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

from_zarr code #22

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
Open

from_zarr code #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
5c72704
Add files via upload
SultanOrazbayev May 2, 2022
3a67453
Update to_datetime code
SultanOrazbayev May 3, 2022
9ae092a
Add from_zarr code
SultanOrazbayev May 6, 2022
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
161 changes: 161 additions & 0 deletions local/from_zarr.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,161 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "240d8ca9-3dd4-4df6-8fa7-2ac9c4a697cf",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"from dask.array import from_zarr\n",
"\n",
"zar_file = \"s3://coiled-datasets/synthetic-data/array-random-390KB.zarr\"\n",
"x = from_zarr(zar_file)\n",
"\n",
"print(x)\n",
"# dask.array<from-zarr, shape=(100, 100, 5), dtype=float64, chunksize=(10, 10, 1), chunktype=numpy.ndarray>"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e43b65f6-17a1-439d-bd1e-ff6e9bf4c7b6",
"metadata": {},
"outputs": [],
"source": [
"from dask.array import from_zarr\n",
"\n",
"x = from_zarr(\"group.zarr\", component=\"group_foo/sample_array\")\n",
"print(x)\n",
"# dask.array<from-zarr, shape=(10, 10), dtype=int32, chunksize=(2, 2), chunktype=numpy.ndarray>\n",
"\n",
"product = x @ x.T\n",
"print(f\"Number of tasks: {len((product).dask)}\")\n",
"# Number of tasks: 376"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6fac7a32-f4be-45f7-a822-3734604894eb",
"metadata": {},
"outputs": [],
"source": [
"from dask.array import from_zarr\n",
"\n",
"x = from_zarr(\"group.zarr\", component=\"group_foo/sample_array\", chunks=(2, 10))\n",
"print(x)\n",
"# dask.array<from-zarr, shape=(10, 10), dtype=int32, chunksize=(2, 2), chunktype=numpy.ndarray>\n",
"\n",
"product = x @ x.T\n",
"print(f\"Number of tasks: {len((product).dask)}\")\n",
"# Number of tasks: 61"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "971518f6-025a-4fbf-81df-9b5b957c0500",
"metadata": {},
"outputs": [],
"source": [
"from dask.array import from_zarr\n",
"\n",
"x = from_zarr(\"group.zarr\", component=\"group_foo/sample_array\")\n",
"print(x)\n",
"# dask.array<from-zarr, shape=(10, 10), dtype=int32, chunksize=(2, 2), chunktype=numpy.ndarray>"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "3083b34f-1f20-4524-b71b-caef7f3f9a51",
"metadata": {},
"outputs": [],
"source": [
"from dask.array import from_zarr\n",
"\n",
"x = from_zarr(\"sample.zarr\")\n",
"print(x.dask)\n",
"# HighLevelGraph with 2 layers.\n",
"# <dask.highlevelgraph.HighLevelGraph object at 0x1877b8f40>\n",
"# 0. original-from-zarr-aa89d568fa5d6a465403e4a4457083a9\n",
"# 1. from-zarr-aa89d568fa5d6a465403e4a4457083a9"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "76a334c4-af0c-4bd5-a33b-e3081c3d9f22",
"metadata": {},
"outputs": [],
"source": [
"from dask.array import from_zarr\n",
"\n",
"x = from_zarr(\"sample.zarr\", inline_array=True)\n",
"print(x.dask)\n",
"# HighLevelGraph with 1 layers.\n",
"# <dask.highlevelgraph.HighLevelGraph object at 0x1877ecac0>\n",
"# 0. from-zarr-dd5aae068dabbf1fea826d7abea7b6f8"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6e51e2cc-6254-4d16-af9b-ddd0c2e4ba73",
"metadata": {},
"outputs": [],
"source": [
"import zarr\n",
"from dask.array import from_zarr, stack\n",
"from matplotlib.pyplot import imshow\n",
"\n",
"# load the list of components inside the zarr\n",
"zarr_file = \"weather_group.zarr\"\n",
"list_components = list(zarr.open(zarr_file, mode=\"r\")[\"temperature\"])\n",
"\n",
"# create a list of dask arrays\n",
"arrays = [from_zarr(zarr_file, component=f\"temperature/{c}\") for c in list_components]\n",
"print(len(arrays))\n",
"\n",
"# stack the arrays into a single array\n",
"temperature = stack(arrays, axis=0)\n",
"\n",
"print(temperature)\n",
"# dask.array<stack, shape=(31, 5760, 11520), dtype=float64, chunksize=(1, 500, 500), chunktype=numpy.ndarray>\n",
"\n",
"# calculate average temperature (at a single location across all dates)\n",
"result = temperature.mean(axis=0)\n",
"\n",
"print(result)\n",
"# dask.array<mean_agg-aggregate, shape=(5760, 11520), dtype=float64, chunksize=(500, 500), chunktype=numpy.ndarray>\n",
"\n",
"# visualize the result\n",
"imshow(result, cmap=\"RdBu_r\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.4"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
Loading