diff --git a/workflow/scripts/tif_to_zarr_gcs.py b/workflow/scripts/tif_to_zarr_gcs.py index 41ed921..7db8ca8 100644 --- a/workflow/scripts/tif_to_zarr_gcs.py +++ b/workflow/scripts/tif_to_zarr_gcs.py @@ -127,11 +127,11 @@ def build_zstack_from_single(gcs_uri,zstack_metadata,fs): tiles=[] for i_tile,(tilex,tiley) in enumerate(product(metadata['tiles_x'],metadata['tiles_y'])): - print(f'tile {tilex}x{tiley}, {i_tile}') + #print(f'tile {tilex}x{tiley}, {i_tile}') zstacks=[] for i_chan,channel in enumerate(metadata['channels']): - print(f'channel {i_chan}') + #print(f'channel {i_chan}') if is_zstack: tif_file = in_tif_pattern.format(tilex=tilex,tiley=tiley,prefix=metadata['prefixes'][0],channel=channel) @@ -161,7 +161,7 @@ def build_zstack_from_single(gcs_uri,zstack_metadata,fs): #now we can do the computation itself, storing to zarr print('writing images to zarr with dask') -with ProgressBar(): +with ProgressBar(dt=10): da.to_zarr(darr,snakemake.output.zarr,overwrite=True,dimension_separator='/')