diff --git a/catalog/alaska_et_2020_era-interim_reanalysis/collection.json b/catalog/alaska_et_2020_era-interim_reanalysis/collection.json
new file mode 100644
index 0000000000000000000000000000000000000000..74d43c545453805e9e4e90ba5f23a6bc7b78fdbe
--- /dev/null
+++ b/catalog/alaska_et_2020_era-interim_reanalysis/collection.json
@@ -0,0 +1,152 @@
+{
+ "type": "Collection",
+ "id": "alaska_et_2020_era-interim_reanalysis",
+ "stac_version": "1.0.0",
+ "description": "alaska_et_2020_era-interim_reanalysis",
+ "links": [
+ {
+ "rel": "root",
+ "href": "../catalog.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "parent",
+ "href": "../catalog.json",
+ "type": "application/json"
+ }
+ ],
+ "stac_extensions": [
+ "https://stac-extensions.github.io/datacube/v2.2.0/schema.json"
+ ],
+ "cube:dimensions": {
+ "time": {
+ "type": "temporal",
+ "description": "time",
+ "extent": [
+ "1979-04-01T00:00:00Z",
+ "2017-09-30T00:00:00Z"
+ ],
+ "step": "NaT"
+ },
+ "x": {
+ "type": "spatial",
+ "description": "x coordinate of projection",
+ "axis": "x",
+ "extent": [
+ -2610000.0,
+ 2610000.0
+ ],
+ "step": 20000.0,
+ "reference_system": "{\"$schema\":\"https://proj.org/schemas/v0.5/projjson.schema.json\",\"type\":\"ProjectedCRS\",\"name\":\"unknown\",\"base_crs\":{\"name\":\"unknown\",\"datum\":{\"type\":\"GeodeticReferenceFrame\",\"name\":\"unknown\",\"ellipsoid\":{\"name\":\"WGS 84\",\"semi_major_axis\":6378137,\"inverse_flattening\":298.257223563}},\"coordinate_system\":{\"subtype\":\"ellipsoidal\",\"axis\":[{\"name\":\"Longitude\",\"abbreviation\":\"lon\",\"direction\":\"east\",\"unit\":\"degree\"},{\"name\":\"Latitude\",\"abbreviation\":\"lat\",\"direction\":\"north\",\"unit\":\"degree\"}]}},\"conversion\":{\"name\":\"unknown\",\"method\":{\"name\":\"Polar Stereographic (variant B)\",\"id\":{\"authority\":\"EPSG\",\"code\":9829}},\"parameters\":[{\"name\":\"Latitude of standard parallel\",\"value\":64,\"unit\":\"degree\",\"id\":{\"authority\":\"EPSG\",\"code\":8832}},{\"name\":\"Longitude of origin\",\"value\":-152,\"unit\":\"degree\",\"id\":{\"authority\":\"EPSG\",\"code\":8833}},{\"name\":\"False easting\",\"value\":0,\"unit\":\"metre\",\"id\":{\"authority\":\"EPSG\",\"code\":8806}},{\"name\":\"False northing\",\"value\":0,\"unit\":\"metre\",\"id\":{\"authority\":\"EPSG\",\"code\":8807}}]},\"coordinate_system\":{\"subtype\":\"Cartesian\",\"axis\":[{\"name\":\"Easting\",\"abbreviation\":\"E\",\"direction\":\"south\",\"meridian\":{\"longitude\":90},\"unit\":\"metre\"},{\"name\":\"Northing\",\"abbreviation\":\"N\",\"direction\":\"south\",\"meridian\":{\"longitude\":180},\"unit\":\"metre\"}]}}"
+ },
+ "y": {
+ "type": "spatial",
+ "axis": "y",
+ "description": "y coordinate of projection",
+ "extent": [
+ -5413582.2906,
+ -193582.29059999995
+ ],
+ "step": 20000.0,
+ "reference_system": "{\"$schema\":\"https://proj.org/schemas/v0.5/projjson.schema.json\",\"type\":\"ProjectedCRS\",\"name\":\"unknown\",\"base_crs\":{\"name\":\"unknown\",\"datum\":{\"type\":\"GeodeticReferenceFrame\",\"name\":\"unknown\",\"ellipsoid\":{\"name\":\"WGS 84\",\"semi_major_axis\":6378137,\"inverse_flattening\":298.257223563}},\"coordinate_system\":{\"subtype\":\"ellipsoidal\",\"axis\":[{\"name\":\"Longitude\",\"abbreviation\":\"lon\",\"direction\":\"east\",\"unit\":\"degree\"},{\"name\":\"Latitude\",\"abbreviation\":\"lat\",\"direction\":\"north\",\"unit\":\"degree\"}]}},\"conversion\":{\"name\":\"unknown\",\"method\":{\"name\":\"Polar Stereographic (variant B)\",\"id\":{\"authority\":\"EPSG\",\"code\":9829}},\"parameters\":[{\"name\":\"Latitude of standard parallel\",\"value\":64,\"unit\":\"degree\",\"id\":{\"authority\":\"EPSG\",\"code\":8832}},{\"name\":\"Longitude of origin\",\"value\":-152,\"unit\":\"degree\",\"id\":{\"authority\":\"EPSG\",\"code\":8833}},{\"name\":\"False easting\",\"value\":0,\"unit\":\"metre\",\"id\":{\"authority\":\"EPSG\",\"code\":8806}},{\"name\":\"False northing\",\"value\":0,\"unit\":\"metre\",\"id\":{\"authority\":\"EPSG\",\"code\":8807}}]},\"coordinate_system\":{\"subtype\":\"Cartesian\",\"axis\":[{\"name\":\"Easting\",\"abbreviation\":\"E\",\"direction\":\"south\",\"meridian\":{\"longitude\":90},\"unit\":\"metre\"},{\"name\":\"Northing\",\"abbreviation\":\"N\",\"direction\":\"south\",\"meridian\":{\"longitude\":180},\"unit\":\"metre\"}]}}"
