def test_with_just_nodes_and_depths():
expected = two_triangles()
del expected.faces
del expected.edges
depth = UVar('depth',
'node',
np.array([1.0, 2.0, 3.0, 4.0]),
{'units': 'm',
'positive': 'down',
'standard_name': 'sea_floor_depth_below_geoid'})
expected.add_data(depth)
fname = '2_triangles_depth.nc'
with chdir(test_files):
expected.save_as_netcdf(fname)
grid = UGrid.from_ncfile(fname, load_data=True)
os.remove(fname)
assert grid.faces is None
assert grid.edges is None
assert np.array_equal(expected.nodes, grid.nodes)
assert np.array_equal(expected.data['depth'].data, grid.data['depth'].data)
assert expected.data['depth'].attributes == grid.data['depth'].attributes
def test_build_face_coordinates():
grid = two_triangles()
grid.build_face_coordinates()
coords = grid.face_coordinates
assert coords.shape == (2, 2)
assert np.allclose(coords, [(1.1, 0.76666667), (2.1, 1.43333333)])
def test_build_edges():
ugrid = two_triangles()
ugrid.build_edges()
edges = ugrid.edges
edges.sort(axis=0)
assert np.array_equal(edges, [[0, 1], [0, 2], [1, 2], [1, 3], [2, 3]])
def test_build_face_face_connectivity_small():
ugrid = two_triangles()
ugrid.build_face_face_connectivity()
face_face = ugrid.face_face_connectivity
assert np.array_equal(face_face[0], [-1, 1, -1])
assert np.array_equal(face_face[1], [-1, -1, 0])
def test_write_with_depths():
"""Tests writing a netcdf file with depth data."""
grid = two_triangles()
grid.mesh_name = 'mesh1'
# Create a UVar object for the depths:
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0, 4.0])
depths.attributes['units'] = 'm'
depths.attributes['standard_name'] = 'sea_floor_depth_below_geoid'
depths.attributes['positive'] = 'down'
grid.add_data(depths)
fname = 'temp.nc'
with chdir(test_files):
grid.save_as_netcdf(fname)
ds = netCDF4.Dataset(fname)
os.remove(fname)
assert nc_has_variable(ds, 'mesh1')
assert nc_has_variable(ds, 'depth')
assert nc_var_has_attr_vals(ds, 'depth', {
'coordinates': 'mesh1_node_lon mesh1_node_lat',
'location': 'node',
'mesh': 'mesh1'})
ds.close()
def test_write_with_edge_data():
"""Tests writing a netcdf file with data on the edges (fluxes, maybe?)."""
grid = two_triangles()
grid.mesh_name = 'mesh2'
# Create a UVar object for fluxes:
flux = UVar('flux', location='edge', data=[0.0, 0.0, 4.1, 0.0, 5.1, ])
flux.attributes['units'] = 'm^3/s'
flux.attributes['long_name'] = 'volume flux between cells'
flux.attributes['standard_name'] = 'ocean_volume_transport_across_line'
grid.add_data(flux)
