set chunking in bdv n5 (default 32x32x32)

To hopefully address performance issues in the bigstitcher step when
dealing with large datasets.

Also sets dtype to int16 instead of uint16 for this only -- some imagesc
posts describing the black bars had this as a fix..

workflow/rules/bigstitcher.smk

@@ -40,7 +40,7 @@ rule zarr_to_bdv:
             )
             / "dataset.xml"
         ),
-        chunks=(1,1,32,32,32)
+        chunks=(32,32,32) #the previous default was 1 x Nx x Ny (Nx Ny were full tile size!)
     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,chunks=snakemake.params.chunks).astype(np.int16)
+darr = da.from_zarr(in_zarr)
 
 (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=(snakemake.params.chunks[2:]))
+                                blockdim=((1,256,256),))
 
 bdv_writer.set_attribute_labels('channel', metadata['channels'])
 
@@ -90,6 +90,7 @@ def update_xml_h5_to_n5(in_xml,out_xml,in_n5):
 print('removing empty bdv h5/xml')
 rmtree(temp_bdv_dir)
 
+
 print('writing data to n5')
 n5_store = zarr.n5.N5Store(snakemake.output.bdv_n5)
 
@@ -98,7 +99,7 @@ def update_xml_h5_to_n5(in_xml,out_xml,in_n5):
     ds_list=[] #for setup-level attrs
     for ds in range(max_downsampling_layers):
         step=2**ds  #1,2,4,8.. 
-        zstack = da.squeeze(darr[tile_i,chan_i,:,::step,::step])
+        zstack = da.squeeze(darr[tile_i,chan_i,:,::step,::step]).rechunk(snakemake.params.chunks).astype(np.int16)
         print(f'writing to setup{setup_i}/timepoint0/s{ds}')
         with ProgressBar():
             zstack.to_zarr(n5_store,component=f'setup{setup_i}/timepoint0/s{ds}',overwrite=True,compute=True) 

workflow/scripts/zarr_to_ome_zarr.py

@@ -68,6 +68,7 @@
 
     darr_list.append(da.from_zarr(in_zarr,component=f'{group_name}/s0',chunks=rechunk_size))
 
+
     #append to omero metadata
     channel_metadata={key:val for key,val in snakemake.config['ome_zarr']['omero_metadata']['channels']['defaults'].items()}
     channel_name=stains[zarr_i]