+ }
+ },
+ "cube:variables": {
+ "lat": {
+ "dimensions": [
+ "y",
+ "x"
+ ],
+ "type": "auxiliary",
+ "description": "latitude",
+ "unit": "degrees_north"
+ },
+ "lon": {
+ "dimensions": [
+ "y",
+ "x"
+ ],
+ "type": "auxiliary",
+ "description": "longitude",
+ "unit": "degrees_east"
+ },
+ "et0": {
+ "dimensions": [
+ "time",
+ "y",
+ "x"
+ ],
+ "type": "data",
+ "description": "Reference Evapotranspiration",
+ "unit": "mm"
+ },
+ "polar_stereographic": {
+ "dimensions": [],
+ "type": "data",
+ "description": "CRS definition",
+ "unit": null
+ }
+ },
+ "extent": {
+ "spatial": {
+ "bbox": [
+ [
+ -179.9994659423828,
+ 37.233001708984375,
+ 179.9990692138672,
+ 88.26099395751953
+ ]
+ ]
+ },
+ "temporal": {
+ "interval": [
+ [
+ "1979-04-01T00:00:00Z",
+ "2017-09-30T00:00:00Z"
+ ]
+ ]
+ }
+ },
+ "license": "CC0-1.0",
+ "assets": {
+ "zarr-s3-osn": {
+ "href": "s3://mdmf/gdp/alaska_et_2020_era-interim_reanalysis.zarr/",
+ "type": "application/vnd+zarr",
+ "description": "Open Storage Network Pod S3 API access to collection zarr group",
+ "xarray:open_kwargs": {
+ "chunks": {},
+ "engine": "zarr",
+ "consolidated": true
+ },
+ "xarray:storage_options": {
+ "anon": true,
+ "client_kwargs": {
+ "endpoint_url": "https://usgs.osn.mghpcc.org/"
+ }
+ },
+ "roles": [
+ "data",
+ "zarr",
+ "s3"
+ ]
+ },
+ "zarr-s3": {
+ "href": "s3://nhgf-development/workspace/DataConversion/alaska_et_2020_era-interim_reanalysis.zarr/",
+ "type": "application/vnd+zarr",
+ "description": "S3 access to collection zarr group",
+ "xarray:open_kwargs": {
+ "chunks": {},
+ "engine": "zarr",
+ "consolidated": true
+ },
+ "xarray:storage_options": {
+ "requester_pays": true
+ },
+ "roles": [
+ "data",
+ "zarr",
+ "s3"
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/catalog/catalog.json b/catalog/catalog.json
index 008d97940bcf02795e944300589326695ae61c59..cd528551849400fa40ebd2519d3a4ed0ee6286ca 100644
--- a/catalog/catalog.json
+++ b/catalog/catalog.json
@@ -18,6 +18,11 @@
"rel": "child",
"href": "./alaska_et_2020_ccsm4_historical_simulation/collection.json",
"type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./alaska_et_2020_era-interim_reanalysis/collection.json",
+ "type": "application/json"
}
]
}
\ No newline at end of file
diff --git a/workflows/archive/alaska_et_2020_ccsm4_historical_simulation_create_collection_from_zarr.ipynb b/workflows/archive/alaska_et_2020_ccsm4_historical_simulation_create_collection_from_zarr.ipynb
index 33c18edf188b43b856a1b1b0d1a8d3b6ce430a11..af637ec4f8940ddf56a5caa2c236863496c15112 100644
--- a/workflows/archive/alaska_et_2020_ccsm4_historical_simulation_create_collection_from_zarr.ipynb
+++ b/workflows/archive/alaska_et_2020_ccsm4_historical_simulation_create_collection_from_zarr.ipynb
@@ -730,18 +730,6 @@
"# print(*find_paths(d))"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "bca0536f-6d72-4640-b540-5ce5d13e7006",
- "metadata": {
- "tags": []
- },
- "outputs": [],
- "source": [
- "if catalog.get_child(collection_id)"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
diff --git a/workflows/archive/alaska_et_2020_era-interim_reanalysis_create_collection_from_zarr.ipynb b/workflows/archive/alaska_et_2020_era-interim_reanalysis_create_collection_from_zarr.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..e385f15e621602e1d087d1421fb83f914cdf9b6a
