Rechunking#
This example uses Xarray to rechunk a dataset.
Install the package pre-requisites by running the following:
pip install cubed cubed-xarray xarray pooch netCDF4
Open dataset#
Start by importing Xarray - note that we don’t need to import Cubed or cubed-xarray, since they will be picked up automatically.
import xarray as xr
xr.set_options(display_expand_attrs=False);
We open an Xarray dataset (in netCDF format) using the usual open_dataset function. By specifying chunks={} we ensure that the dataset is chunked using the on-disk chunking (here it is the netCDF file chunking). The chunked_array_type argument specifies which chunked array type to use - Cubed in this case.
ds = xr.tutorial.open_dataset(
"air_temperature", chunked_array_type="cubed", chunks={}
)
The air data variable is a cubed.Array, and we can see that this small dataset has a single on-disk chunk.
ds["air"]
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/IPython/core/formatters.py:406, in BaseFormatter.__call__(self, obj)
404 method = get_real_method(obj, self.print_method)
405 if method is not None:
--> 406 return method()
407 return None
408 else:
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/common.py:189, in AbstractArray._repr_html_(self)
187 if OPTIONS["display_style"] == "text":
188 return f"<pre>{escape(repr(self))}</pre>"
--> 189 return formatting_html.array_repr(self)
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/formatting_html.py:339, in array_repr(arr)
331 arr_name = escape(repr(arr.name)) if getattr(arr, "name", None) else ""
333 header_components = [
334 f"<div class='xr-obj-type'>{obj_type}</div>",
335 f"<div class='xr-obj-name'>{arr_name}</div>",
336 format_dims(dims, indexed_dims),
337 ]
--> 339 sections = [array_section(arr)]
341 if hasattr(arr, "coords"):
342 if arr.coords:
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/formatting_html.py:249, in array_section(obj)
247 variable = getattr(obj, "variable", obj)
248 preview = escape(inline_variable_array_repr(variable, max_width=70))
--> 249 data_repr = short_data_repr_html(obj)
250 data_icon = _icon("icon-database")
252 return (
253 "<div class='xr-array-wrap'>"
254 f"<input id='{data_id}' class='xr-array-in' type='checkbox' {collapsed}>"
(...) 258 "</div>"
259 )
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/formatting_html.py:43, in short_data_repr_html(array)
41 internal_data = getattr(array, "variable", array)._data
42 if hasattr(internal_data, "_repr_html_"):
---> 43 return internal_data._repr_html_()
44 text = escape(short_data_repr(array))
45 return f"<pre>{text}</pre>"
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/cubed/array_api/array_object.py:50, in Array._repr_html_(self)
49 def _repr_html_(self):
---> 50 from cubed.diagnostics.widgets import get_template
52 try:
53 grid = self.to_svg(size=ARRAY_SVG_SIZE)
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/cubed/diagnostics/__init__.py:1
----> 1 from .rich import RichProgressBar as ProgressBar
3 __all__ = ["ProgressBar"]
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/cubed/diagnostics/rich.py:6
3 import time
4 from contextlib import contextmanager
----> 6 from rich.console import RenderableType
7 from rich.progress import (
8 BarColumn,
9 MofNCompleteColumn,
(...) 15 TimeElapsedColumn,
16 )
17 from rich.text import Text
ModuleNotFoundError: No module named 'rich'
<xarray.DataArray 'air' (time: 2920, lat: 25, lon: 53)> Size: 31MB
cubed.Array<array-003, shape=(2920, 25, 53), dtype=float64, chunks=((2920,), (25,), (53,))>
Coordinates:
* time (time) datetime64[ns] 23kB 2013-01-01 ... 2014-12-31T18:00:00
* lat (lat) float32 100B 75.0 72.5 70.0 67.5 65.0 ... 22.5 20.0 17.5 15.0
* lon (lon) float32 212B 200.0 202.5 205.0 207.5 ... 325.0 327.5 330.0
Attributes: (11)
Rechunk#
To change the chunking we use Xarray’s chunk function:
rds = ds.chunk({'time':1}, chunked_array_type="cubed")
Looking at the air data variable again, we can see that it is now chunked along the time dimension.
