diff --git a/lumicks/pylake/force_calibration/tests/test_touchdown.py b/lumicks/pylake/force_calibration/tests/test_touchdown.py index aa2665ab3..dee583396 100644 --- a/lumicks/pylake/force_calibration/tests/test_touchdown.py +++ b/lumicks/pylake/force_calibration/tests/test_touchdown.py @@ -145,6 +145,7 @@ def test_exp_sine_fits(decay, amplitude, frequency, phase_shift): np.testing.assert_allclose(par, frequency, rtol=1e-6) +@pytest.mark.filterwarnings("ignore:Covariance of the parameters could not be estimated") def test_insufficient_data(mack_parameters): stage_positions, simulation = simulate_touchdown(102.5, 103.5, 0.01, mack_parameters) diff --git a/lumicks/pylake/kymotracker/tests/conftest.py b/lumicks/pylake/kymotracker/tests/conftest.py index b0812408f..f5d1d953b 100644 --- a/lumicks/pylake/kymotracker/tests/conftest.py +++ b/lumicks/pylake/kymotracker/tests/conftest.py @@ -66,7 +66,7 @@ def two_gaussians_1d(): @pytest.fixture def blank_kymo(): - return generate_kymo( + kymo = generate_kymo( "", np.ones((1, 10)), pixel_size_nm=1000, @@ -75,6 +75,8 @@ def blank_kymo(): samples_per_pixel=1, line_padding=0, ) + kymo._motion_blur_constant = 0 + return kymo @pytest.fixture diff --git a/lumicks/pylake/kymotracker/tests/test_kymotrack.py b/lumicks/pylake/kymotracker/tests/test_kymotrack.py index 6e57a3acf..248c182f5 100644 --- a/lumicks/pylake/kymotracker/tests/test_kymotrack.py +++ b/lumicks/pylake/kymotracker/tests/test_kymotrack.py @@ -867,7 +867,9 @@ def test_fit_binding_times_nonzero(blank_kymo, blank_kymo_track_args): r"analysis. If you wish to not see this warning, filter the tracks with " r"`lk.filter_tracks` with a minimum length of 2 samples.", ): - dwelltime_model = tracks.fit_binding_times(1) + dwelltime_model = tracks.fit_binding_times( + n_components=1, observed_minimum=True, discrete_model=False + ) np.testing.assert_equal(dwelltime_model.dwelltimes, [4, 4, 4, 4]) np.testing.assert_equal(dwelltime_model._observation_limits[0], 4) np.testing.assert_allclose(dwelltime_model.lifetimes[0], [0.4]) @@ -1145,6 +1147,7 @@ def test_kymotrack_group_diffusion_filter(): image = np.random.randint(0, 20, size=(10, 10, 3)) kwargs = dict(line_time_seconds=10e-3, start=np.int64(20e9), pixel_size_um=0.05, name="test") kymo = _kymo_from_array(image, "rgb", **kwargs) + kymo._motion_blur_constant = 0 base_coordinates = ( np.arange(1, 10), @@ -1408,7 +1411,12 @@ def test_ensemble_diffusion_different_attributes(): line_times = (1, 0.5) pixel_sizes = (0.1, 0.05) kwargs = [{"line_time_seconds": t, "pixel_size_um": s} for t in line_times for s in pixel_sizes] - kymos = [_kymo_from_array(np.random.poisson(5, (25, 25, 3)), "rgb", **k) for k in kwargs] + kymos = [] + for k in kwargs: + kymo = _kymo_from_array(np.random.poisson(5, (25, 25, 3)), "rgb", **k) + kymo._motion_blur_constant = 0 + kymos.append(kymo) + tracks = [ KymoTrackGroup( [KymoTrack(np.arange(5), np.random.uniform(3, 5, 5), k, "green", 0) for _ in range(5)]