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Added combining and loading of netcdf to dask tutorial #38

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Added combining and loading of netcdf to dask tutorial #38

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69 changes: 67 additions & 2 deletions notebooks/foundations/03_kerchunk_dask.ipynb
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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