rds["air"]
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/IPython/core/formatters.py:406, in BaseFormatter.__call__(self, obj)
404 method = get_real_method(obj, self.print_method)
405 if method is not None:
--> 406 return method()
407 return None
408 else:
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/common.py:189, in AbstractArray._repr_html_(self)
187 if OPTIONS["display_style"] == "text":
188 return f"<pre>{escape(repr(self))}</pre>"
--> 189 return formatting_html.array_repr(self)
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/formatting_html.py:339, in array_repr(arr)
331 arr_name = escape(repr(arr.name)) if getattr(arr, "name", None) else ""
333 header_components = [
334 f"<div class='xr-obj-type'>{obj_type}</div>",
335 f"<div class='xr-obj-name'>{arr_name}</div>",
336 format_dims(dims, indexed_dims),
337 ]
--> 339 sections = [array_section(arr)]
341 if hasattr(arr, "coords"):
342 if arr.coords:
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/formatting_html.py:249, in array_section(obj)
247 variable = getattr(obj, "variable", obj)
248 preview = escape(inline_variable_array_repr(variable, max_width=70))
--> 249 data_repr = short_data_repr_html(obj)
250 data_icon = _icon("icon-database")
252 return (
253 "<div class='xr-array-wrap'>"
254 f"<input id='{data_id}' class='xr-array-in' type='checkbox' {collapsed}>"
(...) 258 "</div>"
259 )
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/xarray/core/formatting_html.py:43, in short_data_repr_html(array)
41 internal_data = getattr(array, "variable", array)._data
42 if hasattr(internal_data, "_repr_html_"):
---> 43 return internal_data._repr_html_()
44 text = escape(short_data_repr(array))
45 return f"<pre>{text}</pre>"
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/cubed/array_api/array_object.py:50, in Array._repr_html_(self)
49 def _repr_html_(self):
---> 50 from cubed.diagnostics.widgets import get_template
52 try:
53 grid = self.to_svg(size=ARRAY_SVG_SIZE)
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/cubed/diagnostics/__init__.py:1
----> 1 from .rich import RichProgressBar as ProgressBar
3 __all__ = ["ProgressBar"]
File /opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/cubed/diagnostics/rich.py:6
3 import time
4 from contextlib import contextmanager
----> 6 from rich.console import RenderableType
7 from rich.progress import (
8 BarColumn,
9 MofNCompleteColumn,
(...) 15 TimeElapsedColumn,
16 )
17 from rich.text import Text
ModuleNotFoundError: No module named 'rich'
<xarray.DataArray 'air' (time: 2920, lat: 25, lon: 53)> Size: 31MB
cubed.Array<array-005, shape=(2920, 25, 53), dtype=float64, chunks=((1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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Coordinates:
* time (time) datetime64[ns] 23kB 2013-01-01 ... 2014-12-31T18:00:00
* lat (lat) float32 100B 75.0 72.5 70.0 67.5 65.0 ... 22.5 20.0 17.5 15.0
* lon (lon) float32 212B 200.0 202.5 205.0 207.5 ... 325.0 327.5 330.0
Attributes: (11)
Save to Zarr#
Since Cubed has a lazy computation model, the data has not been loaded from disk yet. We can save a copy of the rechunked dataset by calling to_zarr:
rds.to_zarr("rechunked_air_temperature.zarr", mode="w", consolidated=True);
/tmp/ipykernel_2342/973971337.py:1: SerializationWarning: saving variable None with floating point data as an integer dtype without any _FillValue to use for NaNs
rds.to_zarr("rechunked_air_temperature.zarr", mode="w", consolidated=True);
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/zarr/api/asynchronous.py:247: ZarrUserWarning: Consolidated metadata is currently not part in the Zarr format 3 specification. It may not be supported by other zarr implementations and may change in the future.
warnings.warn(
This will run a computation that loads the input data and writes it out to a Zarr store on the local filesystem with the new chunking. We can check that it worked by re-loading from disk using xarray.open_dataset and checking that the chunks are the same:
ds = xr.open_dataset(
"rechunked_air_temperature.zarr", chunked_array_type="cubed", chunks={}
)
assert ds.chunks == rds.chunks