--- /dev/null
+++ b/workflows/archive/alaska_et_2020_era-interim_reanalysis_create_collection_from_zarr.ipynb
@@ -0,0 +1,771 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "6c10e07b-1e60-4926-af1d-fa75dc78e5d4",
+ "metadata": {
+ "tags": []
+ },
+ "source": [
+ "# CONUS404 Daily Zarr -> Collection Exploratory Workflow\n",
+ "This is a workflow for transforming the CONUS404 daily zarr dataset into a [STAC collection](https://github.com/radiantearth/stac-spec/blob/master/collection-spec/collection-spec.md). We use the [datacube extension](https://github.com/stac-extensions/datacube) to define the spatial and temporal dimensions of the zarr store, as well as the variables it contains.\n",
+ "\n",
+ "To simplify this workflow so that it can scale to many datasets, a few simplifying suggestions and assumptions are made:\n",
+ "1. For USGS data, we can use the CC0-1.0 license. For all other data we can use Unlicense. Ref: https://spdx.org/licenses/\n",
+ "2. I am assuming all coordinates are from the WGS84 datum if not specified."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "201e0945-de55-45ff-b095-c2af009a4e62",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "import pystac\n",
+ "from pystac.extensions.datacube import CollectionDatacubeExtension, AssetDatacubeExtension, AdditionalDimension, DatacubeExtension\n",
+ "import xarray as xr\n",
+ "import cf_xarray\n",
+ "import os\n",
+ "import fsspec\n",
+ "import cf_xarray\n",
+ "import hvplot.xarray\n",
+ "import pandas as pd\n",
+ "import json\n",
+ "import numpy as np\n",
+ "import metpy\n",
+ "import cartopy.crs as ccrs\n",
+ "import cfunits\n",
+ "import json"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "20b00e88-5a13-46b3-9787-d9ac2d4e7bd6",
+ "metadata": {},
+ "source": [
+ "## Open up NHGF STAC Catalog"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "adf6c59d-58cd-48b1-a5fd-3bb205a3ef56",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# define folder location where your STAC catalog json file is\n",
+ "catalog_path = os.path.join('..', '..', 'catalog')\n",
+ "# open catalog\n",
+ "catalog = pystac.Catalog.from_file(os.path.join(catalog_path, 'catalog.json'))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "996e60ba-13e4-453a-8534-e62ce747f0fa",
+ "metadata": {},
+ "source": [
+ "## Collection Metadata Input"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "482d204d-b5b6-40e5-ac42-55b459be1097",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# name for STAC collection\n",
+ "collection_id = 'alaska_et_2020_era-interim_reanalysis'\n",
+ "# description of STAC collection\n",
+ "collection_description = 'alaska_et_2020_era-interim_reanalysis'\n",
+ "# license for dataset\n",
+ "collection_license = 'CC0-1.0'"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "116b5837-8e85-4ae7-964a-803533ded714",
+ "metadata": {},
+ "source": [
+ "## Asset Metadata Input"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "dd6fa323-132a-4794-8c80-576933f547a0",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# url to zarr store that you want to create a collection for\n",
+ "zarr_url = 's3://mdmf/gdp/alaska_et_2020_era-interim_reanalysis.zarr/'\n",
+ "\n",
+ "# define keyword arguments needed for opening the dataset with xarray\n",
+ "# ref: https://github.com/stac-extensions/xarray-assets\n",
+ "xarray_opendataset_kwargs = {\"xarray:open_kwargs\":{\"chunks\":{},\"engine\":\"zarr\",\"consolidated\":True},\n",
+ " \"xarray:storage_options\": {\"anon\": True, \"client_kwargs\": {\"endpoint_url\":\"https://usgs.osn.mghpcc.org/\"}}}\n",
+ "# description for zarr url asset attached to collection (zarr_url)\n",
+ "asset_description = \"Open Storage Network Pod S3 API access to collection zarr group\"\n",