# Add coordinates for edges.
grid.build_edge_coordinates()
fname = 'temp.nc'
with chdir(test_files):
grid.save_as_netcdf(fname)
ds = netCDF4.Dataset(fname)
os.remove(fname)
assert nc_has_variable(ds, 'mesh2')
assert nc_has_variable(ds, 'flux')
assert nc_var_has_attr_vals(ds, 'flux', {
'coordinates': 'mesh2_edge_lon mesh2_edge_lat',
'location': 'edge',
'units': 'm^3/s',
'mesh': 'mesh2'})
assert np.array_equal(ds.variables['mesh2_edge_lon'],
grid.edge_coordinates[:, 0])
assert np.array_equal(ds.variables['mesh2_edge_lat'],
grid.edge_coordinates[:, 1])
ds.close()
def test_set_mesh_name():
grid = two_triangles()
grid.mesh_name = 'mesh_2'
fname = 'temp.nc'
with chdir(test_files):
grid.save_as_netcdf(fname)
ds = netCDF4.Dataset(fname)
os.remove(fname)
assert nc_has_variable(ds, 'mesh_2')
assert nc_var_has_attr_vals(ds, 'mesh_2', {
'cf_role': 'mesh_topology',
'topology_dimension': 2,
'long_name': u'Topology data of 2D unstructured mesh'})
assert nc_var_has_attr_vals(ds, 'mesh_2', {
'cf_role': 'mesh_topology',
'topology_dimension': 2,
'long_name': u'Topology data of 2D unstructured mesh',
'node_coordinates': 'mesh_2_node_lon mesh_2_node_lat'})
assert nc_has_variable(ds, 'mesh_2_node_lon')
assert nc_has_variable(ds, 'mesh_2_node_lat')
assert nc_has_variable(ds, 'mesh_2_face_nodes')
assert nc_has_variable(ds, 'mesh_2_edge_nodes')
assert nc_has_dimension(ds, 'mesh_2_num_node')
assert nc_has_dimension(ds, 'mesh_2_num_edge')
assert nc_has_dimension(ds, 'mesh_2_num_face')
assert nc_has_dimension(ds, 'mesh_2_num_vertices')
assert not nc_var_has_attr(ds, 'mesh_2', 'face_edge_connectivity')
ds.close()
def test_with_just_nodes_and_depths():
expected = two_triangles()
del expected.faces
del expected.edges
depth = UVar(
"depth",
"node",
np.array([1.0, 2.0, 3.0, 4.0]),
{"units": "m", "positive": "down", "standard_name": "sea_floor_depth_below_geoid"},
)
expected.add_data(depth)
fname = "2_triangles_depth.nc"
with chdir(test_files):
expected.save_as_netcdf(fname)
grid = UGrid.from_ncfile(fname, load_data=True)
os.remove(fname)
assert grid.faces is None
assert grid.edges is None
assert np.array_equal(expected.nodes, grid.nodes)
assert np.array_equal(expected.data["depth"].data, grid.data["depth"].data)
assert expected.data["depth"].attributes == grid.data["depth"].attributes
def test_build_edges():
ugrid = two_triangles()
ugrid.build_edges()
edges = ugrid.edges
edges.sort(axis=0)
assert np.array_equal(edges, [[0, 1], [0, 2], [1, 2], [1, 3], [2, 3]])
def test_build_face_face_connectivity_small():
ugrid = two_triangles()
ugrid.build_face_face_connectivity()
face_face = ugrid.face_face_connectivity
assert np.array_equal(face_face[0], [-1, 1, -1])
assert np.array_equal(face_face[1], [-1, -1, 0])
def test_build_face_coordinates():
grid = two_triangles()
grid.build_face_coordinates()
coords = grid.face_coordinates
assert coords.shape == (2, 2)
assert np.allclose(coords, [(1.1, 0.76666667),
(2.1, 1.43333333)])
def test_build_boundaries_small():
ugrid = two_triangles()
ugrid.build_face_face_connectivity()
ugrid.build_boundaries()
boundaries = sorted(ugrid.boundaries.tolist())
expected_boundaries = [[0, 1], [1, 3], [2, 0], [3, 2]]
assert boundaries == expected_boundaries
def test_build_boundaries_small():
ugrid = two_triangles()
ugrid.build_face_face_connectivity()
ugrid.build_boundaries()
boundaries = sorted(ugrid.boundaries.tolist())
expected_boundaries = [[0, 1], [1, 3], [2, 0], [3, 2]]
assert boundaries == expected_boundaries
def test_build_edge_coordinates():
grid = two_triangles()
grid.build_edge_coordinates()
coords = grid.edge_coordinates
assert coords.shape == (5, 2)
assert np.allclose(
coords, [[1.1, 0.1], [2.6, 1.1], [2.1, 2.1], [0.6, 1.1], [1.6, 1.1]])
def test_add_edge_data_wrong():
"""Too long an array."""
grid = two_triangles()
# Create a UVar object for velocity:
# a miss-matched set.
bnds = UVar('bounds', location='edge', data=[0, 1, 0, 0, 1, 3, 3])
with pytest.raises(ValueError):
grid.add_data(bnds)
def test_build_boundary_coordinates():
grid = two_triangles()
grid.boundaries = [(0, 1), (0, 2), (2, 3), (1, 3)]
grid.build_boundary_coordinates()
coords = grid.boundary_coordinates
assert coords.shape == (4, 2)
assert np.allclose(coords,
[[1.1, 0.1], [0.6, 1.1], [2.1, 2.1], [2.6, 1.1]])
def test_add_edge_data_wrong():
"""Too long an array."""
