def test_face_polygons_exception():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -3**0.5 / 2]]
tri_edges_valid = [[0, 1, 0], [1, 2, 0], [2, 0, 0], [0, 3, 1], [3, 1, 1],
[1, 0, 1], [0, 2, 2], [2, 3, 2], [3, 0, 2]]
tri_edges_invalid = [[0, 1, 0], [1, 2, 0], [2, 0, 0], [0, 3, 1], [3, 1, 1],
[1, 0, 1], [0, 2, 2], [2, 3, 2],
[3, 1, 2]] # changed 0 to 1 to create an invalid face
datasets['edge'] = pd.DataFrame(data=np.array(tri_edges_valid),
columns=['srce', 'trgt', 'face'])
datasets['edge'].index.name = 'edge'
datasets['face'] = pd.DataFrame(data=np.zeros((3, 2)), columns=['x', 'y'])
datasets['face'].index.name = 'face'
datasets['vert'] = pd.DataFrame(data=np.array(tri_verts),
columns=['x', 'y'])
datasets['vert'].index.name = 'vert'
specs = config.geometry.planar_spec()
eptm = Epithelium('valid', datasets, specs, coords=['x', 'y'])
PlanarGeometry.update_all(eptm)
eptm.face_polygons(['x', 'y'])
def test_sort_eastwest():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -(3**0.5) / 2]]
tri_edges = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 0, 2],
]
datasets["edge"] = pd.DataFrame(data=np.array(tri_edges),
columns=["srce", "trgt", "face"])
datasets["edge"].index.name = "edge"
datasets["face"] = pd.DataFrame(data=np.zeros((3, 2)), columns=["x", "y"])
datasets["face"].index.name = "face"
datasets["vert"] = pd.DataFrame(data=np.array(tri_verts),
columns=["x", "y"])
datasets["vert"].index.name = "vert"
specs = config.geometry.planar_spec()
eptm = Sheet("extra", datasets, specs, coords=["x", "y"])
PlanarGeometry.update_all(eptm)
eptm.edge_df["opposite"] = get_opposite(eptm.edge_df)
eptm.sort_edges_eastwest()
assert_array_equal(np.asarray(eptm.free_edges), [0, 1, 2])
assert_array_equal(np.asarray(eptm.east_edges), [3, 4, 5])
assert_array_equal(np.asarray(eptm.west_edges), [6, 7, 8])
def test_model():
h5store = os.path.join(stores_dir, "small_hexagonal.hf5")
datasets = load_datasets(h5store, data_names=["face", "vert", "edge"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("emin", datasets, specs)
model_tester(sheet, model)
model_tester(sheet, PlanarModel)
flat = Sheet.planar_sheet_2d("flat", 5, 5, 1, 1)
flat.sanitize()
PlanarGeometry.update_all(flat)
model_tester(flat, PlanarModel)
def test_extra_indices():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -(3**0.5) / 2]]
tri_edges = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 0, 2],
]
datasets["edge"] = pd.DataFrame(data=np.array(tri_edges),
columns=["srce", "trgt", "face"])
datasets["edge"].index.name = "edge"
datasets["face"] = pd.DataFrame(data=np.zeros((3, 2)), columns=["x", "y"])
datasets["face"].index.name = "face"
datasets["vert"] = pd.DataFrame(data=np.array(tri_verts),
columns=["x", "y"])
datasets["vert"].index.name = "vert"
specs = config.geometry.planar_spec()
eptm = Sheet("extra", datasets, specs, coords=["x", "y"])
PlanarGeometry.update_all(eptm)
eptm.edge_df["opposite"] = get_opposite(eptm.edge_df)
eptm.get_extra_indices()
assert (2 * eptm.Ni + eptm.No) == eptm.Ne
assert eptm.west_edges.size == eptm.Ni
assert eptm.Nd == 2 * eptm.Ni
for edge in eptm.free_edges:
opps = eptm.edge_df[eptm.edge_df["srce"] == eptm.edge_df.loc[
