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Use skimage for image reading direct to numpy arrays instead of dask #12

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Merged
cjfuller merged 1 commit into from
Jan 16, 2025
Merged

Use skimage for image reading direct to numpy arrays instead of dask #12

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4 changes: 3 additions & 1 deletion image_stitcher/stitcher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import numpy as np
import ome_zarr
import psutil
import skimage
import zarr
from aicsimageio import types as aics_types
from aicsimageio.writers import OmeTiffWriter, OmeZarrWriter
Expand Down Expand Up @@ -282,7 +283,7 @@ def stitch_region(self, timepoint: int, region: str) -> AnyArray:
# Process each tile with progress tracking
for key, tile_info in region_metadata.items():
t, _, _, z_level, channel = key
tile = dask_imread(tile_info.filepath)[0]
tile = skimage.io.imread(tile_info.filepath)

if self.params.use_registration:
col_index = self.computed_parameters.x_positions.index(tile_info.x)
Expand Down Expand Up @@ -981,6 +982,7 @@ def run(self) -> None:

# Stitch region
self.callbacks.starting_stitching()

stitched_region = self.stitch_region(timepoint, region)
with debug_timing("rechunking"):
if isinstance(stitched_region, da.Array):
Expand Down