+ "# roles to tag zarr url asset with\n",
+ "asset_roles = [\"data\",\"zarr\",\"s3\"]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e1441cd4-e94c-4902-af46-8f1af470eb6b",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# url to zarr store that you want to create a collection for\n",
+ "zarr_url2 = 's3://nhgf-development/workspace/DataConversion/alaska_et_2020_era-interim_reanalysis.zarr/'\n",
+ "\n",
+ "# define keyword arguments needed for opening the dataset with xarray\n",
+ "# ref: https://github.com/stac-extensions/xarray-assets\n",
+ "xarray_opendataset_kwargs2 = {\"xarray:open_kwargs\":{\"chunks\":{},\"engine\":\"zarr\",\"consolidated\":True},\n",
+ " \"xarray:storage_options\":{\"requester_pays\":True}}\n",
+ "# description for zarr url asset attached to collection (zarr_url)\n",
+ "asset_description2 = \"S3 access to collection zarr group\"\n",
+ "# roles to tag zarr url asset with\n",
+ "asset_roles2 = [\"data\",\"zarr\",\"s3\"]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "b213b74f-ad17-4774-93b6-3b62be616b45",
+ "metadata": {
+ "tags": []
+ },
+ "source": [
+ "## Data Exploration"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "708f2cf5-79ab-49af-8067-de31d0d13ee6",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# open and view zarr dataset\n",
+ "fs2 = fsspec.filesystem('s3', anon=True, endpoint_url='https://usgs.osn.mghpcc.org/')\n",
+ "ds = xr.open_dataset(fs2.get_mapper(zarr_url), engine='zarr', \n",
+ " backend_kwargs={'consolidated':True}, chunks={})\n",
+ "ds"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "0bc7e9b3-ad62-4b10-a18e-66b7ed2d35dc",
+ "metadata": {},
+ "source": [
+ "## Identify x, y, t dimensions of dataset\n",
+ "May require user input if dimensions cannot be auto-detected."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "ab91268f-7200-4cb1-979a-c7d75531d2c0",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "dims_auto_extract = ['X', 'Y', 'T']\n",
+ "def extract_dim(ds, d):\n",
+ " try:\n",
+ " dim_list = ds.cf.axes[d]\n",
+ " assert len(dim_list)==1, f'There are too many {d} dimensions in this dataset.'\n",
+ " dim = dim_list[0]\n",
+ " except KeyError:\n",
+ " print(f\"Could not auto-extract {d} dimension name.\")\n",
+ " print(\"Look at the xarray output above showing the dataset dimensions.\")\n",
+ " dim = str(input(f\"What is the name of the {d} dimension of this dataset?\"))\n",
+ " assert dim in ds.dims, \"That is not a valid dimension name for this dataset\"\n",
+ " print(f\"name of {d} dimension: {dim}\\n\")\n",
+ " return dim\n",
+ "\n",
+ "dim_names_dict = {}\n",
+ "for d in dims_auto_extract:\n",
+ " dim_names_dict[d] = extract_dim(ds, d)\n",
+ "print(f\"Dimension dictionary: {dim_names_dict}\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "bad1118b-32ce-4191-939a-21fd58167ea6",
+ "metadata": {},
+ "source": [
+ "## Get crs info"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "8307fb3a-ca11-4c19-bcdc-c95ac7275b1c",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "ds = ds.metpy.parse_cf()\n",
+ "crs = ds[list(ds.keys())[0]].metpy.cartopy_crs"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "8fbfecfb-9886-4d06-a34c-6471cb0a6053",
+ "metadata": {},
+ "source": [
+ "## Plot a map"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "4eb4d027-4266-4a0b-8f16-bacfbef06242",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# # plot a map of a single variable\n",
+ "# var_to_plot = 'SNOW'\n",
+ "# da = ds[var_to_plot].sel(time='2014-03-01 00:00').load()\n",
+ "# da.hvplot.quadmesh(x='lon', y='lat', rasterize=True,\n",
+ "# geo=True, tiles='OSM', alpha=0.7, cmap='turbo')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "5e057a6c-06fb-4406-823b-e81c58e520e4",
+ "metadata": {},
+ "source": [
