def test_with_time(tmpdir):
field = RasterModelGrid(4, 3)
field.add_field("node", "topographic__elevation",
np.ones(12, dtype=np.int64))
with tmpdir.as_cwd():
write_raster_netcdf("test.nc",
field,
append=False,
format="NETCDF4",
time=0.)
root = nc.Dataset("test.nc", "r", format="NETCDF4")
for name in ["topographic__elevation"]:
assert name in root.variables
assert_array_equal(root.variables[name][:],
[[[1, 1, 1], [1, 1, 1], [1, 1, 1], [1, 1, 1]]])
assert root.variables[name][:].dtype == "int64"
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
assert "t" in root.variables
assert_array_equal(root.variables["t"][:], [0.])
root.close()
def test_names_keyword(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("topographic__elevation", np.arange(12.0), at="node")
field.add_field("uplift_rate", 2.0 * np.arange(12.0), at="node")
with tmpdir.as_cwd():
write_raster_netcdf("test.nc",
field,
format="NETCDF3_64BIT",
names="uplift_rate")
root = nc.Dataset("test.nc", "r", format="NETCDF3_64BIT")
assert "topographic__elevation" not in root.variables
assert "uplift_rate" in root.variables
assert_array_equal(
root.variables["uplift_rate"],
[[
[0.0, 2.0, 4.0],
[6.0, 8.0, 10.0],
[12.0, 14.0, 16.0],
[18.0, 20.0, 22.0],
]],
)
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
root.close()
def test_append_without_time_netcdf3(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("topographic__elevation", np.ones(12), at="node")
with tmpdir.as_cwd():
write_raster_netcdf("test.nc",
field,
append=False,
format="NETCDF3_64BIT")
field.at_node["topographic__elevation"] *= 2
write_raster_netcdf("test.nc",
field,
append=True,
format="NETCDF3_64BIT")
root = nc.Dataset("test.nc", "r", format="NETCDF3_64BIT")
for name in ["topographic__elevation"]:
assert name in root.variables
assert_array_equal(root.variables[name][:],
[[[2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2]]])
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
assert "t" not in root.variables
root.close()
def write_output(self):
"""Write output to file as a netCDF.
Filenames will have the value of ``"output_filename"`` from the
input file or parameter dictionary as the first part of the file
name and the model run iteration as the second part of the
filename.
"""
self.calculate_cumulative_change()
filename = self._out_file_name + str(self.iteration).zfill(4) + ".nc"
self._output_files.append(filename)
try:
write_raster_netcdf(filename,
self.grid,
names=self.output_fields,
format="NETCDF4")
except NotImplementedError:
graph = Graph.from_dict({
"y_of_node": self.grid.y_of_node,
"x_of_node": self.grid.x_of_node,
"nodes_at_link": self.grid.nodes_at_link,
})
for field_name in self.output_fields:
graph._ds.__setitem__(field_name,
("node", self.grid.at_node[field_name]))
graph.to_netcdf(path=filename, mode="w", format="NETCDF4")
self.run_output_writers()
def test_without_time_netcdf3(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("node", "topographic__elevation", 2.0 * np.arange(12.0))
field.add_field("node", "uplift_rate", 2.0 * np.arange(12.0))
with tmpdir.as_cwd():
write_raster_netcdf("test.nc", field, format="NETCDF3_64BIT")
root = nc.Dataset("test.nc", "r", format="NETCDF3_64BIT")
for name in ["uplift_rate", "topographic__elevation"]:
assert name in root.variables
assert_array_equal(
root.variables[name][:],
[[
[0.0, 2.0, 4.0],
[6.0, 8.0, 10.0],
[12.0, 14.0, 16.0],
[18.0, 20.0, 22.0],
]],
)
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
assert "t" not in root.variables
root.close()
def test_append_with_time(tmpdir):
field = RasterModelGrid(4, 3)
field.add_field("node", "topographic__elevation", np.ones(12, dtype=np.int64))
with tmpdir.as_cwd():
write_raster_netcdf("test.nc", field, append=False, format="NETCDF4", time=0)
field.at_node["topographic__elevation"] *= 2
write_raster_netcdf("test.nc", field, append=True, format="NETCDF4", time=1.)
