change chunksize in bdv (32x32x32 instead of default 1x4096x4096)

also set dtype to int16 (in case it is related to the black bars bug)

workflow/rules/bigstitcher.smk

@@ -40,6 +40,7 @@ rule zarr_to_bdv:
             )
             / "dataset.xml"
         ),
+        chunks=(1,1,32,32,32)
     output:
         bdv_n5=temp(
             directory(

workflow/scripts/zarr_to_n5_bdv.py

@@ -34,7 +34,7 @@ def update_xml_h5_to_n5(in_xml,out_xml,in_n5):
 max_downsampling_layers=snakemake.params.max_downsampling_layers
 
 #load data  (tiles,chans,zslices,x,y)
-darr = da.from_zarr(in_zarr)
+darr = da.from_zarr(in_zarr,chunks=snakemake.params.chunks).astype(np.int16)
 
 (n_tiles,n_chans,n_z,n_x,n_y) = darr.shape
 
@@ -52,7 +52,7 @@ def update_xml_h5_to_n5(in_xml,out_xml,in_n5):
                                 overwrite=True,
                                 nchannels=len(metadata['channels']), 
                                 ntiles=len(metadata['tiles_x'])*len(metadata['tiles_y']),
-                                blockdim=((1,256,256),))
+                                blockdim=(snakemake.params.chunks[2:]))
 
 bdv_writer.set_attribute_labels('channel', metadata['channels'])
 
@@ -110,6 +110,6 @@ def update_xml_h5_to_n5(in_xml,out_xml,in_n5):
     #add attributes for downsampling as a list, and datatype to the setup# level
     g = zarr.open_group(store=n5_store,path=f'setup{setup_i}',mode='r+')
     g.attrs['downsamplingFactors']=ds_list
-    g.attrs['dataType']='uint16'
+    g.attrs['dataType']='int16'