Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 10 additions & 0 deletions conda_package/docs/api.rst
Original file line number Diff line number Diff line change
Expand Up @@ -369,6 +369,16 @@ Visualization

extract_vtk

.. currentmodule:: mpas_tools.viz.mpas_to_xdmf.mpas_to_xdmf

.. autosummary::
:toctree: generated/

MpasToXdmf
MpasToXdmf.load()
MpasToXdmf.convert_to_xdmf()
main

.. currentmodule:: mpas_tools.viz.mesh_to_triangles

.. autosummary::
Expand Down
39 changes: 28 additions & 11 deletions conda_package/mpas_tools/viz/mpas_to_xdmf/io.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import glob
import importlib.resources
import os

Expand Down Expand Up @@ -47,14 +48,30 @@ def _load_dataset(mesh_filename, time_series_filenames, variables, xtime_var):
if time_series_filenames is None:
ds = ds_mesh
else:
ds = xr.open_mfdataset(
time_series_filenames,
combine='nested',
concat_dim='Time',
data_vars='minimal',
coords='minimal',
compat='override',
)
if isinstance(time_series_filenames, str):
# Deterministic ordering for reproducibility
file_list = sorted(glob.glob(time_series_filenames))
else:
file_list = time_series_filenames

if len(file_list) == 0:
raise ValueError(
f'No time series files found matching '
f"'{time_series_filenames}'"
)

if len(file_list) == 1:
# If only one file, open it directly
ds = xr.open_dataset(file_list[0])
else:
ds = xr.open_mfdataset(
file_list,
combine='nested',
concat_dim='Time',
data_vars='minimal',
coords='minimal',
compat='override',
)

ds_mesh = _get_ds_mesh(ds_mesh)
if variables is not None:
Expand Down Expand Up @@ -180,18 +197,18 @@ def _write_xdmf(ds_geom, ds_data, out_dir, suffix, quiet=False):
ds_data.data_vars, total=total_steps, desc=f'Writing {suffix}'
)
for var_name in ds_data.data_vars:
if not quiet:
if iterator is not None:
iterator.set_description(f'Processing {var_name}')
if 'Time' in ds_data[var_name].dims:
for t_idx in range(ds_data.sizes['Time']):
dataset_name = f'{var_name}_t{t_idx}'
da = ds_data[var_name].isel(Time=t_idx)
h5_file.create_dataset(dataset_name, data=da.values)
if not quiet:
if iterator is not None:
iterator.update(1)
else:
h5_file.create_dataset(var_name, data=ds_data[var_name].values)
if not quiet:
if iterator is not None:
iterator.update(1)

# Preprocess variable metadata for the template
Expand Down
Loading