edge, "trgt"]]["trgt"]
assert eptm.edge_df.loc[edge, "srce"] not in opps
for edge in eptm.east_edges:
srce, trgt = eptm.edge_df.loc[edge, ["srce", "trgt"]]
opp = eptm.edge_df[(eptm.edge_df["srce"] == trgt)
& (eptm.edge_df["trgt"] == srce)].index
assert opp[0] in eptm.west_edges
for edge in eptm.west_edges:
srce, trgt = eptm.edge_df.loc[edge, ["srce", "trgt"]]
opp = eptm.edge_df[(eptm.edge_df["srce"] == trgt)
& (eptm.edge_df["trgt"] == srce)].index
assert opp[0] in eptm.east_edges
def test_face_projected_pos():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 0.75], [-0.5, -0.75]]
tri_edges = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 0, 2],
]
datasets["edge"] = pd.DataFrame(
data=np.array(tri_edges), columns=["srce", "trgt", "face"]
)
datasets["edge"].index.name = "edge"
datasets["face"] = pd.DataFrame(data=np.zeros((3, 2)), columns=["x", "y"])
datasets["face"].index.name = "face"
datasets["vert"] = pd.DataFrame(data=np.array(tri_verts), columns=["x", "y"])
datasets["vert"].index.name = "vert"
specs = config.geometry.planar_spec()
eptm = Epithelium("extra", datasets, specs, coords=["x", "y"])
PlanarGeometry.update_all(eptm)
res_rot_pos_pi2 = PlanarGeometry.face_projected_pos(eptm, 0, pi / 2.0)
res_rot_pos_face1_2pi = PlanarGeometry.face_projected_pos(eptm, 1, 2.0 * pi)
expected_rot_pos_pi2 = pd.DataFrame.from_dict(
{
"vert": [0, 1, 2, 3],
"x": [0.25, 0.25, -0.5, 1.0],
"y": [-0.166667, 0.8333333, -0.666667, -0.666667],
}
).set_index("vert")
expected_rot_pos_face1_2pi = pd.DataFrame.from_dict(
{
"vert": [0, 1, 2, 3],
"x": [-0.166667, 0.833333, -0.666667, -0.666667],
"y": [0.25, 0.25, 1.00, -0.5],
}
).set_index("vert")
tolerance = 1e-16
assert all((expected_rot_pos_pi2 - res_rot_pos_pi2) ** 2 < tolerance)
assert all((expected_rot_pos_face1_2pi - res_rot_pos_face1_2pi) ** 2 < tolerance)
def test_get_force_inference():
# INIT TISSUE
sheet = Sheet.planar_sheet_2d("jam", 10, 10, 1, 1, noise=0)
PlanarGeometry.update_all(sheet)
model = model_factory(
[
effectors.FaceAreaElasticity,
],
effectors.FaceAreaElasticity,
)
sheet.remove(sheet.cut_out([[0, 10], [0, 10]]))
sheet.sanitize(trim_borders=True)
PlanarGeometry.scale(sheet, sheet.face_df.area.mean()**-0.5, ["x", "y"])
PlanarGeometry.center(sheet)
PlanarGeometry.update_all(sheet)
sheet.reset_index()
sheet.reset_topo()
sheet.face_df["area_elasticity"] = 1
sheet.face_df["prefered_area"] = 1
solver = QSSolver(with_t1=False, with_t3=False, with_collisions=False)
solver.find_energy_min(sheet,
PlanarGeometry,
model,
options={"gtol": 1e-8})
sheet.vert_df.y *= 0.5
solver.find_energy_min(sheet,
PlanarGeometry,
model,
options={"gtol": 1e-8})
sheet.get_force_inference(column="tension", free_border_edges=True)
sheet = sheet.extract_bounding_box(x_boundary=[-2, 2], y_boundary=[-1, 1])
sheet.edge_df["angle"] = (
np.arctan2(sheet.edge_df["dx"], sheet.edge_df["dy"]) * 180 / np.pi)
sheet.edge_df["angle"] = sheet.edge_df["angle"].apply(lambda x: 180 + x
if x < 0 else x)
sheet.edge_df["angle"] = sheet.edge_df["angle"].apply(lambda x: 180 - x
if x > 90 else x)
for _, edge in sheet.edge_df[sheet.edge_df.angle > 45].iterrows():