root = nc.Dataset("test.nc", "r", format="NETCDF4")
for name in ["topographic__elevation"]:
assert name in root.variables
assert_array_equal(
root.variables[name][:],
[
[[1, 1, 1], [1, 1, 1], [1, 1, 1], [1, 1, 1]],
[[2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2]],
],
)
assert root.variables[name][:].dtype == "int64"
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 2
assert "t" in root.variables
assert_array_equal(root.variables["t"][:], [0., 1.])
root.close()
def test_with_time_netcdf3(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("node", "topographic__elevation", 2.0 * np.arange(12.0))
field.add_field("node", "uplift_rate", 2.0 * np.arange(12.0))
with tmpdir.as_cwd():
write_raster_netcdf("test.nc", field, format="NETCDF3_64BIT", time=10.0)
root = nc.Dataset("test.nc", "r", format="NETCDF3_64BIT")
for name in ["uplift_rate", "topographic__elevation"]:
assert name in root.variables
assert_array_equal(
root.variables[name][:],
[
[
[0.0, 2.0, 4.0],
[6.0, 8.0, 10.0],
[12.0, 14.0, 16.0],
[18.0, 20.0, 22.0],
]
],
)
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
assert "t" in root.variables
assert_array_equal(root.variables["t"][:], [10.0])
root.close()
def run_one_step(self, dt=None, output=None, names=None):
"""Run each component for one time step."""
dt = dt or self.clock.step
self.advance_components(dt)
self.clock.advance(step=dt)
if output:
write_raster_netcdf(output, self.grid, append=True, names=names)
def run(self, output=None, names=None):
"""Run the model until complete."""
if output:
write_raster_netcdf(output, self.grid, append=False, names=names)
try:
while 1:
self.run_one_step(output=output, names=names)
except StopIteration:
pass
def main():
parser = argparse.ArgumentParser()
parser.add_argument('file', nargs='?', help='plume config file')
parser.add_argument('--output', help='output file')
parser.add_argument('--verbose', action='store_true',
help='be verbose')
parser.add_argument('--plot', choices=('c', 'cs', 'dz'), default=None,
help='value to plot')
parser.add_argument('--set', action='append', default=[],
help='set plume parameters')
args = parser.parse_args()
params = DEFAULT_PARAMS
if args.file:
params_from_file = load_params(args.file)
for group in params.keys():
params[group].update(params_from_file.get(group, {}))
params_from_cl = load_params_from_strings(args.set)
for group in params.keys():
params[group].update(params_from_cl.get(group, {}))
if args.verbose:
print(yaml.dump(params, default_flow_style=False))
params['river']['angle'] = np.deg2rad(params['river']['angle'])
grid = RasterModelGrid(params['grid']['shape'],
spacing=params['grid']['spacing'],
origin=params['grid']['origin'])
plume = Plume(grid,
river_width=params['river']['width'],
river_depth=params['river']['depth'],
river_velocity=params['river']['velocity'],
river_angle=params['river']['angle'],
river_loc=params['river']['location'],
ocean_velocity=params['ocean']['along_shore_velocity'],
)
plume.grid.at_grid['sediment__removal_rate'] = params['sediment']['removal_rate']
plume.grid.at_grid['sediment__bulk_density'] = params['sediment']['bulk_density']
deposit = plume.calc_deposit_thickness(params['sediment']['removal_rate'])
if args.plot:
imshow_grid(plume.grid, plume.grid.at_node[LONG_NAME[args.plot]],
at='node', show=True)
if args.output:
write_raster_netcdf(args.output, plume.grid)
def run_one_step(self):
""" Write output to file as a netCDF. """
filename_prefix = self.filename_prefix
filename = f"{filename_prefix}.nc"
filepath = os.path.join(self.output_dir, filename)
grid = self.model.grid
if isinstance(grid, RasterModelGrid):
write_raster_netcdf(filepath,
grid,
names=self.output_fields,
format="NETCDF4")
else:
to_netcdf(grid, filepath, format="NETCDF4")
self.register_output_filepath(filepath)
def write_output(self, params, field_names=None):
"""Write output to file (currently netCDF)."""