grid = two_triangles()
# Create a UVar object for velocity:
# a miss-matched set.
bnds = UVar('bounds', location='edge', data=[0, 1, 0, 0, 1, 3, 3])
with pytest.raises(ValueError):
grid.add_data(bnds)
def test_add_node_data_wrong():
"""Too short an array."""
grid = two_triangles()
# Create a UVar object for the depths:
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0])
with pytest.raises(ValueError):
grid.add_data(depths)
def two_triangles_with_depths():
grid = two_triangles()
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0, 4.0])
depths.attributes['units'] = 'unknown'
depths.attributes['standard_name'] = 'sea_floor_depth_below_geoid'
depths.attributes['positive'] = 'down'
grid.add_data(depths)
return grid
def test_add_all_data():
"""You should not be able add a data dict directly."""
grid = two_triangles()
assert grid.data == {}
with pytest.raises(AttributeError):
grid.data = {
'depth': UVar('depth', location='node', data=[1.0, 2.0, 3.0, 4.0])
}
def test_add_face_data_wrong():
"""Too short an array."""
grid = two_triangles()
# Create a UVar object for velocity:
u_vel = UVar('u', location='face', data=[1.0])
with pytest.raises(ValueError):
grid.add_data(u_vel)
def test_add_face_data_wrong():
"""Too short an array."""
grid = two_triangles()
# Create a UVar object for velocity:
u_vel = UVar('u', location='face', data=[1.0])
with pytest.raises(ValueError):
grid.add_data(u_vel)
def test_add_node_data_wrong():
"""Too short an array."""
grid = two_triangles()
# Create a UVar object for the depths:
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0])
with pytest.raises(ValueError):
grid.add_data(depths)
def test_add_all_data():
"""You should not be able add a data dict directly."""
grid = two_triangles()
assert grid.data == {}
with pytest.raises(AttributeError):
grid.data = {'depth': UVar('depth',
location='node',
data=[1.0, 2.0, 3.0, 4.0])}
def two_triangles_with_depths():
grid = two_triangles()
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0, 4.0])
depths.attributes['units'] = 'unknown'
depths.attributes['standard_name'] = 'sea_floor_depth_below_geoid'
depths.attributes['positive'] = 'down'
grid.add_data(depths)
return grid
def test_add_edge_data():
grid = two_triangles()
# Create a UVar object for velocity:
bnds = UVar('bounds', location='edge', data=[0, 1, 0, 0, 1])
bnds.attributes['standard_name'] = 'boundary type'
grid.add_data(bnds)
assert grid.data['bounds'].name == 'bounds'
assert np.array_equal(grid.data['bounds'].data, [0, 1, 0, 0, 1])
def test_add_edge_data():
grid = two_triangles()
# Create a UVar object for velocity:
bnds = UVar('bounds', location='edge', data=[0, 1, 0, 0, 1])
bnds.attributes['standard_name'] = 'boundary type'
grid.add_data(bnds)
assert grid.data['bounds'].name == 'bounds'
assert np.array_equal(grid.data['bounds'].data, [0, 1, 0, 0, 1])
def test_build_edge_coordinates():
grid = two_triangles()
grid.build_edge_coordinates()
coords = grid.edge_coordinates
assert coords.shape == (5, 2)
assert np.allclose(coords, [[1.1, 0.1],
[2.6, 1.1],
[2.1, 2.1],
[0.6, 1.1],
[1.6, 1.1]])
def test_build_boundary_coordinates():
grid = two_triangles()
grid.boundaries = [(0, 1), (0, 2), (2, 3), (1, 3)]
grid.build_boundary_coordinates()
coords = grid.boundary_coordinates
assert coords.shape == (4, 2)
assert np.allclose(coords, [[1.1, 0.1],
[0.6, 1.1],
[2.1, 2.1],
[2.6, 1.1]])
def test_add_face_data():
grid = two_triangles()
# Create a UVar object for velocity:
u_vel = UVar('u', location='face', data=[1.0, 2.0])
u_vel.attributes['units'] = 'm/s'
u_vel.attributes['standard_name'] = 'eastward_sea_water_velocity'