assert edge.tension > 1.5
for _, edge in sheet.edge_df[sheet.edge_df.angle < 45].iterrows():
assert edge.tension < 1.5
def test_face_projected_pos():
datasets = {}
tri_verts = [[0, 0],
[1, 0],
[-0.5, 0.75],
[-0.5, -0.75]]
tri_edges = [[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 0, 2]]
datasets['edge'] = pd.DataFrame(data=np.array(tri_edges),
columns=['srce', 'trgt', 'face'])
datasets['edge'].index.name = 'edge'
datasets['face'] = pd.DataFrame(data=np.zeros((3, 2)),
columns=['x', 'y'])
datasets['face'].index.name = 'face'
datasets['vert'] = pd.DataFrame(data=np.array(tri_verts),
columns=['x', 'y'])
datasets['vert'].index.name = 'vert'
specs = config.geometry.planar_spec()
eptm = Epithelium('extra', datasets, specs, coords=['x', 'y'])
PlanarGeometry.update_all(eptm)
res_rot_pos_pi2 = PlanarGeometry.face_projected_pos(eptm, 0, pi/2.)
res_rot_pos_face1_2pi = PlanarGeometry.face_projected_pos(eptm, 1, 2.*pi)
expected_rot_pos_pi2 = pd.DataFrame.from_dict({'vert':[0,1,2,3],\
'x':[0.25, 0.25, -0.5, 1.0],\
'y':[-0.166667, 0.8333333, -0.666667,\
-0.666667]}).set_index('vert')
expected_rot_pos_face1_2pi = pd.DataFrame.from_dict({'vert':[0,1,2,3],\
'x':[-0.166667, 0.833333, -0.666667, -0.666667],\
'y':[0.25,0.25,1.00,-0.5]}).set_index('vert')
tolerance = 1e-16
assert all( (expected_rot_pos_pi2 - res_rot_pos_pi2)**2 < tolerance )
assert all( (expected_rot_pos_face1_2pi - res_rot_pos_face1_2pi)**2 < tolerance )
def test_face_polygons_exception():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -(3**0.5) / 2]]
tri_edges_valid = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 0, 2],
]
tri_edges_invalid = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 1, 2],
] # changed 0 to 1 to create an invalid face
datasets["edge"] = pd.DataFrame(data=np.array(tri_edges_valid),
columns=["srce", "trgt", "face"])
datasets["edge"].index.name = "edge"
datasets["face"] = pd.DataFrame(data=np.zeros((3, 2)), columns=["x", "y"])
datasets["face"].index.name = "face"
datasets["vert"] = pd.DataFrame(data=np.array(tri_verts),
columns=["x", "y"])
datasets["vert"].index.name = "vert"
specs = config.geometry.planar_spec()
eptm = Epithelium("valid", datasets, specs, coords=["x", "y"])
PlanarGeometry.update_all(eptm)
eptm.reset_index(order=True)
eptm.face_polygons(["x", "y"])
def test_extra_indices():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -3**0.5 / 2]]
tri_edges = [[0, 1, 0], [1, 2, 0], [2, 0, 0], [0, 3, 1], [3, 1, 1],
[1, 0, 1], [0, 2, 2], [2, 3, 2], [3, 0, 2]]
datasets['edge'] = pd.DataFrame(data=np.array(tri_edges),
columns=['srce', 'trgt', 'face'])
datasets['edge'].index.name = 'edge'
datasets['face'] = pd.DataFrame(data=np.zeros((3, 2)), columns=['x', 'y'])
datasets['face'].index.name = 'face'
datasets['vert'] = pd.DataFrame(data=np.array(tri_verts),
columns=['x', 'y'])
datasets['vert'].index.name = 'vert'
specs = config.geometry.planar_spec()
eptm = Epithelium('extra', datasets, specs, coords=['x', 'y'])
PlanarGeometry.update_all(eptm)
eptm.edge_df['opposite'] = get_opposite(eptm.edge_df)
eptm.get_extra_indices()
assert (2 * eptm.Ni + eptm.No) == eptm.Ne
assert eptm.west_edges.size == eptm.Ni
