def test_no_files(self, tmp_path):
files_dir = tmp_path.joinpath("data")
files_dir.mkdir()
with pytest.raises(IOError):
path = files_dir.joinpath("run*/example.*.nc")
actual_filepaths = _expand_filepaths(path)
def test_no_files(self, tmpdir):
files_dir = tmpdir.mkdir("data")
with pytest.raises(IOError):
path = Path(str(files_dir.join('run*/example.*.nc')))
actual_filepaths = _expand_filepaths(path)
print(actual_filepaths)
def open_fastoutput(datapath="BOUT.fast.*.nc"):
"""
Opens fast output data and combines into a single dataset.
"""
# Get list of all files
filepaths, filetype = _expand_filepaths(datapath)
# Iterate over all files, extracting DataArrays ready for combining
fo_data = []
for i, filepath in enumerate(filepaths):
fo = xr.open_dataset(filepath)
if i == 0:
# Get time coordinate from first file
time = fo["time"]
# Time is global, and we already extracted it
fo = fo.drop_vars("time", errors="ignore")
# There might be no virtual probe in this region
if len(fo.data_vars) > 0:
for name, da in fo.items():
# Save the physical position (in index units)
da = da.expand_dims(x=1, y=1, z=1)
da = da.assign_coords(
x=xr.DataArray([da.attrs["ix"]], dims=["x"]),
y=xr.DataArray([da.attrs["iy"]], dims=["y"]),
z=xr.DataArray([da.attrs["iz"]], dims=["z"]),
)
# Re-attach the time coordinate
da = da.assign_coords(time=time)
# We saved the position, so don't care what number the variable was
# Only need it's name (i.e. n, T, etc.)
regex = re.compile(r"(\D+)([0-9]+)")
match = regex.match(name)
if match is None:
raise ValueError(
f"Regex could not parse the variable named {name}")
var, num = match.groups()
da.name = var
# Must promote DataArrays to Datasets until we require xarray-0.19.0
# where xarray GH #3248 is fixed
ds = xr.Dataset({var: da})
fo_data.append(ds)
fo.close()
# This will merge different variables, and arrange by physical position
full_fo = xr.combine_by_coords(fo_data, combine_attrs="drop_conflicts")
return full_fo