pydata / pydata/xarray

Round tripping Zarr datasets with scaling

Open
#9,780 3 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug needs mcve
Dominant language
Python
Stars
4.2k
Forks
1.4k
Avg merge
2d 15h
Merged PRs (30d)
14

Description

What happened?

Data was loaded into Xarray via OpenDataCube dc.load method. This Xarray was persisted to Zarr using

xx.time.encoding['units'] = "seconds since 1970-01-01 00:00:00"
xx.time.attrs = {}
xx.to_zarr('test.zarr',mode='w',consolidated=True)

When this zarr is loaded back using

ds_z = xr.open_dataset('test.zarr',  engine = 'zarr', consolidated = True)

The round tripped dataset has scaling applied with encodings saved in bands e.g. ds_z.red.encoding as

ds_z.red.encoding
{'chunks': (1, 610, 522),
 'preferred_chunks': {'time': 1, 'y': 610, 'x': 522},
 'compressor': Blosc(cname='lz4', clevel=5, shuffle=SHUFFLE, blocksize=0),
 'filters': None,
 'scale_factor': 0.0001,
 'add_offset': -0.1,
 'dtype': dtype('uint16'),
 'coordinates': 'spatial_ref'}

The values returned do not have the scaling auto-applied.

What did you expect to happen?

Scaling to DataArrays is auto-applied when rounding tripping to-from Zarr via Xarray.

Minimal Complete Verifiable Example
ds.time.encoding['units'] = "seconds since 1970-01-01 00:00:00"
ds.time.attrs = {}
ds.to_zarr('test.zarr',mode='w',consolidated=True)

ds_z = xr.open_dataset('test.zarr',  engine = 'zarr', consolidated = True)
MVCE confirmation
  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.
  • Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output

No response

Anything else we need to know?

No response

Environment
INSTALLED VERSIONS ------------------ commit: None python: 3.12.3 (main, Sep 11 2024, 14:17:37) [GCC 13.2.0] python-bits: 64 OS: Linux OS-release: 5.10.227-219.884.amzn2.x86_64 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: C.UTF-8 LANG: C.UTF-8 LOCALE: ('C', 'UTF-8') libhdf5: 1.10.10 libnetcdf: 4.9.2

xarray: 2024.10.0
pandas: 2.2.3
numpy: 1.26.4
scipy: 1.14.1
netCDF4: 1.7.2
pydap: 3.5
h5netcdf: 1.4.0
h5py: 3.12.1
zarr: 2.18.3
cftime: 1.6.4.post1
nc_time_axis: 1.4.1
iris: None
bottleneck: 1.4.2
dask: 2024.7.1
distributed: 2024.7.1
matplotlib: 3.8.4
cartopy: 0.24.1
seaborn: 0.13.2
numbagg: 0.8.2
fsspec: 2024.10.0
cupy: None
pint: 0.24.4
sparse: 0.15.4
flox: 0.9.14
numpy_groupies: 0.11.2
setuptools: 75.3.0
pip: 24.3.1
conda: None
pytest: 8.3.3
mypy: None
IPython: 8.29.0
sphinx: None

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the minimal example using to_zarr and xr.open_dataset with the supplied environment details, then inspect how the scale_factor and add_offset encodings are written and read. Confirm the expected decoded values after round-tripping and add coverage for the demonstrated scaling case; done means the reopened DataArray automatically applies the stored scaling.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.