assert eptm.Nd == 2 * eptm.Ni
for edge in eptm.free_edges:
opps = eptm.edge_df[eptm.edge_df['srce'] == eptm.edge_df.loc[
edge, 'trgt']]['trgt']
assert eptm.edge_df.loc[edge, 'srce'] not in opps
for edge in eptm.east_edges:
srce, trgt = eptm.edge_df.loc[edge, ['srce', 'trgt']]
opp = eptm.edge_df[(eptm.edge_df['srce'] == trgt)
& (eptm.edge_df['trgt'] == srce)].index
assert opp[0] in eptm.west_edges
for edge in eptm.west_edges:
srce, trgt = eptm.edge_df.loc[edge, ['srce', 'trgt']]
opp = eptm.edge_df[(eptm.edge_df['srce'] == trgt)
& (eptm.edge_df['trgt'] == srce)].index
assert opp[0] in eptm.east_edges
def test_sort_eastwest():
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -3**0.5 / 2]]
tri_edges = [[0, 1, 0], [1, 2, 0], [2, 0, 0], [0, 3, 1], [3, 1, 1],
[1, 0, 1], [0, 2, 2], [2, 3, 2], [3, 0, 2]]
datasets['edge'] = pd.DataFrame(data=np.array(tri_edges),
columns=['srce', 'trgt', 'face'])
datasets['edge'].index.name = 'edge'
datasets['face'] = pd.DataFrame(data=np.zeros((3, 2)), columns=['x', 'y'])
datasets['face'].index.name = 'face'
datasets['vert'] = pd.DataFrame(data=np.array(tri_verts),
columns=['x', 'y'])
datasets['vert'].index.name = 'vert'
specs = config.geometry.planar_spec()
eptm = Epithelium('extra', datasets, specs, coords=['x', 'y'])
PlanarGeometry.update_all(eptm)
eptm.edge_df['opposite'] = get_opposite(eptm.edge_df)
eptm.sort_edges_eastwest()
assert_array_equal(np.asarray(eptm.free_edges), [0, 1, 2])
assert_array_equal(np.asarray(eptm.east_edges), [3, 4, 5])
assert_array_equal(np.asarray(eptm.west_edges), [6, 7, 8])
def test_invalid_valid_sanitize():
# get_invalid and get_valid
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -(3**0.5) / 2]]
tri_edges_valid = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 0, 2],
]
tri_edges_invalid = [
[0, 1, 0],
[1, 2, 0],
[2, 0, 0],
[0, 3, 1],
[3, 1, 1],
[1, 0, 1],
[0, 2, 2],
[2, 3, 2],
[3, 1, 2],
] # changed 0 to 1 to create an invalid face
# Epithelium whose faces are all valid
##
datasets["edge"] = pd.DataFrame(data=np.array(tri_edges_valid),
columns=["srce", "trgt", "face"])
datasets["edge"].index.name = "edge"
datasets["face"] = pd.DataFrame(data=np.zeros((3, 2)), columns=["x", "y"])
datasets["face"].index.name = "face"
datasets["vert"] = pd.DataFrame(data=np.array(tri_verts),
columns=["x", "y"])
datasets["vert"].index.name = "vert"
specs = config.geometry.planar_spec()
eptm = Epithelium("valid", datasets, specs, coords=["x", "y"])
PlanarGeometry.update_all(eptm)
# Epithelium with invalid faces (last 3)
datasets_invalid = datasets.copy()
datasets_invalid["edge"] = pd.DataFrame(data=np.array(tri_edges_invalid),
columns=["srce", "trgt", "face"])
datasets_invalid["edge"].index.name = "edge"
eptm_invalid = Epithelium("invalid",
datasets_invalid,
specs,
coords=["x", "y"])
PlanarGeometry.update_all(eptm_invalid)
eptm.get_valid()
eptm_invalid.get_valid()
res_invalid_expect_all_false = eptm.get_invalid()
res_invalid_expect_some_true = eptm_invalid.get_invalid()
assert eptm.edge_df["is_valid"].all()
assert not eptm_invalid.edge_df["is_valid"][6:].all()
assert not res_invalid_expect_all_false.all()
assert res_invalid_expect_some_true[6:].all()