grid.add_data(u_vel)
assert grid.data['u'].name == 'u'
assert grid.data['u'].attributes['units'] == 'm/s'
assert np.array_equal(grid.data['u'].data, [1.0, 2.0])
def test_add_face_data():
grid = two_triangles()
# Create a UVar object for velocity:
u_vel = UVar('u', location='face', data=[1.0, 2.0])
u_vel.attributes['units'] = 'm/s'
u_vel.attributes['standard_name'] = 'eastward_sea_water_velocity'
grid.add_data(u_vel)
assert grid.data['u'].name == 'u'
assert grid.data['u'].attributes['units'] == 'm/s'
assert np.array_equal(grid.data['u'].data, [1.0, 2.0])
def test_add_node_data():
grid = two_triangles()
# Create a UVar object for the depths:
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0, 4.0])
depths.attributes['units'] = 'm'
depths.attributes['standard_name'] = 'sea_floor_depth'
depths.attributes['positive'] = 'down'
grid.add_data(depths)
assert grid.data['depth'].name == 'depth'
assert grid.data['depth'].attributes['units'] == 'm'
assert np.array_equal(grid.data['depth'].data, [1.0, 2.0, 3.0, 4.0])
def test_add_node_data():
grid = two_triangles()
# Create a UVar object for the depths:
depths = UVar('depth', location='node', data=[1.0, 2.0, 3.0, 4.0])
depths.attributes['units'] = 'm'
depths.attributes['standard_name'] = 'sea_floor_depth'
depths.attributes['positive'] = 'down'
grid.add_data(depths)
assert grid.data['depth'].name == 'depth'
assert grid.data['depth'].attributes['units'] == 'm'
assert np.array_equal(grid.data['depth'].data, [1.0, 2.0, 3.0, 4.0])
def test_without_faces():
expected = two_triangles()
del expected.faces
assert expected.faces is None
fname = '2_triangles.nc'
with chdir(test_files):
expected.save_as_netcdf(fname)
grid = UGrid.from_ncfile(fname)
os.remove(fname)
assert grid.faces is None
assert np.array_equal(expected.faces, grid.faces)
assert np.array_equal(expected.edges, grid.edges)
def test_without_faces():
expected = two_triangles()
del expected.faces
assert expected.faces is None
fname = "2_triangles.nc"
with chdir(test_files):
expected.save_as_netcdf(fname)
grid = UGrid.from_ncfile(fname)
os.remove(fname)
assert grid.faces is None
assert np.array_equal(expected.faces, grid.faces)
assert np.array_equal(expected.edges, grid.edges)
def test_simple_write():
grid = two_triangles()
fname = 'temp.nc'
with chdir(test_files):
grid.save_as_netcdf(fname)
ds = netCDF4.Dataset(fname)
os.remove(fname)
# TODO: Could be lots of tests here.
assert nc_has_variable(ds, 'mesh')
assert nc_var_has_attr_vals(ds, 'mesh', {
'cf_role': 'mesh_topology',
'topology_dimension': 2,
'long_name': u'Topology data of 2D unstructured mesh'})
ds.close()
def test_with_faces():
"""
Test with faces, edges, but no `face_coordinates` or `edge_coordinates`.
"""
expected = two_triangles()
fname = "2_triangles.nc"
with chdir(test_files):
expected.save_as_netcdf(fname)
grid = UGrid.from_ncfile(fname)
os.remove(fname)
assert np.array_equal(expected.nodes, grid.nodes)
assert np.array_equal(expected.faces, grid.faces)
assert np.array_equal(expected.edges, grid.edges)
def test_with_faces():
"""
Test with faces, edges, but no `face_coordinates` or `edge_coordinates`.
"""
expected = two_triangles()
fname = '2_triangles.nc'
with chdir(test_files):
expected.save_as_netcdf(fname)
grid = UGrid.from_ncfile(fname)
os.remove(fname)
assert np.array_equal(expected.nodes, grid.nodes)
assert np.array_equal(expected.faces, grid.faces)
assert np.array_equal(expected.edges, grid.edges)
def test_write_with_bound_data():
"""
Tests writing a netcdf file with data on the boundaries
suitable for boundary conditions, for example fluxes.
