def test_hexagrid3d_noise():
np.random.seed(1)
grid = hexa_grid3d(6, 4, 3, noise=0.1)
datasets = from_3d_voronoi(Voronoi(grid))
assert datasets["vert"].shape[0] == 318
assert datasets["edge"].shape[0] == 3300
assert datasets["face"].shape[0] == 335
assert datasets["cell"].shape[0] == 72
def test_from_3d_voronoi():
grid = hexa_grid3d(6, 4, 3)
datasets = from_3d_voronoi(Voronoi(grid))
assert datasets["vert"].shape[0] == 139
assert datasets["edge"].shape[0] == 1272
assert datasets["face"].shape[0] == 141
assert datasets["cell"].shape[0] == 70
bulk = Epithelium("bulk", datasets, config.geometry.bulk_spec())
bulk.reset_index()
bulk.reset_topo()
BulkGeometry.update_all(bulk)
bulk.sanitize()
assert bulk.validate()
def test_from_3d_voronoi():
grid = hexa_grid3d(6, 4, 3)
datasets = from_3d_voronoi(Voronoi(grid))
assert datasets["vert"].shape[0] == 139
assert datasets["edge"].shape[0] == 1272
assert datasets["face"].shape[0] == 282
assert datasets["cell"].shape[0] == 70
bulk = Epithelium("bulk", datasets, config.geometry.bulk_spec())
bulk.reset_index()
bulk.reset_topo()
BulkGeometry.update_all(bulk)
bulk.sanitize()
# GH 137
assert (bulk.edge_df.groupby("face").apply(
lambda df: df["cell"].unique().size).max() == 1)
assert bulk.validate()
def test_bulk_division():
cells = hexa_grid3d(4, 4, 6)
datasets = from_3d_voronoi(Voronoi(cells))
specs = bulk_spec()
bulk = Epithelium("bulk", datasets, specs)
bulk.reset_topo()
bulk.reset_index()
bulk.sanitize()
bulk.reset_topo()
bulk.reset_index()
cell_division(bulk, 4, BulkGeometry)
dsets = hdf5.load_datasets(Path(stores_dir) / "with_4sided_cell.hf5")
bulk = Monolayer("4", dsets)
BulkGeometry.update_all(bulk)
# daughter = cell_division(bulk, 12, BulkGeometry)
with pytest.warns(UserWarning):
cell_division(bulk, 4, BulkGeometry)
assert bulk.validate()
def test_single_cell():
grid = hexa_grid3d(6, 4, 3)
datasets = from_3d_voronoi(Voronoi(grid))
sheet = Sheet("test", datasets)
eptm = utils.single_cell(sheet, 1)
assert len(eptm.edge_df) == len(sheet.edge_df[sheet.edge_df["cell"] == 1])