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])