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Solving bug in mesh attribute access and default behavior when loading meshes #90

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Merged
jules-vanaret merged 3 commits into from
Sep 25, 2025
Merged

Solving bug in mesh attribute access and default behavior when loading meshes #90

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52e6fd7
updated mesh dictionary format
jules-vanaret Sep 23, 2025
93a6ea1
Merge remote-tracking branch 'origin/v3.x' into mesh_bug
jules-vanaret Sep 25, 2025
dbbe3d5
changed default behavior
jules-vanaret Sep 25, 2025
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16 changes: 9 additions & 7 deletions src/lineagetree/_io/_loaders.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,12 +106,16 @@ def _load_meshdict_from_bmfmesh(bmfmesh, pos_multipliers, translation):
translation = np.array(translation, dtype=float)
vertices = vertices * pos_multipliers + translation

return {"vertices": vertices, "faces": faces} # could be a class
return { # could be a class
'vertices': vertices,
'faces': faces,
'center_mass': np.mean(vertices, axis=0),
}


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,
Expand Down Expand Up @@ -146,11 +150,9 @@ 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
)
pos[cell_id] = mesh.center_mass

mesh = _load_meshdict_from_bmfmesh(mesh, pos_multipliers, translation)
pos[cell_id] = mesh["center_mass"]

if store_meshes:
lT_mesh[cell_id] = mesh

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