Python with_gaps_df Examples

Example #1

File: test_transformation.py Project: glyg/scikit-tracker

def test_back_proj_pca():

    trajs = Trajectories(data.with_gaps_df())
    rotated, pca = transformation.do_pca(trajs, suffix='',
                                         append=False, return_pca=True)
    back_proj = transformation.back_proj_pca(rotated, pca, coords=['x', 'y', 'z'])
    assert_almost_equal(back_proj.iloc[0].x, trajs.iloc[0].x)

Example #2

File: test_brownian_cost_function.py Project: bnoi/scikit-tracker

def test_brownian_gap_close():

    trajs = Trajectories(data.with_gaps_df())
    max_speed = 10.

    cost_func = BrownianGapCloseCostFunction(parameters={'max_speed': max_speed})

    in_idxs = [(3, 0), (3, 0), (5, 1), (13, 2), (13, 2), (16, 3)]
    out_idxs = [(5, 3), (7, 4), (7, 4), (15, 5), (18, 6), (18, 6)]

    cost_func.context['trajs'] = trajs
    cost_func.context['idxs_in'] = in_idxs
    cost_func.context['idxs_out'] = out_idxs

    cost_func.get_block()
    m = cost_func.mat

    m_true = [[np.nan, np.nan, np.nan, 2.0553543815820543, 45.74823093541038, np.nan, np.nan],
              [np.nan, np.nan, np.nan, np.nan, 1.1530875267623917, np.nan, np.nan],
              [np.nan, np.nan, np.nan, np.nan, np.nan, 0.8254178191605767, 23.84513283483594],
              [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, 4.916599888362159],
              [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan],
              [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan],
              [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan]]

    assert_array_almost_equal(m, m_true)

Example #3

File: test_brownian_cost_function.py Project: felix-r/scikit-tracker

def test_brownian_gap_close():

    trajs = Trajectories(data.with_gaps_df())
    max_speed = 10.

    cost_func = BrownianGapCloseCostFunction(
        parameters={'max_speed': max_speed})

    in_idxs = [(3, 0), (3, 0), (5, 1), (13, 2), (13, 2), (16, 3)]
    out_idxs = [(5, 3), (7, 4), (7, 4), (15, 5), (18, 6), (18, 6)]

    cost_func.context['trajs'] = trajs
    cost_func.context['idxs_in'] = in_idxs
    cost_func.context['idxs_out'] = out_idxs

    cost_func.get_block()
    m = cost_func.mat

    m_true = [[
        np.nan, np.nan, np.nan, 2.0553543815820543, 45.74823093541038, np.nan,
        np.nan
    ], [np.nan, np.nan, np.nan, np.nan, 1.1530875267623917, np.nan, np.nan],
              [
                  np.nan, np.nan, np.nan, np.nan, np.nan, 0.8254178191605767,
                  23.84513283483594
              ],
              [
                  np.nan, np.nan, np.nan, np.nan, np.nan, np.nan,
                  4.916599888362159
              ], [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan],
              [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan],
              [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan]]

    assert_array_almost_equal(m, m_true)

Example #4

File: test_transformation.py Project: felix-r/scikit-tracker

def test_back_proj_pca():

    trajs = Trajectories(data.with_gaps_df())
    rotated, pca = transformation.do_pca(trajs, suffix='',
                                         append=False, return_pca=True)
    back_proj = transformation.back_proj_pca(rotated, pca, coords=['x', 'y', 'z'])
    assert_almost_equal(back_proj.iloc[0].x, trajs.iloc[0].x)

Example #5

def test_radial_speed():
    trajs = Trajectories(data.with_gaps_df())
    trajs.reset_index(level='label', drop=True, inplace=True)
    trajs.set_index('true_label', drop=True, append=True, inplace=True)
    trajs.index.set_names(['t_stamp', 'label'], inplace=True)
    rd_speeds = rotation.radial_speed(trajs,
                                      in_coords=['x', 'y'],
                                      from_polar=False)

Example #6

File: test_by_frame_solver.py Project: bnoi/scikit-tracker

def test_by_frame_solver_with_missing_data():

    true_trajs = data.with_gaps_df()

    solver = ByFrameSolver.for_brownian_motion(true_trajs, max_speed=5, penalty=2.)
    trajs = solver.track()

    min_chi_square, conserved_trajectories_number, scores = get_scores_on_trajectories(trajs)

    assert min_chi_square == 0 and conserved_trajectories_number == 3 / 7.

