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restore option to compress raster - #944

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melonora merged 18 commits into
scverse:mainfrom
melonora:restore_storage_options
May 21, 2026
Merged

restore option to compress raster#944
melonora merged 18 commits into
scverse:mainfrom
melonora:restore_storage_options

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@melonora

@melonoramelonora commented Jun 10, 2025•
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closes#37

This PR adds the capability back of using either lz4 or zstd compression at various compression levels. It is exposed through a compressor argument in write and write_element that takes as value a dict with key being the compression name and the value being the compression level. By default if compression is specified bytes will be reordered for more efficient compression SHUFFLE in blosc.

@melonora

melonora commented Jun 10, 2025

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perhaps still some refactoring to clean up the code a bit, but first want opinions on the exposed parameter.

@melonoramelonora mentioned this pull request Jun 10, 2025
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codecovBot commented Jun 10, 2025•
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Codecov Report

❌ Patch coverage is 76.00000% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.44%. Comparing base (06e6981) to head (eea7a7f).
⚠️ Report is 20 commits behind head on main.

Files with missing linesPatch %Lines
src/spatialdata/_io/io_raster.py71.05%11 Missing ⚠️
src/spatialdata/_io/_utils.py90.00%1 Missing ⚠️
Additional details and impacted files
@@ Coverage Diff @@## main #944 +/- ##
==========================================
- Coverage 92.55% 92.44% -0.11% 
==========================================
Files 51 51 Lines 7763 7811 +48 ==========================================
+ Hits 7185 7221 +36 - Misses 578 590 +12
Files with missing linesCoverage Δ
src/spatialdata/_core/spatialdata.py93.86% <100.00%> (+<0.01%)⬆️
src/spatialdata/_io/_utils.py86.66% <90.00%> (+0.13%)⬆️
src/spatialdata/_io/io_raster.py89.25% <71.05%> (-3.97%)⬇️
🚀 New features to boost your workflow:
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@LucaMarconato

LucaMarconato commented Jan 4, 2026•
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Thanks @melonora, I picked this up and merged the conflicts arising after the Zarr v3 support.

The tests currently fail mainly due to the disconnect between the new format options and dask, but it should be straightforward to make the PR green again after https://github.com/ome/ome-zarr-py/pull/510/changes is merged.

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LucaMarconato commented May 5, 2026

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Sharding support has been added to ome-zarr-py ome/ome-zarr-py#534 and is being added to spatialdata via #1106.

LucaMarconatoand others added 3 commits May 12, 2026 17:39
@LucaMarconato
Merge branch 'main' into restore_storage_options
fac4cbc
@LucaMarconato@claude
Fix zarr v3 compression: use native codecs and bump min deps
0710fbf
Use "compressors" (plural) with native zarr v3 codec objects (ZstdCodec,
BloscCodec) in storage_options, which ome-zarr-py >= 0.16.0 + dask >= 2026.3.0
correctly forwards to zarr_array_kwargs. Bump minimum deps accordingly and fix
test assertions for lz4 (.clevel) vs zstd (.level) and the s0 array path.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconato
bump min dask test in ci
d3607f1
@LucaMarconato

LucaMarconato commented May 12, 2026

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@melonora I merged the latest main and bumped the min ome-zarr and dask versions to be aligned with the sharding PR. Now the tests pass.

Can you please do a review of the changes? If you also think it's ok, feel free to merge (before the sharding PR).

melonora
melonora commented May 21, 2026
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Comment threadtests/io/test_readwrite.py
melonora
melonora commented May 21, 2026
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Comment threadsrc/spatialdata/_io/io_raster.py
melonora
melonora commented May 21, 2026
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Comment threadsrc/spatialdata/_io/_utils.py Outdated
melonora
melonora commented May 21, 2026
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Comment threadsrc/spatialdata/_io/io_raster.py Outdated
if zarr_format == 2:
from numcodecs import Blosc as BloscV2

assert BloscV2.SHUFFLE == 1

@melonoramelonoraMay 21, 2026

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Why this assert if you hardcode shuffle to be 1 in any case?

@melonora
melonora enabled auto-merge (squash) May 21, 2026 18:46
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melonora disabled auto-merge May 21, 2026 18:46
@melonora
melonora merged commit 68dade6 into scverse:mainMay 21, 2026
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Re-enable compression

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@melonora@LucaMarconato