rm zarr tools

zarr_tools/__main__.py

-from calendar import c
-from .convert import to_zarr
-import fire
-import nd2
-import os
-
-def main(nd2_path:str, output:str=None, channel_axis:int=1, steps:int=6, dry_run=False):
-    data = (d := nd2.ND2File(nd2_path)).to_dask().rechunk()
-    print(d.sizes)
-    try:
-        channel_axis = list(d.sizes.keys()).index('C')
-    except ValueError:
-        channel_axis = None
-
-    if output is None:
-        output = nd2_path.replace('.nd2', '.zarr')
-    out = to_zarr(data, output, steps=steps, dry_run=dry_run, channel_axis=channel_axis)
-    assert os.path.exists(out), "Failed..."
-    exit(0)
-
-if __name__=="__main__":
-    fire.Fire(main)
\ No newline at end of file

zarr_tools/convert.py

-import zarr
-import dask.array as da
-import os
-import nd2
-
-def nd2_to_zarr(path_nd2, out=None, steps=6, dry_run=False):
-    '''
-    Converts nd2 to zarr, multiscale
-    '''
-    data = nd2.ND2File(path_nd2)
-    print(sizes := data.sizes)
-    channel_axis = list(sizes.keys()).index('C')
-    out = (path_nd2.replace('.nd2', '.zarr') if out is None else path_nd2)
-    dask_input = data.to_dask()
-    _ = to_zarr(
-        dask_input=dask_input,
-        path=out,
-        steps=steps,
-        channel_axis=channel_axis,
-        dry_run=dry_run
-        )
-
-
-def to_zarr(dask_input:da.Array, path:str=None, steps=3, channel_axis=1, dry_run=False):
-    store = zarr.DirectoryStore(baseurl := path.replace('.nd2', '.zarr') if path is None else path)
-    grp = zarr.group(store)
-    grp.attrs['multiscales'] = {
-        "multiscales": [
-            {
-                "datasets": [
-                    {
-                        "path": str(i)
-                    } for i in range(steps)
-                ],
-                "name": os.path.basename(baseurl),
-                "type": "nd2",
-                "channel_axis": channel_axis,
-                "version": "0.1"
-            },
-
-        ]
-    }
-    print(baseurl)
-    for i in range(steps):
-        data = dask_input[...,::2**i,::2**i]
-        try:
-            data = data.rechunk()
-            print(data.chunksize, data.shape)
-            if not dry_run:
-                data.to_zarr(ppp:=os.path.join(baseurl, str(i)))
-                print(f'saved {ppp}')
-            else:
-                print(f'dry-run `to save to` {os.path.join(baseurl, str(i))}')
-                
-        except Exception as e:
-            print(e.args)
-        
-    return baseurl
-