def test_fix_pinch():
dsets = hdf5.load_datasets(Path(stores_dir) / "with_pinch.hf5")
pinched = Monolayer("pinched", dsets)
assert not pinched.validate()
fix_pinch(pinched)
assert pinched.validate()
edf = pinched.edge_df[["srce", "trgt", "face", "cell"]].copy()
# Nothing happens here
fix_pinch(pinched)
assert pinched.validate()
assert np.all(pinched.edge_df[["srce", "trgt", "face", "cell"]] == edf)
def test_remove_cell():
dsets = hdf5.load_datasets(Path(stores_dir) / "with_4sided_cell.hf5")
mono = Monolayer("4", dsets)
Nci = mono.Nc
cell = mono.cell_df.query("num_faces == 4").index[0]
res = remove_cell(mono, cell)
MonolayerGeometry.update_all(mono)
assert not res
assert mono.validate()
assert mono.Nc == Nci - 1
with pytest.warns(UserWarning):
cell = mono.cell_df.query("num_faces != 4").index[0]
res = remove_cell(mono, cell)
assert mono.validate()
def test_close_cell():
dsets = hdf5.load_datasets(Path(stores_dir) / "with_4sided_cell.hf5")
mono = Monolayer("4", dsets)
cell = mono.cell_df.query("num_faces != 4").index[0]
Nfi = mono.cell_df.loc[cell, "num_faces"]
Nei = mono.Ne
edges = mono.edge_df.query(f"cell == {cell}")
face = edges["face"].iloc[0]
face_edges = edges.query(f"face == {face}").index
Nsi = len(face_edges)
mono.face_df.drop(face, axis=0, inplace=True)
mono.edge_df.drop(face_edges, axis=0, inplace=True)
mono.reset_index()
mono.reset_topo()
assert mono.cell_df.loc[cell, "num_faces"] == Nfi - 1
assert mono.Ne == Nei - Nsi
res = close_cell(mono, cell)
MonolayerGeometry.update_all(mono)
mono.reset_index()
mono.reset_topo()
assert not res
assert mono.validate()
assert mono.cell_df.loc[cell, "num_faces"] == Nfi
assert mono.Ne == Nei
def test_monolayer_division():
datasets_2d, _ = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, method="translation")
eptm = Monolayer("test_volume", datasets, bulk_spec(), coords=["x", "y", "z"])
eptm.vert_df[eptm.coords] += np.random.normal(scale=1e-6, size=(eptm.Nv, 3))
MonolayerGeometry.update_all(eptm)
for orientation in ["vertical", "horizontal", "apical"]:
monolayer_division(eptm, 0, orientation=orientation)
eptm.reset_topo()
eptm.reset_index()
assert eptm.validate()
assert eptm.Nc == 6
def test_monolayer_division():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, method="translation")
eptm = Monolayer("test_volume",
datasets,
bulk_spec(),
coords=["x", "y", "z"])
MonoLayerGeometry.update_all(eptm)
for orientation in ["vertical", "horizontal"]:
daughter = cell_division(eptm, 0, orientation=orientation)
eptm.reset_topo()
eptm.reset_index()
assert eptm.validate()
assert eptm.Nc == 5