+ "## Plot a time series at a specific point\n",
+ "This can help you verify a variable's values"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c7de2681-88c2-4597-857c-8f169c596f8b",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# # enter lat, lon of point you want to plot time series for\n",
+ "# lat,lon = 39.978322,-105.2772194\n",
+ "# time_start = '2013-01-01 00:00'\n",
+ "# time_end = '2013-12-31 00:00'\n",
+ "# x, y = crs.transform_point(lon, lat, src_crs=ccrs.PlateCarree()) # PlateCaree = Lat,Lon\n",
+ "# da = ds[var_to_plot].sel(x=x, y=y, method='nearest').sel(time=slice(time_start,time_end)).load()\n",
+ "# da.hvplot(x=dim_names_dict['T'], grid=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "a8c3ed37-8564-400b-a7fb-25bd5e43d21c",
+ "metadata": {},
+ "source": [
+ "## Create Collection Extent"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "69f0d837-68a5-4fed-9a14-5d75cfbb0da4",
+ "metadata": {},
+ "source": [
+ "### Spatial Extent"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "d46805e0-8e94-4ebe-aa01-d9a2d7051459",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# pull out lat/lon bbox for data\n",
+ "# coordinates must be from WGS 84 datum\n",
+ "# left, bottom, right, top\n",
+ "# Note: I'm not sure why but I have some trouble getting the data type right here - \n",
+ "# I've included all the options I've had to run to get it to not be a regular float rather \n",
+ "# than a numpy float below - switch the commented line if you have this issue\n",
+ "#coord_bounds = [ds.lon.data.min().compute().astype(float).tolist(), ds.lat.data.min().compute().astype(float), ds.lon.data.max().compute().astype(float), ds.lat.data.max().compute().astype(float)]\n",
+ "coord_bounds = [ds.lon.data.min().compute().astype(float).tolist(), ds.lat.data.min().compute().astype(float).tolist(), ds.lon.data.max().compute().astype(float).tolist(), ds.lat.data.max().compute().astype(float).tolist()]\n",
+ "#coord_bounds = [ds.lon.data.min().astype(float).item(), ds.lat.data.min().astype(float).item(), ds.lon.data.max().astype(float).item(), ds.lat.data.max().astype(float).item()]\n",
+ "print(coord_bounds)\n",
+ "# create a spatial extent object \n",
+ "spatial_extent = pystac.SpatialExtent(bboxes=[coord_bounds])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "a04c8fca-1d33-43ac-9e2b-62d7be2887f7",
+ "metadata": {},
+ "source": [
+ "### Temporal Extent"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "41a84995-867c-4152-8c57-85e3758bbb77",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# pull out first and last timestamps\n",
+ "temporal_extent_lower = pd.Timestamp(ds[dim_names_dict['T']].data.min())\n",
+ "temporal_extent_upper = pd.Timestamp(ds[dim_names_dict['T']].data.max())\n",
+ "print(f'min: {temporal_extent_lower} \\nmax: {temporal_extent_upper}')\n",
+ "# create a temporal extent object\n",
+ "temporal_extent = pystac.TemporalExtent(intervals=[[temporal_extent_lower, temporal_extent_upper]])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "1b1e37c4-5348-46ad-abc9-e005b5d6c02b",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "collection_extent = pystac.Extent(spatial=spatial_extent, temporal=temporal_extent)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "cfb71202-03df-45b5-ac2f-0dc2ee1ab780",
+ "metadata": {},
+ "source": [
+ "## Create pystac collection"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "7e96811b-95ae-406a-9728-55fc429d4e1f",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "if catalog.get_child(collection_id):\n",
+ " collection = catalog.get_child(collection_id)\n",
+ " print(\"existing collection opened\")\n",
+ " collection.extent=collection_extent\n",
+ " collection.description=collection_description\n",
+ " collection.license=collection_license\n",
