Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Added combining and loading of netcdf to dask tutorial #38

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Added combining and loading of netcdf to dask tutorial #38

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
69 changes: 67 additions & 2 deletions notebooks/foundations/03_kerchunk_dask.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@
"outputs": [],
"source": [
"import logging\n",
"import glob\n",
"\n",
"from distributed import Client\n",
"\n",
Expand Down Expand Up @@ -135,6 +136,7 @@
"import dask\n",
"import fsspec\n",
"import ujson\n",
"import s3fs\n",
"import xarray as xr\n",
"from kerchunk.combine import MultiZarrToZarr\n",
"from kerchunk.hdf import SingleHdf5ToZarr"
Expand Down Expand Up @@ -182,7 +184,7 @@
"metadata": {},
"outputs": [],
"source": [
"file_pattern = file_pattern[0:40]"
"file_pattern = file_pattern[0:2]"
]
},
{
Expand Down Expand Up @@ -278,6 +280,69 @@
"dask.compute(tasks)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Combine .json `Kerchunk` reference files and write a combined `Kerchunk` index\n",
"\n",
"Next, we are going to combine the created Kerchunk reference files into a single reference file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Create a list of reference json files\n",
"output_files = glob.glob(f\"{temp_dir}/*.json\")\n",
"\n",
"# combine individual references into single consolidated reference\n",
"mzz = MultiZarrToZarr(\n",
" output_files,\n",
" concat_dims=[\"Tijme\"],\n",
" identical_dims=[\"XLAT\", \"XLON\", \"interp_levels\"],\n",
")\n",
"# save translate reference in memory for later visualization\n",
"multi_kerchunk = mzz.translate()\n",
"\n",
"# Write kerchunk .json record\n",
"output_fname = \"combined.json\"\n",
"with open(f\"{output_fname}\", \"wb\") as f:\n",
" f.write(ujson.dumps(multi_kerchunk).encode())"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Load kerchunked dataset\n",
"\n",
"Now the dataset is a logical view over all of the files we scanned."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# create an fsspec reference filesystem from the Kerchunk output\n",
"\n",
"fs = fsspec.filesystem(\n",
" \"reference\",\n",
" fo=\"combined.json\",\n",
" remote_protocol=\"s3\",\n",
" remote_options={\"anon\": True},\n",
" skip_instance_cache=True,\n",
")\n",
"m = fs.get_mapper(\"\")\n",
"ds = xr.open_dataset(m, engine=\"zarr\")"
]
},
{
"attachments": {},
"cell_type": "markdown",
Expand Down Expand Up @@ -344,7 +409,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.0"
"version": "3.10.12"
},
"vscode": {
"interpreter": {
Expand Down
Loading