def test_3d_eptm_cell_getter_setter():
datasets_2d, specs = three_faces_sheet()
datasets = extrude(datasets_2d)
eptm = Epithelium("3faces_3D", datasets)
assert eptm.cell_df is not None
datasets_3d = extrude(datasets_2d, method="translation")
eptm.cell_df = datasets_3d["cell"]
for key in eptm.cell_df:
assert key in datasets_3d["cell"]
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_retrieve_bulk():
eptm = Epithelium("3", extrude(three_faces_sheet()[0]))
RNRGeometry.update_all(eptm)
history = History(eptm)
eptm_ = history.retrieve(0)
RNRGeometry.update_all(eptm_)
def test_modify():
datasets, _ = three_faces_sheet()
extruded = extrude(datasets, method="translation")
mono = Monolayer("test", extruded, config.geometry.bulk_spec())
mono.update_specs(config.dynamics.quasistatic_bulk_spec(), reset=True)
modifiers = {
"apical": {
"edge": {
"line_tension": 1.0
},
"face": {
"contractility": 0.2
}
},
"basal": {
"edge": {
"line_tension": 3.0
},
"face": {
"contractility": 0.1
}
},
}
utils.modify_segments(mono, modifiers)
assert mono.edge_df.loc[mono.apical_edges,
"line_tension"].unique()[0] == 1.0
assert mono.edge_df.loc[mono.basal_edges,
"line_tension"].unique()[0] == 3.0
def test_cell_cell_connectivity():
data, _ = three_faces_sheet()
mono = Monolayer("test", extrude(data), bulk_spec())
ccc = connectivity.cell_cell_connectivity(mono)
expected = np.array([[0, 36, 36], [36, 0, 36], [36, 36, 0]])
np.testing.assert_array_equal(ccc, expected)
def test_verts_in_cell_connectivity():
data, specs = three_faces_sheet()
mono = Monolayer("test", extrude(data), bulk_spec())
ccc = connectivity.verts_in_cell_connectivity(mono)
assert ccc[0][ccc[0] == 9].shape == (18, )
assert ccc[0][ccc[0] == 18].shape == (6, )
assert ccc[0][ccc[0] == 27].shape == (1, )
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_extrude():
datasets, specs = generation.three_faces_sheet()
sheet = Sheet("test", datasets, specs)
extruded = extrude(sheet.datasets, method="translation")
assert extruded["cell"].shape[0] == 3
assert extruded["face"].shape[0] == 24
assert extruded["edge"].shape[0] == 108
assert extruded["vert"].shape[0] == 26
def test_number_getters():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d)
eptm = Epithelium("3faces_3D", datasets, specs)
assert eptm.Nc == datasets["cell"].shape[0]
assert eptm.Nv == datasets["vert"].shape[0]
assert eptm.Nf == datasets["face"].shape[0]
assert eptm.Ne == datasets["edge"].shape[0]
def test_get_simple_index():
tri_face = Epithelium("3", *three_faces_sheet())
idx = get_simple_index(tri_face.edge_df)
assert idx.shape == (15, )
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, scale=1 / 3.0)
eptm = Epithelium("3faces_3D", datasets, specs)
idx = get_simple_index(eptm.edge_df)
assert idx.shape == (43, )
def test_cell_centered_patch():
grid = hexa_grid2d(6, 4, 3, 3)
datasets = from_2d_voronoi(Voronoi(grid))
_ = Sheet("test", datasets)
extruded = extrude(datasets, method="translation")
mono = Monolayer("test", extruded, config.geometry.bulk_spec())
submono = utils.cell_centered_patch(mono, 5, 1)
assert submono.Nc == 4
def test_highlight():
dsets = extrude(three_faces_sheet()[0])
mono3 = Epithelium("3", dsets, config.geometry.bulk_spec())
RNRGeometry.update_all(mono3)
highlight_cells(mono3, 0)
assert mono3.face_df.visible.sum() == 8
highlight_cells(mono3, [0, 1], reset_visible=False)
assert mono3.face_df.visible.sum() == 16
highlight_cells(mono3, 2, reset_visible=True)
assert mono3.face_df.visible.sum() == 8
def test_orbits():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d)
eptm = Epithelium("3faces_3D", datasets, specs)
expected_res_cell = datasets["edge"].groupby("srce").apply(
lambda df: df["cell"])
expected_res_face = datasets["edge"].groupby("face").apply(
lambda df: df["trgt"])
assert_array_equal(expected_res_cell, eptm.get_orbits("srce", "cell"))
assert_array_equal(expected_res_face, eptm.get_orbits("face", "trgt"))
def test_polygons():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, scale=1 / 3.0)
eptm = Epithelium("3faces_3D", datasets, specs)
RNRGeometry.update_all(eptm)
with raises(ValueError):
fp = eptm.face_polygons()
eptm.reset_index(order=True)
res = eptm.face_polygons(["x", "y", "z"])
shapes = res.apply(lambda s: s.shape in ((6, 3), (4, 3)))
assert all(shapes)
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_face_centered_patch():
grid = hexa_grid2d(6, 4, 3, 3)
