounds_e),
_add_small_rand(lon_bounds_e),
Expand All @@ -77,7 +77,7 @@ def _test_data(grid_label="gn", z_axis=True):
],
dim="vertex",
)
lat_verticies = xr.concat(
lat_vertices = xr.concat(
[
_add_small_rand(lat_bounds_s),
_add_small_rand(lat_bounds_n),
Expand All @@ -94,8 +94,8 @@ def _test_data(grid_label="gn", z_axis=True):
lat=lat,
lon_bounds=lon_bounds,
lat_bounds=lat_bounds,
lon_verticies=lon_verticies,
lat_verticies=lat_verticies,
lon_vertices=lon_vertices,
lat_vertices=lat_vertices,
)

if z_axis:
Expand All @@ -115,7 +115,7 @@ def test_parse_bounds_vertex():
data = np.random.rand(4)

da = xr.DataArray(
data, dims=["vertex"], coords={"lon_verticies": lon_b, "lat_verticies": lat_b}
data, dims=["vertex"], coords={"lon_vertices": lon_b, "lat_vertices": lat_b}
)
test = _parse_bounds_vertex(da, "vertex", position=[0, 3])
print(test)
Expand Down Expand Up @@ -214,15 +214,15 @@ def test_recreate_metrics(xshift, yshift, z_axis):
if yshift == "left":
# dx
lon0, lon1 = grid.axes["X"]._get_neighbor_data_pairs(
_interp_vertex_to_bounds(ds_metrics.lon_verticies, "y").isel(bnds=0),
_interp_vertex_to_bounds(ds_metrics.lon_vertices, "y").isel(bnds=0),
xshift,
)
lat0, lat1 = grid.axes["X"]._get_neighbor_data_pairs(
ds_metrics.lat_bounds.isel(bnds=0), xshift
)
elif yshift == "right":
lon0, lon1 = grid.axes["X"]._get_neighbor_data_pairs(
_interp_vertex_to_bounds(ds_metrics.lon_verticies, "y").isel(bnds=1),
_interp_vertex_to_bounds(ds_metrics.lon_vertices, "y").isel(bnds=1),
xshift,
)
lat0, lat1 = grid.axes["X"]._get_neighbor_data_pairs(
Expand All @@ -234,15 +234,15 @@ def test_recreate_metrics(xshift, yshift, z_axis):
if xshift == "left":
# dx
lat0, lat1 = grid.axes["Y"]._get_neighbor_data_pairs(
_interp_vertex_to_bounds(ds_metrics.lat_verticies, "x").isel(bnds=0),
_interp_vertex_to_bounds(ds_metrics.lat_vertices, "x").isel(bnds=0),
yshift,
)
lon0, lon1 = grid.axes["Y"]._get_neighbor_data_pairs(
ds_metrics.lon_bounds.isel(bnds=0), yshift
)
elif xshift == "right":
lat0, lat1 = grid.axes["Y"]._get_neighbor_data_pairs(
_interp_vertex_to_bounds(ds_metrics.lat_verticies, "x").isel(bnds=1),
_interp_vertex_to_bounds(ds_metrics.lat_vertices, "x").isel(bnds=1),
yshift,
)
lon0, lon1 = grid.axes["Y"]._get_neighbor_data_pairs(
Expand All @@ -255,12 +255,12 @@ def test_recreate_metrics(xshift, yshift, z_axis):
else:
vertex_points = [2, 3]
lon0, lon1 = (
ds_metrics.lon_verticies.isel(vertex=vertex_points[0]),
ds_metrics.lon_verticies.isel(vertex=vertex_points[1]),
ds_metrics.lon_vertices.isel(vertex=vertex_points[0]),
ds_metrics.lon_vertices.isel(vertex=vertex_points[1]),
)
lat0, lat1 = (
ds_metrics.lat_verticies.isel(vertex=vertex_points[0]),
ds_metrics.lat_verticies.isel(vertex=vertex_points[1]),
ds_metrics.lat_vertices.isel(vertex=vertex_points[0]),
ds_metrics.lat_vertices.isel(vertex=vertex_points[1]),
)
dy_gx_expected = distance(lon0, lat0, lon1, lat1)

