def test_apoptosis(): specs = config.geometry.bulk_spec() sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1) sheet.sanitize() datasets = extrude(sheet.datasets, method="translation") mono = Monolayer("mono", datasets, specs) mono.face_df["id"] = mono.face_df.index.values geom.center(mono) geom.update_all(mono) mono.face_df["contractility"] = 1.0 manager = EventManager("face") cell_id = 0 apical_face = mono.face_df[ (mono.face_df.index.isin(mono.get_orbits("cell", "face")[cell_id])) & (mono.face_df.segment == "apical")].index[0] sheet.settings["apoptosis"] = {"cell_id": cell_id} initial_cell_event = [(apoptosis, sheet.settings["apoptosis"])] manager.extend(initial_cell_event) manager.execute(mono) manager.update() assert len(manager.current) == 1 i = 0 while i < 5: manager.execute(mono) manager.update() i = i + 1 assert mono.face_df.loc[apical_face, "contractility"] > 1.0
def test_find_transitions(): 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) eptm.settings["threshold_length"] = 1e-3 IH_transition(eptm, 26) BulkGeometry.update_all(eptm) eptm.settings["threshold_length"] = 1e-2 ih, hi = find_rearangements(eptm) assert len(ih) == 0 assert len(hi) == 2 assert len(find_HIs(eptm)) face = eptm.face_df.index[-1] HI_transition(eptm, face) BulkGeometry.update_all(eptm) eptm.settings["threshold_length"] = 2e-1 ih, hi = find_rearangements(eptm) assert len(ih) == 1 assert len(hi) == 0 assert len(find_IHs(eptm))
def test_ab_pull_edge(): specs = config.geometry.bulk_spec() sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1) sheet.sanitize() datasets = extrude(sheet.datasets, method="translation") mono = Monolayer("mono", datasets, specs) geom.center(mono) geom.update_all(mono) mono.edge_df["line_tension"] = 1.0 mono.specs["edge"]["line_tension"] = 1.0 assert len(mono.edge_df.line_tension.unique()) == 1 ab_pull_edge(mono, 1, 2, False) assert len(mono.edge_df.line_tension.unique()) == 2
def test_shrink(): specs = config.geometry.bulk_spec() sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1) sheet.sanitize() datasets = extrude(sheet.datasets, method="translation") mono = Monolayer("mono", datasets, specs) geom.center(mono) geom.update_all(mono) mono.cell_df["prefered_vol"] = 1.0 mono.cell_df["prefered_area"] = 1.0 shrink(mono, 0, 0.2) assert round(mono.cell_df.loc[0, "prefered_vol"], 4) == 0.8333 assert round(mono.cell_df.loc[0, "prefered_area"], 4) == 0.8855
def test_contract(): specs = config.geometry.bulk_spec() sheet = Sheet.planar_sheet_3d("flat", 4, 5, 1, 1) sheet.sanitize() datasets = extrude(sheet.datasets, method="translation") mono = Monolayer("mono", datasets, specs) geom.center(mono) geom.update_all(mono) mono.face_df["contractility"] = 1.0 assert len(mono.face_df.contractility.unique()) == 1 faces = mono.edge_df[mono.edge_df["cell"] == 0]["face"].unique() for f in faces: contract(mono, f, 0.2) assert len(mono.face_df.contractility.unique()) == 2 for f in faces: assert mono.face_df.loc[f, "contractility"] == 1.2
def test_IH_transition(): sheet = Sheet.planar_sheet_3d('sheet', 5, 5, 1, 1) sheet.sanitize() datasets = extrude(sheet.datasets, method='translation') eptm = Epithelium('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)
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_constriction(): specs = config.geometry.bulk_spec() sheet = Sheet.planar_sheet_3d("flat", 6, 8, 1, 1) sheet.sanitize() datasets = extrude(sheet.datasets, method="translation") mono = Monolayer("mono", datasets, specs) geom.center(mono) geom.update_all(mono) dyn_specs = config.dynamics.quasistatic_bulk_spec() dyn_specs["cell"]["area_elasticity"] = 0.05 dyn_specs["cell"]["prefered_area"] = 6.0 dyn_specs["cell"]["vol_elasticity"] = 1.0 dyn_specs["cell"]["prefered_vol"] = 1.2 dyn_specs["face"]["contractility"] = 0.0 dyn_specs["edge"]["line_tension"] = 0.0 mono.update_specs(dyn_specs, reset=True) mono.face_df.loc[mono.apical_faces, "contractility"] = 1.12 mono.face_df.loc[mono.basal_faces, "contractility"] = 1.12 manager = EventManager("face") sheet.face_df["enter_in_process"] = 0 mono.settings["constriction"] = {} mono.cell_df["is_mesoderm"] = False mono.face_df["is_mesoderm"] = False cell_to_constrict = [12] apical_face = mono.face_df[(mono.face_df.index.isin( mono.get_orbits("cell", "face")[cell_to_constrict[0]])) & (mono.face_df.segment == "apical")].index[0] mono.cell_df.loc[cell_to_constrict, "is_mesoderm"] = True mono.cell_df["id"] = mono.cell_df.index.values mono.face_df["id"] = mono.face_df.index.values list_face_in_cell = mono.get_orbits("cell", "face") cell_in_mesoderm = mono.cell_df[mono.cell_df.is_mesoderm].index.values for i in cell_in_mesoderm: faces_in_cell = mono.face_df.loc[list_face_in_cell[i].unique()] for f in faces_in_cell.index.values: mono.face_df.loc[f, "is_mesoderm"] = True for i in cell_to_constrict: delam_kwargs = mono.settings["constriction"].copy() delam_kwargs.update({ "cell_id": i, "contract_rate": 2, "critical_area": 0.02, "shrink_rate": 0.4, "critical_volume": 0.1, "radial_tension": 3, "max_traction": 35, "contract_neighbors": True, "contract_span": 1, "with_rearrangement": True, "critical_area_reduction": 5, }) initial_cell_event = [(constriction, delam_kwargs)] manager.extend(initial_cell_event) manager.execute(mono) manager.update() assert len(manager.current) == 1 i = 0 while i < 10: manager.execute(mono) manager.update() i = i + 1 assert mono.face_df.loc[apical_face, "contractility"] > 1.0 for c in cell_to_constrict: assert mono.cell_df.loc[c, "num_faces"] <= 4