diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index 3e8ff65..2b87710 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/src/lineagetree/_io/_loaders.py @@ -106,10 +106,10 @@ def _load_meshdict_from_bmfmesh(bmfmesh, pos_multipliers, translation): translation = np.array(translation, dtype=float) vertices = vertices * pos_multipliers + translation - return { # could be a class - 'vertices': vertices, - 'faces': faces, - 'center_mass': np.mean(vertices, axis=0), + return { # could be a class + "vertices": vertices, + "faces": faces, + "center_mass": np.mean(vertices, axis=0), } @@ -150,9 +150,11 @@ def read_from_bmf( for track in tracks: pred = None for t, mesh in track.meshes.items(): - mesh = _load_meshdict_from_bmfmesh(mesh, pos_multipliers, translation) + mesh = _load_meshdict_from_bmfmesh( + mesh, pos_multipliers, translation + ) pos[cell_id] = mesh["center_mass"] - + if store_meshes: lT_mesh[cell_id] = mesh @@ -869,6 +871,8 @@ def read_from_mastodon( pos = dict(zip(nodes, spots[:, :3], strict=True)) time = dict(zip(nodes, spots[:, 3], strict=True)) predecessor = {} + labels, labels_name = {}, [] + for succ, pred in zip(links[:, 1], links[:, 0]): predecessor[int(succ)] = int(pred)