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Fix ZarrAvgMerger under zarr 3.3: map chunks=True to auto-chunking #9077

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Merged
ericspod merged 2 commits into from
Oct 13, 2026
Merged

Fix ZarrAvgMerger under zarr 3.3: map chunks=True to auto-chunking #9077

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c5097e2
Fix ZarrAvgMerger under zarr 3.3: map chunks=True to auto-chunking
dhillrigo Aug 28, 2026
f99351d
Merge branch 'dev' into fix/zarr-3.3-boolean-chunks
ericspod Oct 13, 2026
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8 changes: 7 additions & 1 deletion monai/inferers/merger.py
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Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,13 @@ def __init__(
self.value_store = zarr.storage.TempStore() if value_store is None else value_store # type: ignore
self.count_store = zarr.storage.TempStore() if count_store is None else count_store # type: ignore

self.chunks = chunks
# zarr 3.3 rejects boolean chunk arguments; `None` there means auto-chunking,
# which is what `chunks=True` meant before. On zarr < 3.3 `None` instead means
# a single whole-shape chunk, so the substitution must not be applied there.
if chunks is True and version_geq(get_package_version("zarr"), "3.3.0"):
self.chunks: Sequence[int] | bool | None = None
else:
self.chunks = chunks

# Initialize codecs/compressor attributes with proper types
self.codecs: list | None = None
Expand Down
30 changes: 25 additions & 5 deletions tests/inferers/test_zarr_avg_merger.py
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Expand Up @@ -195,11 +195,20 @@
]

# Define zarr v3 codec configurations with proper bytes codec
ZARR_V3_LZ4_CODECS = [{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "lz4"}}]
ZARR_V3_LZ4_CODECS = [
{"name": "bytes", "configuration": {"endian": "little"}},
{"name": "blosc", "configuration": {"cname": "lz4"}},
]

ZARR_V3_PICKLE_CODECS = [{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zstd"}}]
ZARR_V3_PICKLE_CODECS = [
{"name": "bytes", "configuration": {"endian": "little"}},
{"name": "blosc", "configuration": {"cname": "zstd"}},
]

ZARR_V3_LZMA_CODECS = [{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zlib"}}]
ZARR_V3_LZMA_CODECS = [
{"name": "bytes", "configuration": {"endian": "little"}},
{"name": "blosc", "configuration": {"cname": "zlib"}},
]

# test for LZ4 compressor (zarr v2) or codecs (zarr v3)
TEST_CASE_13_COMPRESSOR_LZ4 = [
Expand Down Expand Up @@ -289,7 +298,10 @@
TEST_CASE_19_VALUE_CODECS = [
dict(
merged_shape=TENSOR_4x4.shape,
value_codecs=[{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zstd"}}],
value_codecs=[
{"name": "bytes", "configuration": {"endian": "little"}},
{"name": "blosc", "configuration": {"cname": "zstd"}},
],
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ericspod marked this conversation as resolved.
),
[
(TENSOR_4x4[..., :2, :2], (0, 0)),
Expand All @@ -304,7 +316,10 @@
TEST_CASE_20_COUNT_CODECS = [
dict(
merged_shape=TENSOR_4x4.shape,
count_codecs=[{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zlib"}}],
count_codecs=[
{"name": "bytes", "configuration": {"endian": "little"}},
{"name": "blosc", "configuration": {"cname": "zlib"}},
],
),
[
(TENSOR_4x4[..., :2, :2], (0, 0)),
Expand Down Expand Up @@ -449,6 +464,11 @@ def test_zarr_avg_merge_none_merged_shape_error(self):
with self.assertRaises(ValueError):
ZarrAvgMerger(merged_shape=None, store=self.merged_name)

def test_zarr_avg_merger_default_chunks_auto(self):
"""chunks=True must mean auto-chunking, not one whole-shape chunk (zarr 3.3 removed boolean chunks)."""
merger = ZarrAvgMerger(merged_shape=(4096, 4096), store=self.merged_name)
self.assertNotEqual(merger.output.chunks, (4096, 4096))


if __name__ == "__main__":
unittest.main()
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