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Update data format #8

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merged 1 commit into from
Nov 23, 2020
Merged

Update data format #8

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9 changes: 5 additions & 4 deletions create_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,10 @@ def write_metadata(in_xml, out_xml, out_path):
bucket_name=bucket_name,
path_in_bucket=path_in_bucket,
authentication='Anonymous',
bdv_type='bdv.zarr.s3')
bdv_type='ome.zarr.s3')

with z5py.File(out_path, 'r') as f:
shape = f['setup0/timepoint0/s0'].shape[2:]
shape = f['s0'].shape[2:]

# check if we need to update the shape and resolution
exp_shape = get_size(out_xml, setup_id=0)
Expand Down Expand Up @@ -71,7 +71,7 @@ def add_volume(in_path, vol_name, layer_type, start_scale=0):
# convert to ome zarr
convert_bdv_n5(in_path=in_path,
out_path=out_path,
out_key='setup0/timepoint0',
out_key='',
vol_name=vol_name,
use_nested_store=False,
n_threads=8,
Expand Down Expand Up @@ -117,4 +117,5 @@ def add_all_volumes():


if __name__ == '__main__':
add_all_volumes()
add_myosin()
# add_all_volumes()
2 changes: 1 addition & 1 deletion data/prospr-myosin.xml
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Expand Up @@ -25,7 +25,7 @@
<first>0</first>
<last>0</last>
</Timepoints>
<ImageLoader format="bdv.zarr.s3">
<ImageLoader format="ome.zarr.s3">
<Key>prospr-myosin.ome.zarr</Key>
<SigningRegion>us-west-2</SigningRegion>
<ServiceEndpoint>https://s3.embl.de</ServiceEndpoint>
Expand Down
14 changes: 10 additions & 4 deletions data_conversion/to_ome_zarr.py
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Expand Up @@ -136,17 +136,23 @@ def convert_bdv_n5(in_path, out_path, out_key, vol_name,
if start_scale > 0:
scale_names = scale_names[start_scale:]

g_out = f_out.create_group(out_key)
write_at_root = out_key is None or out_key == ''
if write_at_root:
g_out = f_out
else:
g_out = f_out.create_group(out_key)
out_names = []

for sid, name in enumerate(scale_names):
ds_in = scale_group[name]
out_name = f"s{sid}"

store_path = os.path.join(out_path, out_name) if write_at_root else\
os.path.join(out_path, out_key, out_name)
if use_nested_store:
store = zarr.NestedDirectoryStore(os.path.join(out_path, out_key, out_name))
store = zarr.NestedDirectoryStore(store_path)
else:
store = zarr.DirectoryStore(os.path.join(out_path, out_key, out_name))
store = zarr.DirectoryStore(store_path)
ds_out = zarr.zeros(store=store,
shape=ds_in.shape,
chunks=ds_in.chunks,
Expand All @@ -157,7 +163,7 @@ def convert_bdv_n5(in_path, out_path, out_key, vol_name,

# this invalidates the shape and chunk attributes of our dataset,
# so we can't use it after that (but we also don't need to)
expand_dims(os.path.join(out_path, out_key, out_name), use_nested_store)
expand_dims(store_path, use_nested_store)
out_names.append(out_name)

assert len(out_names) == len(scales)
Expand Down