datasets = from_2d_voronoi(Voronoi(grid))
sheet = Sheet("test", datasets)
subsheet = utils.face_centered_patch(sheet, 5, 2)
assert subsheet.Nf == 6
extruded = extrude(datasets, method="translation")
mono = Monolayer("test", extruded, config.geometry.bulk_spec())
submono = utils.face_centered_patch(mono, 15, 1)
assert submono.Nf == 19
def test_copy():
datasets, specs = three_faces_sheet()
extruded = extrude(datasets, method="translation")
mono = Monolayer("test", extruded, config.geometry.bulk_spec())
assert mono.Nc == 3
assert mono.Nf == 24
assert mono.Ne == 108
assert mono.Nv == 26
mono2 = mono.copy()
assert mono2.Nc == 3
assert isinstance(mono2, Monolayer)
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_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_subdivide():
datasets, specs = generation.three_faces_sheet()
sheet = Sheet("test", datasets, specs)
subdivided = subdivide_faces(sheet, [0])
assert subdivided["face"].shape[0] == 3
assert subdivided["edge"].shape[0] == 30
assert subdivided["vert"].shape[0] == 14
datasets_3d = extrude(datasets, method="translation")
sheet_3d = Sheet("test3d", datasets_3d, specs)
subdivided_3d = subdivide_faces(sheet_3d, [0])
assert subdivided_3d["face"].shape[0] == 24
assert subdivided_3d["edge"].shape[0] == 120
assert subdivided_3d["vert"].shape[0] == 27
assert subdivided_3d["cell"].shape[0] == 3
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_upcast():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d)
eptm = Epithelium("3faces_3D", datasets, specs)
eptm.cell_df["test_data"] = eptm.cell_df.index
eptm.face_df["test_data"] = eptm.face_df.index
eptm.vert_df["test_data"] = eptm.vert_df.index
assert_array_equal(eptm.upcast_srce(eptm.vert_df["test_data"]),
eptm.edge_df["srce"])
assert_array_equal(eptm.upcast_srce("test_data"), eptm.edge_df["srce"])
assert_array_equal(eptm.upcast_trgt(eptm.vert_df["test_data"]),
eptm.edge_df["trgt"])
assert_array_equal(eptm.upcast_trgt("test_data"), eptm.edge_df["trgt"])
assert_array_equal(eptm.upcast_face("test_data"), eptm.edge_df["face"])
assert_array_equal(eptm.upcast_cell("test_data"), eptm.edge_df["cell"])
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_update_rank():
sheet = Sheet("3", *three_faces_sheet())
sheet.update_rank()
np.testing.assert_array_equal(
np.array([3, 3, 2, 2, 2, 3, 2, 2, 2, 3, 2, 2, 2]),
sheet.vert_df["rank"])
mono = Epithelium("3", extrude(sheet.datasets))
mono.update_rank()
mono.vert_df["rank"].values
np.testing.assert_array_equal(
np.array([
4,
4,
3,
3,
3,
4,
3,
3,
3,
4,
3,
3,
3,
4,
4,
3,
3,
3,
4,
3,
3,
3,
4,
3,
3,
3,
]),
mono.vert_df["rank"].values,
)
def test_simple_history():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
assert "dx" in history.datasets["edge"].columns
for element in sheet.datasets:
assert sheet.datasets[element].shape[0] == history.datasets[
element].shape[0]
history.record()
assert sheet.datasets["vert"].shape[0] * 2 == history.datasets[
"vert"].shape[0]
history.record()
assert sheet.datasets["vert"].shape[0] * 3 == history.datasets[
"vert"].shape[0]
assert sheet.datasets["face"].shape[0] * 3 == history.datasets[
"face"].shape[0]
mono = Epithelium("eptm", extrude(sheet.datasets))
histo2 = History(mono)
for element in mono.datasets:
assert mono.datasets[element].shape[0] == histo2.datasets[
element].shape[0]
def test_face_face_connectivity():
data, specs = three_faces_sheet()
sheet = Sheet("test", data, specs)
ffc = connectivity.face_face_connectivity(sheet, exclude_opposites=False)
expected = np.array([[0, 2, 2], [2, 0, 2], [2, 2, 0]])
np.testing.assert_array_equal(ffc, expected)
ffc = connectivity.face_face_connectivity(sheet, exclude_opposites=True)
expected = np.array([[0, 2, 2], [2, 0, 2], [2, 2, 0]])
np.testing.assert_array_equal(ffc, expected)
mono = Monolayer("test", extrude(data), bulk_spec())
ffc = connectivity.face_face_connectivity(mono, exclude_opposites=False)
assert ffc[0][ffc[0] == 2].shape == (10, )
assert ffc[0][ffc[0] == 1].shape == (4, )
assert ffc.max() == 4
ffc = connectivity.face_face_connectivity(mono, exclude_opposites=True)
assert ffc[0][ffc[0] == 2].shape == (10, )
assert ffc[0][ffc[0] == 1].shape == (4, )
assert ffc.max() == 2
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
def test_extrude_invalid_method():
datasets, specs = generation.three_faces_sheet()
with raises(ValueError):
datasets_3d = extrude(datasets, method="invalid_method")
