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add 5th and 95th percentile #317

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Merged
merged 4 commits into from
Oct 17, 2025
Merged

add 5th and 95th percentile #317

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6336578
add 5th and 95th percentile
ritvikvasan Oct 2, 2025
ed936f2
ruff format
ritvikvasan Oct 2, 2025
6ef1829
optimize sorting and test
ziw-liu Oct 17, 2025
5acd8bd
remove scipy
ziw-liu Oct 17, 2025
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10 changes: 9 additions & 1 deletion viscy/utils/meta_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,15 @@ def write_meta_field(position: ngff.Position, metadata, field_name, subfield_nam
"""
if field_name in position.zattrs:
if subfield_name in position.zattrs[field_name]:
position.zattrs[field_name][subfield_name].update(metadata)
# Need to create a new dict and reassign to trigger zarr write
updated_subfield = {
**position.zattrs[field_name][subfield_name],
**metadata,
}
position.zattrs[field_name] = {
**position.zattrs[field_name],
subfield_name: updated_subfield,
}
else:
D1 = position.zattrs[field_name]
field_metadata = {
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5 changes: 5 additions & 0 deletions viscy/utils/mp_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,11 +260,16 @@ def get_val_stats(sample_values):
indices
:return dict meta_row: Dict with intensity data for image
"""
p5 = float(np.nanpercentile(sample_values, 5))
p95 = float(np.nanpercentile(sample_values, 95))

meta_row = {
"mean": float(np.nanmean(sample_values)),
"std": float(np.nanstd(sample_values)),
"median": float(np.nanmedian(sample_values)),
"iqr": float(scipy.stats.iqr(sample_values)),
"p5": p5,
"p95": p95,
"p95_p5": p95 - p5, # Range for normalization
}
return meta_row