remove fused toplevel group

workflow/scripts/ome_zarr_to_nii.py

@@ -10,7 +10,7 @@
 
 zi = zarr.open(in_zarr)
 
-attrs=zi['fused'].attrs.asdict()
+attrs=zi['/'].attrs.asdict()
 
 level=int(snakemake.wildcards.level)
 
@@ -25,7 +25,7 @@
 affine[1,1]=-transforms[0]['scale'][1] #y
 affine[2,2]=-transforms[0]['scale'][0] #x
 
-darr = da.from_zarr(in_zarr,component=f'fused/{level}')
+darr = da.from_zarr(in_zarr,component=f'/{level}')
 
 #input array axes are ZYX 
 #writing to nifti we want XYZ

workflow/scripts/resample_labels_to_zarr.py

@@ -12,8 +12,10 @@
 in_template_dseg=snakemake.input.dseg
 out_zarr=snakemake.output.zarr
 
+level=0
+
 #load dask array from zarr reference image
-darr = da.from_zarr(in_zarr,component='fused/0')
+darr = da.from_zarr(in_zarr,component=f'/{level}')
 
 #load template dseg
 dseg_nib = nib.load(in_template_dseg)
@@ -30,7 +32,7 @@
 
 #read coordinate transform from ome-zarr
 zi = zarr.open(in_zarr)
-attrs=zi['fused'].attrs.asdict()
+attrs=zi['/'].attrs.asdict()
 level=0
 transforms = attrs['multiscales'][0]['datasets'][level]['coordinateTransformations']
 

workflow/scripts/zarr_to_ome_zarr.py

@@ -2,6 +2,7 @@
 import zarr
 import dask.array as da
 from ome_zarr.writer import write_image
+from ome_zarr.format import format_from_version
 from ome_zarr.scale import Scaler
 from dask.diagnostics import ProgressBar
 
@@ -45,7 +46,7 @@
 
 
 store = zarr.DirectoryStore(out_zarr)
-root = zarr.group(store,path='/fused',overwrite=True)
+root = zarr.group(store,path='/',overwrite=True)
 scaler = Scaler(max_layer=max_layer,method=scaling_method)
 
 
@@ -55,6 +56,8 @@
                             group=root,
                             scaler=scaler,
                             coordinate_transformations=coordinate_transformations,
+                            #fmt=format_from_version(0.1),
+#                            fmt=format_from_version(0.4),
                             axes=axes)