# testing sanitize
# edges 6 to 9 should be removed.
edge_df_before = eptm.edge_df.copy()
edge_df_invalid_before = eptm_invalid.edge_df.copy()
eptm.sanitize()
eptm_invalid.sanitize()
assert edge_df_before.equals(eptm.edge_df)
assert edge_df_invalid_before[:6].equals(eptm_invalid.edge_df)
def test_invalid_valid_sanitize():
# get_invalid and get_valid
datasets = {}
tri_verts = [[0, 0], [1, 0], [-0.5, 3**0.5 / 2], [-0.5, -3**0.5 / 2]]
tri_edges_valid = [[0, 1, 0], [1, 2, 0], [2, 0, 0], [0, 3, 1], [3, 1, 1],
[1, 0, 1], [0, 2, 2], [2, 3, 2], [3, 0, 2]]
tri_edges_invalid = [[0, 1, 0], [1, 2, 0], [2, 0, 0], [0, 3, 1], [3, 1, 1],
[1, 0, 1], [0, 2, 2], [2, 3, 2],
[3, 1, 2]] # changed 0 to 1 to create an invalid face
## Epithelium whose faces are all valid
##
datasets['edge'] = pd.DataFrame(data=np.array(tri_edges_valid),
columns=['srce', 'trgt', 'face'])
datasets['edge'].index.name = 'edge'
datasets['face'] = pd.DataFrame(data=np.zeros((3, 2)), columns=['x', 'y'])
datasets['face'].index.name = 'face'
datasets['vert'] = pd.DataFrame(data=np.array(tri_verts),
columns=['x', 'y'])
datasets['vert'].index.name = 'vert'
specs = config.geometry.planar_spec()
eptm = Epithelium('valid', datasets, specs, coords=['x', 'y'])
PlanarGeometry.update_all(eptm)
## Epithelium with invalid faces (last 3)
datasets_invalid = datasets.copy()
datasets_invalid['edge'] = pd.DataFrame(data=np.array(tri_edges_invalid),
columns=['srce', 'trgt', 'face'])
datasets_invalid['edge'].index.name = 'edge'
eptm_invalid = Epithelium('invalid',
datasets_invalid,
specs,
coords=['x', 'y'])
PlanarGeometry.update_all(eptm_invalid)
eptm.get_valid()
eptm_invalid.get_valid()
res_invalid_expect_all_false = eptm.get_invalid()
res_invalid_expect_some_true = eptm_invalid.get_invalid()
assert eptm.edge_df['is_valid'].all()
assert (not eptm_invalid.edge_df['is_valid'][6:].all())
assert (not res_invalid_expect_all_false.all())
assert res_invalid_expect_some_true[6:].all()
### testing sanitize
### edges 6 to 9 should be removed.
edge_df_before = eptm.edge_df.copy()
edge_df_invalid_before = eptm_invalid.edge_df.copy()
eptm.sanitize()
eptm_invalid.sanitize()
assert edge_df_before.equals(eptm.edge_df)
assert edge_df_invalid_before[:6].equals(eptm_invalid.edge_df)