Expand All @@ -269,12 +269,12 @@ def test_recreate_metrics(xshift, yshift, z_axis):
else:
vertex_points = [1, 2]
lon0, lon1 = (
ds_metrics.lon_verticies.isel(vertex=vertex_points[0]),
ds_metrics.lon_verticies.isel(vertex=vertex_points[1]),
ds_metrics.lon_vertices.isel(vertex=vertex_points[0]),
ds_metrics.lon_vertices.isel(vertex=vertex_points[1]),
)
lat0, lat1 = (
ds_metrics.lat_verticies.isel(vertex=vertex_points[0]),
ds_metrics.lat_verticies.isel(vertex=vertex_points[1]),
ds_metrics.lat_vertices.isel(vertex=vertex_points[0]),
ds_metrics.lat_vertices.isel(vertex=vertex_points[1]),
)
dx_gy_expected = distance(lon0, lat0, lon1, lat1)

Expand Down
28 changes: 14 additions & 14 deletions tests/test_preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,8 +242,8 @@ def _lons_parsed_make_sense(
"lon_bounds",
"lat_bounds",
"time_bounds",
"lat_verticies",
"lon_verticies",
"lat_vertices",
"lon_vertices",
],
)
def test_correct_coordinates(coord):
Expand Down Expand Up @@ -293,8 +293,8 @@ def test_parse_lon_lat_bounds():
)

ds_test = parse_lon_lat_bounds(ds)
assert "lon_verticies" in ds_test.coords
assert "lat_verticies" in ds_test.coords
assert "lon_vertices" in ds_test.coords
assert "lat_vertices" in ds_test.coords

# introduce a time diemension
for wrong_coord in ["lon_bounds", "lat_bounds"]:
Expand Down Expand Up @@ -386,7 +386,7 @@ def test_maybe_convert_bounds_to_vertex():
lat_v = lat_v.reset_coords(drop=True)

ds_expected = ds.copy()
ds_expected = ds_expected.assign_coords(lon_verticies=lon_v, lat_verticies=lat_v)
ds_expected = ds_expected.assign_coords(lon_vertices=lon_v, lat_vertices=lat_v)

xr.testing.assert_identical(ds_expected, maybe_convert_bounds_to_vertex(ds))
# check that datasets that already conform to this are not changed
Expand All @@ -396,7 +396,7 @@ def test_maybe_convert_bounds_to_vertex():


def test_maybe_convert_vertex_to_bounds():
# create a ds with verticies
# create a ds with vertices
lon = np.arange(0, 10)
lat = np.arange(20, 30)
data = np.random.rand(len(lon), len(lat))
Expand All @@ -406,10 +406,10 @@ def test_maybe_convert_vertex_to_bounds():
ds.coords["lon"] = ds.x * xr.ones_like(ds.y)
ds.coords["lat"] = xr.ones_like(ds.x) * ds.y

ds.coords["lon_verticies"] = (
ds.coords["lon_vertices"] = (
xr.DataArray([-0.1, -0.1, 0.1, 0.1], dims=["vertex"]) + ds["lon"]
)
ds.coords["lat_verticies"] = (
ds.coords["lat_vertices"] = (
xr.DataArray([-0.1, 0.1, 0.1, -0.1], dims=["vertex"]) + ds["lat"]
)
ds = promote_empty_dims(ds)
Expand Down Expand Up @@ -459,24 +459,24 @@ def test_sort_vertex_order():
.expand_dims(["x", "y"])
.to_dataset(name="test")
)
da = da.assign_coords({"lon_verticies": lon_v, "lat_verticies": lat_v})
da = da.assign_coords({"lon_vertices": lon_v, "lat_vertices": lat_v})

da_sorted = sort_vertex_order(da).squeeze()
new = np.vstack((da_sorted.lon_verticies, da_sorted.lat_verticies)).T
new = np.vstack((da_sorted.lon_vertices, da_sorted.lat_vertices)).T

np.testing.assert_allclose(new, ordered_points)

