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_overwrite_time():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
history.record(time_stamp=1)
history.record(time_stamp=1)
sheet_ = history.retrieve(1)
assert sheet_.Nv == sheet.Nv
def test_create_gif():
geom = SheetGeometry
model = PlanarModel
sheet = Sheet("3", *three_faces_sheet())
geom.update_all(sheet)
sheet.settings["threshold_length"] = 0.1
sheet.update_specs(config.dynamics.quasistatic_plane_spec())
sheet.face_df["prefered_area"] = sheet.face_df["area"].mean()
history = History(sheet)
solver = EulerSolver(sheet, geom, model, history=history, auto_reconnect=True)
sheet.vert_df["viscosity"] = 0.1
sheet.edge_df.loc[[0, 17], "line_tension"] *= 2
sheet.edge_df.loc[[1], "line_tension"] *= 8
res = solver.solve(0.5, dt=0.05)
with pytest.raises(ValueError):
create_gif(history, "frames.gif")
create_gif(history, "frames.gif", num_frames=5)
create_gif(history, "interval.gif", interval=(2, 4))
assert os.path.isfile("frames.gif") == True
assert os.path.isfile("interval.gif") == True
os.remove("frames.gif")
os.remove("interval.gif")
def test_warning():
sheet = Sheet("3", *three_faces_sheet())
with pytest.warns(UserWarning):
History(sheet,
extra_cols={
"edge": ["dx"],
"face": ["area"],
"vert": ["segment"]
})
def test_browse():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
for i in range(30):
history.record(i / 10)
times = [t for t, _ in history.browse()]
np.testing.assert_allclose(times, history.time_stamps)
times_areas = np.array([[t, s.face_df.loc[0, "area"]]
for t, s in history.browse(2, 8, endpoint=True)])
assert times_areas.shape == (7, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[8]
assert set(times_areas[:, 0]).issubset(history.time_stamps)
times_areas = np.array([[t, s.face_df.loc[0, "area"]]
for t, s in history.browse(2, 8, 4, endpoint=False)
])
assert times_areas.shape == (4, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[7]
assert set(times_areas[:, 0]).issubset(history.time_stamps)
times_areas = np.array([[t, s.face_df.loc[0, "area"]]
for t, s in history.browse(2, 8, 4, endpoint=True)
])
assert times_areas.shape == (4, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[8]
assert set(times_areas[:, 0]).issubset(history.time_stamps)
times_areas = np.array([[t, s.face_df.loc[0, "area"]]
for t, s in history.browse(2, 8, 10)])
assert times_areas.shape == (10, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[8]
assert set(times_areas[:, 0]).issubset(history.time_stamps)
times_areas = np.array([[t, s.edge_df.loc[0, "length"]]
for t, s in history.browse(size=40)])
assert times_areas.shape == (40, 2)
assert set(times_areas[:, 0]) == set(history.time_stamps)
def test_to_and_from_archive():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
history.record()
history.record()
history.record()
history.to_archive("test.hf5")
history_h = HistoryHdf5.from_archive("test.hf5")
sheet_ = history_h.retrieve(2)
try:
assert sheet_.Nv == sheet.Nv
finally:
os.remove("test.hf5")
def test_euler():
geom = SheetGeometry
model = PlanarModel
sheet = Sheet("3", *three_faces_sheet())
geom.update_all(sheet)
sheet.settings["threshold_length"] = 1e-3
sheet.update_specs(config.dynamics.quasistatic_plane_spec())
sheet.face_df["prefered_area"] = sheet.face_df["area"].mean()
history = History(sheet)
solver = EulerSolver(sheet, geom, model, with_t1=True, with_t3=True)
sheet.vert_df["viscosity"] = 1.0
sheet.edge_df.loc[[0, 17], "line_tension"] *= 4
l0 = sheet.edge_df.loc[0, "length"]
res = solver.solve(0.2, dt=0.05)
assert sheet.edge_df.loc[0, "length"] < l0
assert len(solver.history) == 5
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_retrieve():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet, {"face": ["area"]})
sheet_ = history.retrieve(0)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert "area" in sheet_.datasets["face"].columns
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
sheet.vert_df.loc[0, "x"] = 100
sheet.face_df["area"] = 100
history.record()
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
print(dset)
assert sheet_.datasets["vert"].loc[0, "x"] == 100
assert sheet_.datasets["face"].loc[0, "area"] != 100
history.record(["vert", "face"])
sheet_ = history.retrieve(2)
assert sheet_.datasets["face"].loc[0, "area"] == 100
sheet_ = history.retrieve(1)
assert sheet_.datasets["face"].loc[0, "area"] != 100
def test_warning():
sheet = Sheet("3", *three_faces_sheet())
with pytest.warns(UserWarning):
history = History(sheet, extra_cols={"vert": ["invalid_column"]})
def test_retrieve():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
sheet_ = history.retrieve(0)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
assert "area" in sheet_.datasets["face"].columns
with pytest.warns(UserWarning):
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
sheet.vert_df.loc[0, "x"] = 100.0
sheet.face_df["area"] = 100.0
history.record()
sheet_ = history.retrieve(1)
for elem, dset in sheet_.datasets.items():
assert dset.shape[0] == sheet.datasets[elem].shape[0]
print(dset)
assert sheet_.datasets["vert"].loc[0, "x"] == 100.0
assert sheet_.datasets["face"].loc[0, "area"] == 100.0
history.record()
sheet_ = history.retrieve(2)
assert sheet_.datasets["face"].loc[0, "area"] == 100.0
sheet_ = history.retrieve(1)
assert sheet_.datasets["face"].loc[0, "area"] == 100.0
def test_retrieve_coords():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
history.record()
assert history.retrieve(0).coords == sheet.coords