+ "else:\n",
+ " collection = pystac.Collection(id=collection_id,\n",
+ " description=collection_description,\n",
+ " extent=collection_extent,\n",
+ " license=collection_license)\n",
+ " print(\"new collection created\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "a21c76e8-cd57-4eb5-a33f-7c668a3b3205",
+ "metadata": {},
+ "source": [
+ "## Add zarr url asset to collection"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "094832af-d22b-4359-b0f6-cf687acce5cc",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "asset_id = \"zarr-s3-osn\"\n",
+ "asset = pystac.Asset(href=zarr_url,\n",
+ " description=asset_description,\n",
+ " media_type=\"application/vnd+zarr\",\n",
+ " roles=asset_roles,\n",
+ " extra_fields = xarray_opendataset_kwargs)\n",
+ "collection.add_asset(asset_id, asset)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0c298d07-f234-4a08-986d-87f4a39e9ae6",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "asset_id2 = \"zarr-s3\"\n",
+ "asset2 = pystac.Asset(href=zarr_url2,\n",
+ " description=asset_description2,\n",
+ " media_type=\"application/vnd+zarr\",\n",
+ " roles=asset_roles2,\n",
+ " extra_fields = xarray_opendataset_kwargs2)\n",
+ "collection.add_asset(asset_id2, asset2)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "f67cd5c9-db33-45c2-bc21-480cd67354f4",
+ "metadata": {},
+ "source": [
+ "## Add datacube extension to collection"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "fc00946d-2880-491d-9b3b-3aeeb4414d6c",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# instantiate extention on collection\n",
+ "dc = DatacubeExtension.ext(collection, add_if_missing=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "8bdd77a2-7587-485e-afb7-42af3a822241",
+ "metadata": {},
+ "source": [
+ "### Add cube dimensions (required field for extension)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "120a4914-3302-44a5-a282-0308ac84f040",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# list out dataset dimensions\n",
+ "# When writing data to Zarr, Xarray sets this attribute on all variables based on the variable dimensions. When reading a Zarr group, Xarray looks for this attribute on all arrays,\n",
+ "# raising an error if it can’t be found.\n",
+ "dims = list(ds.dims)\n",
+ "print(dims)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "00a18a29-fb9a-4b56-8009-493122997b16",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# get x, y bounds for extent of those dimensions (required)\n",
+ "xy_bounds = [ds[dim_names_dict['X']].data.min().astype(float).item(), ds[dim_names_dict['Y']].data.min().astype(float).item(), ds[dim_names_dict['X']].data.max().astype(float).item(), ds[dim_names_dict['Y']].data.max().astype(float).item()]\n",
+ "print(xy_bounds)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0f49d6d7-9e30-4144-909b-fa1238e6c77a",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "def get_step(dim_name):\n",
+ " dim_vals = ds[dim_name].values\n",
+ " diffs = [d2 - d1 for d1, d2 in zip(dim_vals, dim_vals[1:])]\n",
+ " unique_steps = np.unique(diffs)\n",
+ " # set step - if all steps are the same length\n",
+ " # datacube spec specifies to use null for irregularly spaced steps\n",
+ " if len(unique_steps)==1:\n",
+ " step = unique_steps[0].astype(float).item()\n",
+ " else:\n",
+ " step = None\n",
+ " return(step)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "a20d12bf-a511-4c5e-84d0-77e2ec551518",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "def get_long_name(ds, v):\n",
+ " # try to get long_name attribute from variable\n",
+ " try:\n",
+ " long_name = ds[v].attrs['long_name']\n",
+ " # otherwise, leave empty\n",
+ " except:\n",
+ " long_name = None\n",
+ " return long_name"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "e7dc357c-91ec-49ae-83e5-400f791f9792",
