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Add a couple more debug timing spans and suppress spammy third-party logs #14

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Merged
cjfuller merged 1 commit into from
Jan 17, 2025
Merged

Add a couple more debug timing spans and suppress spammy third-party logs #14

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40 changes: 21 additions & 19 deletions image_stitcher/stitcher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -458,10 +458,11 @@ def save_region_ome_zarr(
root = zarr.group(store=store)

# Calculate pyramid using scaler - maintains efficiency for both dask and numpy arrays
scaler = ome_zarr.scale.Scaler(
max_layer=self.computed_parameters.num_pyramid_levels - 1
)
pyramid = scaler.nearest(stitched_region)
with debug_timing("scaler"):
scaler = ome_zarr.scale.Scaler(
max_layer=self.computed_parameters.num_pyramid_levels - 1
)
pyramid = scaler.nearest(stitched_region)

# Define correct physical coordinates with proper micrometer scaling
transforms = []
Expand Down Expand Up @@ -497,21 +498,22 @@ def save_region_ome_zarr(
}

# Write pyramid data with full metadata
ome_zarr.writer.write_multiscale(
pyramid=pyramid,
group=root,
axes=[ # Required for OME-ZARR >= 0.3
{"name": "t", "type": "time", "unit": "second"},
{"name": "c", "type": "channel"},
{"name": "z", "type": "space", "unit": "micrometer"},
{"name": "y", "type": "space", "unit": "micrometer"},
{"name": "x", "type": "space", "unit": "micrometer"},
],
coordinate_transformations=transforms,
storage_options=storage_opts,
name=f"{region}_t{timepoint}",
fmt=ome_zarr.format.CurrentFormat(),
)
with debug_timing(".write_multiscale()"):
ome_zarr.writer.write_multiscale(
pyramid=pyramid,
group=root,
axes=[ # Required for OME-ZARR >= 0.3
{"name": "t", "type": "time", "unit": "second"},
{"name": "c", "type": "channel"},
{"name": "z", "type": "space", "unit": "micrometer"},
{"name": "y", "type": "space", "unit": "micrometer"},
{"name": "x", "type": "space", "unit": "micrometer"},
],
coordinate_transformations=transforms,
storage_options=storage_opts,
name=f"{region}_t{timepoint}",
fmt=ome_zarr.format.CurrentFormat(),
)

# Add complete OMERO metadata for visualization
# Note(colin): this is an unusual API, but reading the Zarr library
Expand Down
2 changes: 2 additions & 0 deletions image_stitcher/stitcher_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@ def main(args: list[str]) -> None:
params = CliApp.run(StitchingParameters, cli_args=args)
log_level = logging.DEBUG if params.verbose else logging.INFO
logging.basicConfig(level=log_level)
# fsspec debug logs are very spammy
logging.getLogger("fsspec.local").setLevel(logging.INFO)
Stitcher(params).run()


Expand Down