assert da_sorted.lon_verticies.isel(vertex=0) < da_sorted.lon_verticies.isel(
assert da_sorted.lon_vertices.isel(vertex=0) < da_sorted.lon_vertices.isel(
vertex=3
)
assert da_sorted.lon_verticies.isel(vertex=1) < da_sorted.lon_verticies.isel(
assert da_sorted.lon_vertices.isel(vertex=1) < da_sorted.lon_vertices.isel(
vertex=2
)

assert da_sorted.lat_verticies.isel(vertex=0) < da_sorted.lat_verticies.isel(
assert da_sorted.lat_vertices.isel(vertex=0) < da_sorted.lat_vertices.isel(
vertex=1
)
assert da_sorted.lat_verticies.isel(vertex=3) < da_sorted.lat_verticies.isel(
assert da_sorted.lat_vertices.isel(vertex=3) < da_sorted.lat_vertices.isel(
vertex=2
)

Expand Down
34 changes: 17 additions & 17 deletions tests/test_preprocessing_cloud.py
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Expand Up @@ -308,7 +308,7 @@ def test_check_dim_coord_values(

# this fixture has to be redifined every time to account for different fail cases for each test
@pytest.fixture
def spec_check_bounds_verticies(request, gl, vi, ei, cat):
def spec_check_bounds_vertices(request, gl, vi, ei, cat):
expected_failures = (
not_supported_failures
+ intake_concat_failures
Expand All @@ -329,15 +329,15 @@ def spec_check_bounds_verticies(request, gl, vi, ei, cat):
return request


@pytest.mark.parametrize("spec_check_bounds_verticies", test_models, indirect=True)
def test_check_bounds_verticies(spec_check_bounds_verticies):
@pytest.mark.parametrize("spec_check_bounds_vertices", test_models, indirect=True)
def test_check_bounds_vertices(spec_check_bounds_vertices):
(
source_id,
variable_id,
experiment_id,
grid_label,
catalog,
) = spec_check_bounds_verticies.param
) = spec_check_bounds_vertices.param
ds, cat = data(
source_id, variable_id, experiment_id, grid_label, True, catalog=catalog
)
Expand All @@ -350,8 +350,8 @@ def test_check_bounds_verticies(spec_check_bounds_verticies):
if "vertex" in ds.dims:
np.testing.assert_allclose(ds.vertex.data, np.arange(4))

# Check for existing bounds and verticies
for co in ["lon_bounds", "lat_bounds", "lon_verticies", "lat_verticies"]:
# Check for existing bounds and vertices
for co in ["lon_bounds", "lat_bounds", "lon_vertices", "lat_vertices"]:
assert co in ds.coords
# make sure that all other dims are eliminated from the bounds.
assert (set(ds[co].dims) - set(["bnds", "vertex"])) == set(["x", "y"])
Expand All @@ -361,18 +361,18 @@ def test_check_bounds_verticies(spec_check_bounds_verticies):
# things are still weird.
test_ds = ds.where(abs(ds.lat) <= 40, drop=True)

vertex_lon_diff1 = test_ds.lon_verticies.isel(
vertex=3
) - test_ds.lon_verticies.isel(vertex=0)
vertex_lon_diff2 = test_ds.lon_verticies.isel(
vertex=2
) - test_ds.lon_verticies.isel(vertex=1)
vertex_lat_diff1 = test_ds.lat_verticies.isel(
vertex_lon_diff1 = test_ds.lon_vertices.isel(vertex=3) - test_ds.lon_vertices.isel(
vertex=0
)
vertex_lon_diff2 = test_ds.lon_vertices.isel(vertex=2) - test_ds.lon_vertices.isel(
vertex=1
) - test_ds.lat_verticies.isel(vertex=0)
vertex_lat_diff2 = test_ds.lat_verticies.isel(
vertex=2
) - test_ds.lat_verticies.isel(vertex=3)
)
vertex_lat_diff1 = test_ds.lat_vertices.isel(vertex=1) - test_ds.lat_vertices.isel(
vertex=0
)
vertex_lat_diff2 = test_ds.lat_vertices.isel(vertex=2) - test_ds.lat_vertices.isel(
vertex=3
)
for vertex_diff in [vertex_lon_diff1, vertex_lon_diff2]:
assert (vertex_diff <= 0).sum() <= (3 * len(vertex_diff.y))
# allowing for a few rows to be negative
Expand Down
24 changes: 12 additions & 12 deletions xmip/grids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@


def _parse_bounds_vertex(da, dim="bnds", position=[0, 1]):
"""Convenience function to extract positions from bounds/verticies"""
"""Convenience function to extract positions from bounds/vertices"""
return tuple([da.isel({dim: i}).load().data for i in position])


