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_HI_transition():
sheet = Sheet.planar_sheet_3d("sheet", 5, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
eptm = Monolayer("test_HIt", datasets, bulk_spec())
BulkGeometry.update_all(eptm)
Nc, Nf, Ne, Nv = eptm.Nc, eptm.Nf, eptm.Ne, eptm.Nv
eptm.settings["threshold_length"] = 1e-3
IH_transition(eptm, 26)
BulkGeometry.update_all(eptm)
face = eptm.face_df.index[-1]
HI_transition(eptm, face)
assert eptm.Nc == Nc
assert eptm.Nf == Nf
assert eptm.Ne == Ne
assert eptm.Nv == Nv
invalid = eptm.get_invalid()
assert np.alltrue(1 - invalid)
assert np.alltrue(eptm.edge_df["sub_vol"] > 0)
def test_IH_transition():
sheet = Sheet.planar_sheet_3d("sheet", 5, 5, 1, 1)
sheet.sanitize()
datasets = extrude(sheet.datasets, method="translation")
eptm = Monolayer("test_IHt", datasets, bulk_spec())
BulkGeometry.update_all(eptm)
Nc, Nf, Ne, Nv = eptm.Nc, eptm.Nf, eptm.Ne, eptm.Nv
eptm.settings["threshold_length"] = 1e-3
IH_transition(eptm, 26)
BulkGeometry.update_all(eptm)
assert eptm.Nc == Nc
assert eptm.Nf == Nf + 2
assert eptm.Ne == Ne + 12
assert eptm.Nv == Nv + 1
invalid = eptm.get_invalid()
assert np.alltrue(1 - invalid)
assert np.alltrue(eptm.edge_df["sub_vol"] > 0)
assert (eptm.face_df[eptm.face_df.segment == "apical"].shape[0] ==
eptm.cell_df.shape[0])
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
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