def test_pinchoff_fit_plot(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
ax, _ = pf.plot_fit(save_figures=True, file_location=str(tmp_path), filename="test")
assert os.path.exists(os.path.join(str(tmp_path), "test.png"))
assert len(ax) == len(pf.readout_methods)
def test_pinchofffit_initial_guess(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
bounds, initial_guess = pf.compute_initial_guess(readout_method='dc_current')
assert math.isclose(bounds[0][0], 0, rel_tol=rtol)
assert math.isclose(bounds[0][1], 0, rel_tol=rtol)
assert math.isclose(bounds[0][2], -np.inf, rel_tol=rtol)
assert math.isclose(bounds[1][0], 1.0, rel_tol=rtol)
assert math.isclose(bounds[1][1], np.inf, rel_tol=rtol)
assert math.isclose(bounds[1][2], np.inf, rel_tol=rtol)
assert math.isclose(initial_guess[0], 1.0, rel_tol=rtol)
assert math.isclose(initial_guess[1], 1.0, rel_tol=rtol)
assert math.isclose(initial_guess[2], 0.5, rel_tol=rtol)
bounds, initial_guess = pf.compute_initial_guess(readout_method='dc_sensor')
assert math.isclose(bounds[0][0], 0, rel_tol=rtol)
assert math.isclose(bounds[0][1], 0, rel_tol=rtol)
assert math.isclose(bounds[0][2], -np.inf, rel_tol=rtol)
assert math.isclose(bounds[1][0], 0.9957971951822472, rel_tol=rtol)
assert math.isclose(bounds[1][1], np.inf, rel_tol=rtol)
assert math.isclose(bounds[1][2], np.inf, rel_tol=rtol)
assert math.isclose(initial_guess[0], 0.9957971951822472, rel_tol=rtol)
assert math.isclose(initial_guess[1], 1.0042205429359374, rel_tol=rtol)
assert math.isclose(initial_guess[2], 0.5, rel_tol=rtol)
def test_pinchofffit__transition_voltage_fitting(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
assert not pf._transition_signal
assert not pf._transition_signal_index
pf.get_transition_from_fit = True
pf.compute_transition_voltage()
assert math.isclose(pf._transition_signal["dc_current"], 0.5926477267201613, rel_tol=rtol)
assert math.isclose(
pf._transition_signal["dc_sensor"], 0.45264142712057776, rel_tol=rtol
)
assert pf._transition_signal_index["dc_current"] == 60
assert pf._transition_signal_index["dc_sensor"] == 59
pf.get_transition_from_fit = False
pf.compute_transition_voltage()
assert math.isclose(pf._transition_signal["dc_current"], 0.4123686284590007, rel_tol=rtol)
assert math.isclose(
pf._transition_signal["dc_sensor"], 0.5620627106146739, rel_tol=rtol
)
assert pf._transition_signal_index["dc_current"] == 59
assert pf._transition_signal_index["dc_sensor"] == 60
def test_pinchofffit_features_property(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
assert not pf._features
feat_dict = pf.features
assert feat_dict
ds = load_by_id(1)
nt_metadata = json.loads(ds.get_metadata(nt.meta_tag))
assert nt_metadata["features"] == feat_dict
def test_pinchoff_fit_fct(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
v = np.linspace(-0.5, 0.5, 100)
with pytest.raises(IndexError):
_ = pf.fit_fct(v, [1])
params = [1, 15, 2]
pf_fit = pf.fit_fct(v, params)
fit = params[0] * (1 + np.tanh(params[1] * v + params[2]))
assert np.allclose(fit, pf_fit, rtol=rtol)
def test_pinchofffit_next_actions(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
assert not pf.next_actions["dc_current"]
assert not pf.next_actions["dc_sensor"]
_, current, sensor = generate_bad_pinchoff_data()