# Exclude fields with int64 (incompatible with netCDF3)
if field_names is None:
field_names = []
for field in self.grid.at_node:
if type(self.grid.at_node[field][0]) is not np.int64:
field_names.append(field)
self.calculate_cumulative_change()
filename = self.params['output_filename'] + str(self.iteration).zfill(4) \
+ '.nc'
write_raster_netcdf(filename,
self.grid,
names=field_names,
format='NETCDF4')
def test_without_time(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("node", "topographic__elevation", np.ones(12, dtype=np.int64))
with tmpdir.as_cwd():
write_raster_netcdf("test.nc", field, append=False, format="NETCDF4")
root = nc.Dataset("test.nc", "r", format="NETCDF4")
for name in ["topographic__elevation"]:
assert name in root.variables
assert_array_equal(
root.variables[name][:], [[[1, 1, 1], [1, 1, 1], [1, 1, 1], [1, 1, 1]]]
)
assert root.variables[name][:].dtype == "int64"
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
assert "t" not in root.variables
root.close()
def test_append_without_time_netcdf3(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("topographic__elevation", np.ones(12), at="node")
with tmpdir.as_cwd():
write_raster_netcdf("test.nc", field, append=False, format="NETCDF3_64BIT")
field.at_node["topographic__elevation"] *= 2
write_raster_netcdf("test.nc", field, append=True, format="NETCDF3_64BIT")
root = nc.Dataset("test.nc", "r", format="NETCDF3_64BIT")
for name in ["topographic__elevation"]:
assert name in root.variables
assert_array_equal(
root.variables[name][:], [[[2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2]]]
)
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
assert "t" not in root.variables
root.close()
def test_append_with_time(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("topographic__elevation",
np.ones(12, dtype=np.int64),
at="node")
with tmpdir.as_cwd():
write_raster_netcdf("test.nc",
field,
append=False,
format="NETCDF4",
time=0)
field.at_node["topographic__elevation"] *= 2
write_raster_netcdf("test.nc",
field,
append=True,
format="NETCDF4",
time=1.0)
root = nc.Dataset("test.nc", "r", format="NETCDF4")
for name in ["topographic__elevation"]:
assert name in root.variables
assert_array_equal(
root.variables[name],
[
[[1, 1, 1], [1, 1, 1], [1, 1, 1], [1, 1, 1]],
[[2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2]],
],
)
assert root.variables[name].dtype == "int64"
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 2
assert "t" in root.variables
assert_array_equal(root.variables["t"], [0.0, 1.0])
root.close()
def test_names_keyword(tmpdir):
field = RasterModelGrid((4, 3))
field.add_field("node", "topographic__elevation", np.arange(12.))
field.add_field("node", "uplift_rate", 2. * np.arange(12.))
with tmpdir.as_cwd():
write_raster_netcdf(
"test.nc", field, format="NETCDF3_64BIT", names="uplift_rate"
)
root = nc.Dataset("test.nc", "r", format="NETCDF3_64BIT")
assert "topographic__elevation" not in root.variables
assert "uplift_rate" in root.variables
assert_array_equal(
root.variables["uplift_rate"][:],
[[[0., 2., 4.], [6., 8., 10.], [12., 14., 16.], [18., 20., 22.]]],
)
assert "nt" in root.dimensions
assert len(root.dimensions["nt"]) == 1
root.close()
