diff --git a/align.py b/align.py index 7963c3a407f45728134479d557f0bf728229f9f9..ba2272aa94fdfbb4652ca26a98f57eccfeddf669 100644 --- a/align.py +++ b/align.py @@ -65,17 +65,7 @@ def align_multichip( counts = [o['counts'] for o in out] tvecs = [o['tvec'] for o in out] - def prep_tvec(transform_dict): - transform_dict["tvec"] = List(transform_dict["tvec"]) - return transform_dict - - try: - transform_data = [map(prep_tvec, tvecs)] - with open(out_path.replace('.zarr', '.transform.json'), 'w') as f: - json.dump(transform_data, fp=f) - except Exception as e: - print('saving transform json failed: ', e.args) - + save_tvecs(tvecs, out_path.replace('.zarr', '.transform.json')) df = pd.concat(counts, ignore_index=True).sort_values(['[AB]','label']) df.to_csv(table_path) @@ -91,7 +81,19 @@ def align_multichip( ) return out_path - +def prep_tvec(transform_dict): + t = transform_dict.copy() + t["tvec"] = list(t["tvec"]) + return t + +def save_tvecs(tvecs, path): + try: + transform_data = list(map(prep_tvec, tvecs)) + with open(path, 'w') as f: + json.dump(transform_data, fp=f) + except Exception as e: + print('saving transform json failed: ', e.args) + def align_parallel(args, **kwargs): return align2D(*args, **kwargs)