pf.data['dc_current'].values = pf._normalize_data(current, "dc_current")
pf.data['dc_sensor'].values = pf._normalize_data(sensor, "dc_sensor")
pf.prepare_filtered_data()
pf.find_fit()
expected_actions = ["x more negative", "x more positive"]
assert sorted(pf.next_actions["dc_current"]) == expected_actions
assert sorted(pf.next_actions["dc_sensor"]) == expected_actions
def test_pinchofffit_init(nt_dataset_pinchoff, tmp_path):
attributes = [
"features",
"gradient_percentile",
"_low_signal",
"_high_signal",
"_transition_voltage",
"_transition_signal",
"_low_signal_index",
"_high_signal_index",
"_transition_signal_index",
"_normalized_voltage",
"_next_actions",
]
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
for attr in attributes:
assert hasattr(pf, attr)
getattr(pf, attr)
def test_pinchofffit_transition_interval_fitting(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
assert not pf._low_signal
assert not pf._high_signal
pf.get_transition_from_fit = True
pf.compute_transition_interval()
assert math.isclose(pf._high_signal["dc_current"], 0.9328689304577482, rel_tol=rtol)
assert math.isclose(pf._high_signal["dc_sensor"], 0.8505814391091593, rel_tol=rtol)
assert math.isclose(pf._low_signal["dc_current"], 0.06741378644796504, rel_tol=rtol)
assert math.isclose(pf._low_signal["dc_sensor"], 0.07404054174629943, rel_tol=rtol)
pf.get_transition_from_fit = False
pf.compute_transition_interval()
assert math.isclose(pf._high_signal["dc_current"], 0.9385653092441386, rel_tol=rtol)
assert math.isclose(pf._high_signal["dc_sensor"], 0.8400070918869458, rel_tol=rtol)
assert math.isclose(pf._low_signal["dc_current"], 0.061434690755860326, rel_tol=rtol)
assert math.isclose(pf._low_signal["dc_sensor"], 0.15260464585587372, rel_tol=rtol)
def test_pinchofffit_fit_result(nt_dataset_pinchoff, tmp_path):
pf = PinchoffFit(1, "temp.db", db_folder=str(tmp_path))
fit_result = pf.features
assert math.isclose(fit_result["dc_current"]["amplitude"], 0.5002276487208445, rel_tol=rtol)
assert math.isclose(fit_result["dc_current"]["offset"], -22.323634339589656, rel_tol=rtol)
assert math.isclose(fit_result["dc_current"]["slope"], 44.645897814266306, rel_tol=rtol)
assert math.isclose(
fit_result["dc_current"]["residuals"], 0.00325722543290063756, rel_tol=rtol
)
val = -0.0504201680672269
assert math.isclose(fit_result["dc_current"]["_transition_voltage"], val, rel_tol=rtol)
val = 0.4123686284590007
assert math.isclose(fit_result["dc_current"]["_transition_signal"], val, rel_tol=rtol)
assert math.isclose(
fit_result["dc_current"]["_high_signal"], 0.9385653092441386, rel_tol=rtol
)
assert math.isclose(
fit_result["dc_sensor"]["amplitude"], 0.4666022945477287, rel_tol=rtol
)
assert math.isclose(
fit_result["dc_sensor"]["offset"], -14.139712322918397, rel_tol=rtol
)
assert math.isclose(
fit_result["dc_sensor"]["slope"], 28.458715102382286, rel_tol=rtol
)
val = 0.11453839742893486
assert math.isclose(fit_result["dc_sensor"]["residuals"], val, rel_tol=rtol)
val = -0.0495798319327731
assert math.isclose(
fit_result["dc_sensor"]["_transition_voltage"], val, rel_tol=rtol
)
val = 0.5620627106146739
assert math.isclose(fit_result["dc_sensor"]["_transition_signal"], val, rel_tol=rtol)
val = 0.8400070918869458
assert math.isclose(fit_result["dc_sensor"]["_high_signal"], val, rel_tol=rtol)