From 52e6fd715f5cf8873166afd3f109a873fa375637 Mon Sep 17 00:00:00 2001 From: jules-vanaret Date: Wed, 24 Sep 2025 00:54:11 +0200 Subject: [PATCH 1/2] updated mesh dictionary format --- src/lineagetree/_io/_loaders.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index c91c897..ad67fee 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/src/lineagetree/_io/_loaders.py @@ -108,7 +108,8 @@ def _load_meshdict_from_bmfmesh(bmfmesh, pos_multipliers, translation): return { # could be a class 'vertices': vertices, - 'faces': faces + 'faces': faces, + 'center_mass': np.mean(vertices, axis=0), } @@ -150,7 +151,7 @@ def read_from_bmf( pred = None for t, mesh in track.meshes.items(): mesh = _load_meshdict_from_bmfmesh(mesh, pos_multipliers, translation) - pos[cell_id] = mesh.center_mass + pos[cell_id] = mesh["center_mass"] if store_meshes: lT_mesh[cell_id] = mesh From dbbe3d56e50c7fe3ac30b4cbf82d01840c68579e Mon Sep 17 00:00:00 2001 From: jules-vanaret Date: Thu, 25 Sep 2025 17:11:10 +0200 Subject: [PATCH 2/2] changed default behavior --- src/lineagetree/_io/_loaders.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index 11addc0..3e8ff65 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/src/lineagetree/_io/_loaders.py @@ -115,7 +115,7 @@ def _load_meshdict_from_bmfmesh(bmfmesh, pos_multipliers, translation): def read_from_bmf( file_path: str, - store_meshes: bool = False, + store_meshes: bool = True, pos_multipliers: tuple[float, float, float] = (1.0, 1.0, 1.0), translation: tuple[float, float, float] = (0.0, 0.0, 0.0), name: None | str = None,