Expand Down Expand Up @@ -151,30 +151,30 @@ def recreate_metrics(ds, grid):
ew_bound_idx = [1]

# infer dx at tracer points
if "lon_bounds" in ds.coords and "lat_verticies" in ds.coords:
if "lon_bounds" in ds.coords and "lat_vertices" in ds.coords:
lon0, lon1 = _parse_bounds_vertex(ds["lon_bounds"])
lat0, lat1 = _parse_bounds_vertex(
_interp_vertex_to_bounds(ds["lat_verticies"], "x")
_interp_vertex_to_bounds(ds["lat_vertices"], "x")
)
dist = distance(lon0, lat0, lon1, lat1)
ds.coords["dx_t"] = xr.DataArray(dist, coords=ds.lon.coords)

# infer dy at tracer points
if "lat_bounds" in ds.coords and "lon_verticies" in ds.coords:
if "lat_bounds" in ds.coords and "lon_vertices" in ds.coords:
lat0, lat1 = _parse_bounds_vertex(ds["lat_bounds"])
lon0, lon1 = _parse_bounds_vertex(
_interp_vertex_to_bounds(ds["lon_verticies"], "y")
_interp_vertex_to_bounds(ds["lon_vertices"], "y")
)
dist = distance(lon0, lat0, lon1, lat1)
ds.coords["dy_t"] = xr.DataArray(dist, coords=ds.lon.coords)

if "lon_verticies" in ds.coords and "lat_verticies" in ds.coords:
if "lon_vertices" in ds.coords and "lat_vertices" in ds.coords:
# infer dx at the north/south face
lon0, lon1 = _parse_bounds_vertex(
ds["lon_verticies"], dim="vertex", position=ns_vertex_idx
ds["lon_vertices"], dim="vertex", position=ns_vertex_idx
)
lat0, lat1 = _parse_bounds_vertex(
ds["lat_verticies"], dim="vertex", position=ns_vertex_idx
ds["lat_vertices"], dim="vertex", position=ns_vertex_idx
)
dist = distance(lon0, lat0, lon1, lat1)
ds.coords["dx_gy"] = xr.DataArray(
Expand All @@ -183,10 +183,10 @@ def recreate_metrics(ds, grid):

# infer dy at the east/west face
lon0, lon1 = _parse_bounds_vertex(
ds["lon_verticies"], dim="vertex", position=ew_vertex_idx
ds["lon_vertices"], dim="vertex", position=ew_vertex_idx
)
lat0, lat1 = _parse_bounds_vertex(
ds["lat_verticies"], dim="vertex", position=ew_vertex_idx
ds["lat_vertices"], dim="vertex", position=ew_vertex_idx
)
dist = distance(lon0, lat0, lon1, lat1)
ds.coords["dy_gx"] = xr.DataArray(
Expand Down Expand Up @@ -223,7 +223,7 @@ def recreate_metrics(ds, grid):

# infer dx at the corner point
lon0, lon1 = grid.axes["X"]._get_neighbor_data_pairs(
_interp_vertex_to_bounds(ds.lon_verticies.load(), "y")
_interp_vertex_to_bounds(ds.lon_vertices.load(), "y")
.isel(bnds=ns_bound_idx)
.squeeze(),
axis_vel_pos["X"],
Expand All @@ -241,7 +241,7 @@ def recreate_metrics(ds, grid):

# infer dy at the corner point
lat0, lat1 = grid.axes["Y"]._get_neighbor_data_pairs(
_interp_vertex_to_bounds(ds.lat_verticies.load(), "x")
_interp_vertex_to_bounds(ds.lat_vertices.load(), "x")
.isel(bnds=ew_bound_idx)
.squeeze(),
axis_vel_pos["Y"],
Expand Down
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