+ "metadata": {},
+ "source": [
+ "#### user input needed - you will need to look at the crs information and create a cartopy crs object after identifying the projection type:\n",
+ "reference list of cartopy projections: https://scitools.org.uk/cartopy/docs/latest/reference/projections.html"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "ea452f62-5644-49b6-8a4e-7dc4f649fd1a",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# print ot crs information in dataset\n",
+ "print(crs)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "686ce5f8-f10f-40a5-9780-0bbf85507f26",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# the datacube extension can accept reference_system information as a numerical EPSG code, \n",
+ "# WKT2 (ISO 19162) string or PROJJSON object.\n",
+ "# we will use a projjson, as was done by Microsoft Planetary Computer here:\n",
+ "# https://planetarycomputer.microsoft.com/dataset/daymet-annual-na\n",
+ "# https://planetarycomputer.microsoft.com/api/stac/v1/collections/daymet-annual-na\n",
+ "projjson = crs.to_json()\n",
+ "print(projjson)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "00a5e041-081d-428d-ac2e-75d16de205e6",
+ "metadata": {},
+ "source": [
+ "#### user input needed - you will need to copy all of the dimensions from above into the dict and fill in the appropriate attributes(type, axis, extent):"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "5a443497-67a9-4dce-a8e9-b08d31a88223",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# create a dictionary of datacube dimensions you would like to assign to this dataset\n",
+ "# dimension name should come from the coordinates printed above\n",
+ "# we do not recommend including redundant dimensions (do not include x,y if you have lon,lat)\n",
+ "# note that the extent of each dimension should be pulled from the dataset\n",
+ "dims_dict = {'time': pystac.extensions.datacube.Dimension({'type': 'temporal', 'description': get_long_name(ds, 'time'), 'extent': [temporal_extent_lower.strftime('%Y-%m-%dT%XZ'), temporal_extent_upper.strftime('%Y-%m-%dT%XZ')], 'step': pd.Timedelta(get_step('time')).isoformat()}),\n",
+ " 'x': pystac.extensions.datacube.Dimension({'type': 'spatial', 'description': get_long_name(ds, 'x'), 'axis': 'x', 'extent': [xy_bounds[0], xy_bounds[2]], 'step': get_step('x'), 'reference_system': projjson}),\n",
+ " 'y': pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'y', 'description': get_long_name(ds, 'y'), 'extent': [xy_bounds[1], xy_bounds[3]], 'step': get_step('y'), 'reference_system': projjson}),\n",
+ " }"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "0f277883-a3fd-425f-966a-ca2140d0ef2f",
+ "metadata": {},
+ "source": [
+ "### Add cube variables (optional field for extension)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "92510876-7853-4d24-8563-c69f9012aeb6",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# define functions to pull out datacube attributes and validate format\n",
+ "def get_unit(ds, v):\n",
+ " # check if unit is defined for variable\n",
+ " try:\n",
+ " unit = ds[v].attrs['units']\n",
+ " except:\n",
+ " unit = None\n",
+ " # check if unit comes from https://docs.unidata.ucar.edu/udunits/current/#Database\n",
+ " # datacube extension specifies: The unit of measurement for the data, preferably compliant to UDUNITS-2 units (singular).\n",
+ " # gdptools expects this format as well\n",
+ " try:\n",
+ " cfunits.Units(unit).isvalid\n",
+ " except:\n",
+ " print(\"Unit is not valid as a UD unit.\")\n",
+ " unit = str(input(\"Please enter a valid unit for {v} from here: https://docs.unidata.ucar.edu/udunits/current/#Database\"))\n",
+ " assert cfunits.Units(unit).isvalid\n",
+ " return unit\n",
+ "\n",
+ "def get_var_type(ds, v):\n",