Example #7

File: test_transformation.py Project: glyg/scikit-tracker

def test_back_proj_interp():
    trajs = Trajectories(data.with_gaps_df())
    interpolated = transformation.time_interpolate(trajs,
                                                   sampling=3, s=0)
    back_proj = transformation.back_proj_interp(interpolated, trajs, 3)
    assert_almost_equal(back_proj.iloc[0].x, trajs.iloc[0].x)

    interpolated = transformation.time_interpolate(trajs,
                                                   sampling=3, s=2)
    back_proj = transformation.back_proj_interp(interpolated, trajs, 3)
    assert_almost_equal(back_proj.iloc[0].x, trajs.iloc[0].x)

Example #8

File: test_transformation.py Project: felix-r/scikit-tracker

def test_back_proj_interp():
    trajs = Trajectories(data.with_gaps_df())
    interpolated = transformation.time_interpolate(trajs,
                                                   sampling=3, s=0)
    back_proj = transformation.back_proj_interp(interpolated, trajs, 3)
    assert_almost_equal(back_proj.iloc[0].x, trajs.iloc[0].x)

    interpolated = transformation.time_interpolate(trajs,
                                                   sampling=3, s=2)
    back_proj = transformation.back_proj_interp(interpolated, trajs, 3)
    assert_almost_equal(back_proj.iloc[0].x, trajs.iloc[0].x)

Example #9

File: test_gap_close_solver.py Project: felix-r/scikit-tracker

def test_gap_close():

    trajs = data.with_gaps_df()
    max_speed = 10.
    maximum_gap = 5
    gc_solver = GapCloseSolver.for_brownian_motion(trajs,
                                                   max_speed=max_speed,
                                                   maximum_gap=maximum_gap,
                                                   use_t_stamp=True)
    gc_solver.track()

    seg_shapes = [seg[1].shape for seg in gc_solver.trajs.iter_segments]
    assert seg_shapes == [(18, 5), (19, 5), (19, 5)]

Example #10

File: test_gap_close_solver.py Project: felix-r/scikit-tracker

def test_gap_close_get_candidates():

    trajs = data.with_gaps_df()
    max_speed = 10.
    maximum_gap = 5
    gc_solver = GapCloseSolver.for_brownian_motion(trajs,
                                                   max_speed=max_speed,
                                                   maximum_gap=maximum_gap,
                                                   use_t_stamp=True)
    in_idxs, out_idxs = gc_solver._get_candidates()

    assert in_idxs == [(3, 0), (3, 0), (5, 1), (13, 2), (13, 2), (16, 3)]
    assert out_idxs == [(5, 3), (7, 4), (7, 4), (15, 5), (18, 6), (18, 6)]

Example #11

File: test_by_frame_solver.py Project: felix-r/scikit-tracker

def test_by_frame_solver_with_missing_data():

    true_trajs = data.with_gaps_df()

    solver = ByFrameSolver.for_brownian_motion(true_trajs,
                                               max_speed=5,
                                               penalty=2.)
    trajs = solver.track()

    min_chi_square, conserved_trajectories_number, scores = get_scores_on_trajectories(
        trajs)

    assert min_chi_square == 0 and conserved_trajectories_number == 3 / 7.

Example #12

File: test_trajectories.py Project: felix-r/scikit-tracker

def test_interpolate():

    trajs = Trajectories(data.with_gaps_df())
    trajs.set_index('true_label', inplace=True, append=True)
    trajs.reset_index(level='label', drop=True, inplace=True)
    trajs.index.set_names(['t_stamp', 'label'], inplace=True)
    interpolated = trajs.time_interpolate(sampling=3, time_step=0.1, s=1)
    # t_stamps_in = interpolated.index.get_level_values('t_stamp')
    # indexer = t_stamps_in % 2 == 0
    # interpolated.loc[indexer].shape, trajs.shape
    # indexer = interpolated.t_stamps % 3 == 0
    # assert interpolated.loc[indexer].shape[0] == trajs.shape[0]
    dts = interpolated.get_segments()[0].t.diff().dropna()
    # All time points should be equaly spaced
    assert_almost_equal(dts.min(), dts.max())

Example #13

File: test_trajectories.py Project: bnoi/scikit-tracker

def test_interpolate():

    trajs = Trajectories(data.with_gaps_df())
    trajs.set_index('true_label', inplace=True, append=True)
    trajs.reset_index(level='label', drop=True, inplace=True)
    trajs.index.set_names(['t_stamp', 'label'], inplace=True)
    interpolated = trajs.time_interpolate(sampling=3, time_step=0.1, s=1)
    # t_stamps_in = interpolated.index.get_level_values('t_stamp')
    # indexer = t_stamps_in % 2 == 0
    # interpolated.loc[indexer].shape, trajs.shape
    # indexer = interpolated.t_stamps % 3 == 0
    # assert interpolated.loc[indexer].shape[0] == trajs.shape[0]
    dts = interpolated.get_segments()[0].t.diff().dropna()
    # All time points should be equaly spaced
    assert_almost_equal(dts.min(), dts.max())

Example #14

File: test_rotation.py Project: bnoi/scikit-tracker

def test_radial_speed():
    trajs = Trajectories(data.with_gaps_df())
    trajs.reset_index(level='label', drop=True, inplace=True)
    trajs.set_index('true_label', drop=True, append=True, inplace=True)
    trajs.index.set_names(['t_stamp', 'label'], inplace=True)
    rd_speeds = rotation.radial_speed(trajs, in_coords=['x', 'y'], from_polar=False)