From eb3d6569b07ea473225e503b3102a89330d7e72a Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 14 Mar 2023 13:50:09 +0000
Subject: [PATCH] Use write_table_points instead of regions

---
 write_kyoda_wormdata.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/write_kyoda_wormdata.py b/write_kyoda_wormdata.py
index 022668f..6188f0a 100644
--- a/write_kyoda_wormdata.py
+++ b/write_kyoda_wormdata.py
@@ -6,7 +6,7 @@
 import numpy as np
 from ome_zarr.io import parse_url
 import zarr
-from ngff_tables_prototype.writer import write_table_regions
+from ngff_tables_prototype.writer import write_table_points
 
 
 df = pd.read_csv('wt-N2-081015-01.csv', names=('t', 'pid', 'cid', 'x', 'y', 'z', 'name', 'sphericity', 'volume', 'phase'))
@@ -55,8 +55,6 @@
 
 
 adata = ad.AnnData(X = dfa, obs = obs_meta)
-# simple 2D table is suitable for obsm data
-adata.obsm["tracking"] = obsp_raw
 
 # write as sparse data to obsp
 adata.obsp["tracking"] = csr_matrix(obsp_raw)
@@ -65,10 +63,7 @@
 root = zarr.group(store=store)
 
 tables_group = root.create_group(name="tables")
-write_table_regions(
+write_table_points(
     group=tables_group,
-    adata=adata,
-    region="labels/label_image",
-    region_key=None,
-    instance_key="cell_id"
+    adata=adata
 )