Merge pull request #8 from constantinpape/main

Update data format
tischi · Nov 23, 2020 · 8b766ec · 8b766ec
2 parents 45941b3 + b0e118d
commit 8b766ec
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/create_data.py b/create_data.py
@@ -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)
@@ -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,
@@ -117,4 +117,5 @@ def add_all_volumes():
 
 
 if __name__ == '__main__':
-    add_all_volumes()
+    add_myosin()
+    # add_all_volumes()
diff --git a/data/prospr-myosin.xml b/data/prospr-myosin.xml
@@ -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>

diff --git a/data_conversion/to_ome_zarr.py b/data_conversion/to_ome_zarr.py
@@ -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,
@@ -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)