+ " if v in ds.coords:\n",
+ " # type = auxiliary for a variable that contains coordinate data, but isn't a dimension in cube:dimensions.\n",
+ " # For example, the values of the datacube might be provided in the projected coordinate reference system, \n",
+ " # but the datacube could have a variable lon with dimensions (y, x), giving the longitude at each point.\n",
+ " var_type = 'auxiliary'\n",
+ " # type = data for a variable indicating some measured value, for example \"precipitation\", \"temperature\", etc.\n",
+ " else:\n",
+ " var_type = 'data'\n",
+ " return var_type"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e9272931-fc0b-4f2a-9546-283033e9cde8",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# pull list of vars from dataset\n",
+ "vars = list(ds.variables)\n",
+ "\n",
+ "# drop metpy_crs coordinate we have added\n",
+ "if 'metpy_crs' in ds.coords:\n",
+ " ds = ds.drop_vars('metpy_crs')\n",
+ "\n",
+ "# spec says that the keys of cube:dimensions and cube:variables should be unique together; a key like lat should not be both a dimension and a variable.\n",
+ "# we will drop all values in dims from vars\n",
+ "vars = [v for v in vars if v not in dims]\n",
+ "\n",
+ "# Microsoft Planetary Computer includes coordinates and crs as variables here:\n",
+ "# https://planetarycomputer.microsoft.com/dataset/daymet-annual-na\n",
+ "# https://planetarycomputer.microsoft.com/api/stac/v1/collections/daymet-annual-na\n",
+ "# we will keep those in the var list\n",
+ "\n",
+ "# create dictionary of dataset variables and associated dimensions\n",
+ "vars_dict={}\n",
+ "for v in vars:\n",
+ " unit = get_unit(ds, v)\n",
+ " var_type = get_var_type(ds, v)\n",
+ " long_name = get_long_name(ds, v)\n",
+ " vars_dict[v] = pystac.extensions.datacube.Variable({'dimensions':list(ds[v].dims), 'type': var_type, 'description': long_name, 'unit': unit})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "11ad5352-884c-4472-8864-4570a96f66e5",
+ "metadata": {},
+ "source": [
+ "### Finalize extension"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "10141fd4-91d6-491d-878b-02653720891d",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# add dimesions and variables to collection extension\n",
+ "dc.apply(dimensions=dims_dict, variables=vars_dict)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "615ca168-75fb-4135-9941-0ef5fe4fd1cb",
+ "metadata": {},
+ "source": [
+ "## Add STAC Collection to Catalog and Save"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e2120a55-3d04-4122-a93f-29afcdb8cb1b",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# # helper to find items of wrong type\n",
+ "# d = collection.to_dict()\n",
+ "# def find_paths(nested_dict, prepath=()):\n",
+ "# for k, v in nested_dict.items():\n",
+ "# try:\n",
+ "# path = prepath + (k,)\n",
+ "# if type(v) is np.float64: # found value\n",
+ "# yield path\n",
+ "# elif hasattr(v, 'items'): # v is a dict\n",
+ "# yield from find_paths(v, path) \n",
+ "# except:\n",
+ "# print(prepath)\n",
+ "\n",
+ "# print(*find_paths(d))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "4b75791b-6b2d-40be-b7c6-330a60888fb5",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "if catalog.get_child(collection_id):\n",
+ " collection.normalize_and_save(root_href=os.path.join(catalog_path, collection_id), catalog_type=pystac.CatalogType.SELF_CONTAINED)\n",
+ "else:\n",
+ " catalog.add_child(collection)\n",
+ " catalog.normalize_and_save(root_href=catalog_path, catalog_type=pystac.CatalogType.SELF_CONTAINED)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "global-global-pangeo",
+ "language": "python",
+ "name": "conda-env-global-global-pangeo-py"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.11.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}