"""
grid = two_triangles()
# Add the boundary definitions:
grid.boundaries = [(0, 1),
(0, 2),
(1, 3),
(2, 3)]
# Create a UVar object for boundary conditions:
bnds = UVar('bnd_cond', location='boundary', data=[0, 1, 0, 0])
bnds.attributes['long_name'] = 'model boundary conditions'
bnds.attributes['flag_values'] = '0 1'
bnds.attributes['flag_meanings'] = 'no_flow_boundary open_boundary'
grid.add_data(bnds)
fname = 'temp.nc'
with chdir(test_files):
grid.save_as_netcdf(fname)
ds = netCDF4.Dataset(fname)
os.remove(fname)
assert nc_has_variable(ds, 'mesh')
assert nc_has_variable(ds, 'bnd_cond')
assert nc_var_has_attr_vals(ds, 'mesh', {
'boundary_node_connectivity': 'mesh_boundary_nodes'})
assert nc_var_has_attr_vals(ds,
'bnd_cond',
{'location': 'boundary',
'flag_values': '0 1',
'flag_meanings': 'no_flow_boundary open_boundary',
'mesh': 'mesh',
})
# There should be no coordinates attribute or variable for the
# boundaries as there is no boundaries_coordinates defined.
assert not nc_has_variable(ds, 'mesh_boundary_lon')
assert not nc_has_variable(ds, 'mesh_boundary_lat')
assert not nc_var_has_attr(ds, 'bnd_cond', 'coordinates')
ds.close()
def test_add_boundary_data():
grid = two_triangles()
# Add the boundary definitions:
grid.boundaries = [(0, 1), (0, 2), (1, 3), (2, 3)]
# Create a UVar object for boundary conditions:
bnds = UVar('bounds', location='boundary', data=[0, 1, 0, 0, 1])
bnds.attributes['long_name'] = 'model boundary conditions'
# Wrong size for data.
with pytest.raises(ValueError):
grid.add_data(bnds)
# Correct data.
bnds.data = [0, 1, 0, 0]
grid.add_data(bnds)
assert grid.data['bounds'].name == 'bounds'
assert np.array_equal(grid.data['bounds'].data, [0, 1, 0, 0])
def test_write_with_velocities():
"""Tests writing a netcdf file with velocities on the faces."""
grid = two_triangles()
grid.mesh_name = 'mesh2'
# Create a UVar object for u velocity:
u_vel = UVar('u', location='face', data=[1.0, 2.0])
u_vel.attributes['units'] = 'm/s'
u_vel.attributes['standard_name'] = 'eastward_sea_water_velocity'
grid.add_data(u_vel)
# Create a UVar object for v velocity:
v_vel = UVar('v', location='face', data=[3.2, 4.3])
v_vel.attributes['units'] = 'm/s'
v_vel.attributes['standard_name'] = 'northward_sea_water_velocity'
grid.add_data(v_vel)
# Add coordinates for face data.
grid.build_face_coordinates()
fname = 'temp.nc'
with chdir(test_files):
grid.save_as_netcdf(fname)
ds = netCDF4.Dataset(fname)
os.remove(fname)
assert nc_has_variable(ds, 'mesh2')
assert nc_has_variable(ds, 'u')
assert nc_has_variable(ds, 'v')
assert nc_var_has_attr_vals(ds, 'u',
{'coordinates': 'mesh2_face_lon mesh2_face_lat',
'location': 'face',
'mesh': 'mesh2',
}
)
ds.close()
def test_add_boundary_data():
grid = two_triangles()
# Add the boundary definitions:
grid.boundaries = [(0, 1),
(0, 2),
(1, 3),
(2, 3)]
# Create a UVar object for boundary conditions:
bnds = UVar('bounds', location='boundary', data=[0, 1, 0, 0, 1])
bnds.attributes['long_name'] = 'model boundary conditions'
# Wrong size for data.
with pytest.raises(ValueError):
grid.add_data(bnds)
# Correct data.
bnds.data = [0, 1, 0, 0]
grid.add_data(bnds)
assert grid.data['bounds'].name == 'bounds'
assert np.array_equal(grid.data['bounds'].data, [0, 1, 0, 0])
