From 58ea5913c128cadd7de364e5ffb03cbd7559392a Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Sun, 7 Apr 2024 00:03:30 -0400 Subject: [PATCH] simplify glob imread --- workflow/scripts/stitched_tif_to_zarr.py | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/workflow/scripts/stitched_tif_to_zarr.py b/workflow/scripts/stitched_tif_to_zarr.py index 1cbca8e..98adcd3 100644 --- a/workflow/scripts/stitched_tif_to_zarr.py +++ b/workflow/scripts/stitched_tif_to_zarr.py @@ -1,4 +1,3 @@ -import tifffile from glob import glob import dask.array as da import dask.array.image @@ -10,18 +9,10 @@ in_tif_glob = snakemake.params.in_tif_glob.format(stain=snakemake.wildcards.stain) -tif_paths = sorted(glob(in_tif_glob)) -zslices=[] -for tif_path in tif_paths[:5]: - - print(tif_path) - zslices.append(dask.array.image.imread(tif_path, imread=tifffile.imread)) +darr = dask.array.image.imread(in_tif_glob) -darr = da.stack(zslices,axis=1) -darr = da.squeeze(darr) - #rescale intensities, and recast -- only recast #darr = darr * snakemake.params.intensity_rescaling darr = darr.astype('uint16')