def test_scale():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, method='translation')
initial_cell_df = pd.DataFrame.from_dict({'cell':[0,1,2],\
'x':[0.5, -1.0, 0.5],\
'y':[8.660000e-01,-6.167906e-18,-8.6600000e-01],\
'z':[-0.5, -0.5, -0.5],\
'is_alive':[True, True, True],
'num_faces':[8,8,8],
'vol':[2.598,2.598,2.598]}).set_index('cell')
x10_cell_df = pd.DataFrame.from_dict({'cell':[0,1,2],\
'x':[5., -10.0, 5.],\
'y':[8.660000e+00,-6.167906e-17,-8.6600000e+00],\
'z':[-5., -5., -5.],\
'is_alive':[True, True, True],
'num_faces':[8,8,8],
'vol':[2.598,2.598,2.598]}).set_index('cell')
eptm = Epithelium('test_volume',datasets, specs, coords=['x','y','z'])
BulkGeometry.update_all(eptm)
scale(eptm, delta = 10.0, coords= ['x','y','z'])
tolerance = 1e-16
assert all( (x10_cell_df[['x','y','z']] - eptm.cell_df[['x', 'y', 'z']])**2 < 1e-16)
def test_bulk_update_vol():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, method='translation')
eptm = Epithelium('test_volume',datasets, specs, coords=['x','y','z'])
BulkGeometry.update_all(eptm)
expected_cell_df = pd.DataFrame.from_dict({'cell':[0,1,2],\
'x':[0.5, -1.0, 0.5],\
'y':[8.660000e-01,-6.167906e-18,-8.6600000e-01],\
'z':[-0.5, -0.5, -0.5],\
'is_alive':[True, True, True],
'num_faces':[8,8,8],
'vol':[2.598,2.598,2.598]}).set_index('cell')
expected_face_centroids = pd.DataFrame.from_dict({'face':list(range(24)),\
'x':[0.5, -1.0, 0.5, 0.5, -1.0, 0.5, 0.5,\
1.25, 1.25, 0.5, -0.25, -0.25, \
-0.25, -1.0, -1.75, -1.75, -1.0, \
-0.25, -0.25, -0.25, 0.5, 1.25, \
1.25, 0.5],\
'y':[0.86599999999999999, 0.0,\
-0.86599999999999999, \
0.86599999999999999, 0.0,\
-0.86599999999999999, 0.0, 0.433,\
1.2989999999999999, 1.732,\
1.2989999999999999, 0.433, 0.433,\
0.86599999999999999, 0.433, -0.433,\
-0.86599999999999999, -0.433, -0.433,\
-1.2989999999999999, -1.732, \
-1.2989999999999999, -0.433, 0.0],\
'z':[0.0, 0.0, 0.0, -1.0, -1.0, -1.0, \
-0.5, -0.5, -0.5, -0.5, -0.5, \
-0.5, -0.5, -0.5, -0.5, -0.5, \
-0.5, -0.5, -0.5, -0.5, -0.5, \
-0.5, -0.5, -0.5]}).set_index('face')
## only update class methods in BulkGeometry : update_vol, update_centroids
tolerance = 1e-16
## check volumes
assert all( (expected_cell_df['vol'] - eptm.cell_df['vol'])**2 < tolerance)
## check centroids
assert all( (expected_face_centroids - eptm.face_df.loc[:, ['x','y','z']])**2 < tolerance )
def test_update():
datasets_2d, specs = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, method='translation')
initial_cell_df = pd.DataFrame.from_dict({'cell':[0,1,2],\
'x':[0.5, -1.0, 0.5],\
'y':[8.660000e-01,-6.167906e-18,-8.6600000e-01],\
'z':[-0.5, -0.5, -0.5],\
'is_alive':[True, True, True],
'num_faces':[8,8,8],
'vol':[2.598,2.598,2.598]}).set_index('cell')
eptm = Epithelium('test_volume',datasets, specs, coords=['x','y','z'])
BulkGeometry.update_all(eptm)
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_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_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_bulk_update_vol():
datasets_2d, _ = three_faces_sheet(zaxis=True)
datasets = extrude(datasets_2d, method="translation")
specs = config.geometry.bulk_spec()
eptm = Epithelium("test_volume", datasets, specs, coords=["x", "y", "z"])
BulkGeometry.update_all(eptm)
expected_cell_df = pd.DataFrame.from_dict({
"cell": [0, 1, 2],
"x": [0.5, -1.0, 0.5],
"y": [8.660000e-01, -6.167906e-18, -8.6600000e-01],
"z": [-0.5, -0.5, -0.5],
"is_alive": [True, True, True],
"num_faces": [8, 8, 8],
"vol": [2.598, 2.598, 2.598],
}).set_index("cell")
expected_face_centroids = pd.DataFrame.from_dict({
"face":
list(range(24)),
"x": [
0.5,
-1.0,
0.5,
0.5,
-1.0,
0.5,
0.5,
1.25,
1.25,
0.5,
-0.25,
-0.25,
-0.25,
-1.0,
-1.75,
-1.75,
-1.0,
-0.25,
-0.25,
-0.25,
0.5,
1.25,
1.25,
0.5,
],
"y": [
0.86599999999999999,
0.0,
-0.86599999999999999,
0.86599999999999999,
0.0,
-0.86599999999999999,
0.0,
0.433,
1.2989999999999999,
1.732,
1.2989999999999999,
0.433,
0.433,
0.86599999999999999,
0.433,
-0.433,
-0.86599999999999999,
-0.433,
-0.433,
-1.2989999999999999,
-1.732,
-1.2989999999999999,
-0.433,
0.0,
],
"z": [
0.0,
0.0,
0.0,
-1.0,
-1.0,
-1.0,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
-0.5,
],
}).set_index("face")
## only update class methods in BulkGeometry : update_vol, update_centroids
tolerance = 1e-16
## check volumes
assert all((expected_cell_df["vol"] - eptm.cell_df["vol"])**2 < tolerance)
## check centroids
assert all((expected_face_centroids -
eptm.face_df.loc[:, ["x", "y", "z"]])**2 < tolerance)