def test_proc_matmul():
restart_seed()
random_markers_1 = Markers.from_random_data()
random_markers_2 = Markers.from_random_data()
markers_matmul = random_markers_1.meca.matmul(random_markers_2)
ref_markers_matmul = random_markers_1 @ random_markers_2
np.testing.assert_almost_equal(markers_matmul, -33729.52497131, decimal=6)
np.testing.assert_almost_equal(markers_matmul,
ref_markers_matmul,
decimal=6)
def test_markers_creation():
dims = ("axis", "channel", "time")
array = Markers()
np.testing.assert_array_equal(x=array, y=xr.DataArray())
assert array.dims == dims
array = Markers(MARKERS_DATA.values)
is_expected_array(array, **EXPECTED_VALUES[57])
size = 3, 10, 100
array = Markers.from_random_data(size=size)
assert array.shape == (4, size[1], size[2])
assert array.dims == dims
with pytest.raises(ValueError):
Markers(ANALOGS_DATA)
def test_rotate():
n_frames = 100
n_markers = 10
angles = Angles.from_random_data(size=(3, 1, n_frames))
rt = Rototrans.from_euler_angles(angles, "xyz")
markers = Markers.from_random_data(size=(3, n_markers, n_frames))
rotated_markers = Markers.from_rototrans(markers, rt)
expected_rotated_marker = np.ndarray((4, n_markers, n_frames))
for marker in range(n_markers):
for frame in range(n_frames):
expected_rotated_marker[:, marker, frame] = np.dot(
rt.isel(time=frame),
markers.isel(channel=marker, time=frame),
)
np.testing.assert_array_almost_equal(rotated_markers,
expected_rotated_marker,
decimal=10)
rotated_markers = Markers.from_rototrans(markers.isel(time=0),
rt.isel(time=0))
expected_rotated_marker = np.ndarray(rotated_markers.shape)
for marker in range(n_markers):
expected_rotated_marker[:, marker] = np.dot(
rt.isel(time=0), markers.isel(channel=marker, time=0))
np.testing.assert_array_almost_equal(rotated_markers,
expected_rotated_marker,
decimal=10)
rotated_markers = Markers.from_rototrans(markers, rt.isel(time=0))
expected_rotated_marker = np.ndarray(rotated_markers.shape)
for marker in range(n_markers):
expected_rotated_marker[:,
marker] = np.dot(rt.isel(time=0),
markers.isel(channel=marker))
np.testing.assert_array_almost_equal(rotated_markers,
expected_rotated_marker,
decimal=10)
with pytest.raises(ValueError):
Markers.from_rototrans(markers.isel(time=0), rt)
def test_proc_norm_marker():
n_frames = 100
n_markers = 10
random_marker = Markers.from_random_data(size=(3, n_markers, n_frames))
norm = random_marker.meca.norm(dim="axis")
norm_without_ones = random_marker.drop_sel(axis="ones").meca.norm(
dim="axis")
np.testing.assert_array_equal(norm, norm_without_ones)
expected_norm = np.ndarray((n_markers, n_frames))
for marker in range(n_markers):
for frame in range(n_frames):
expected_norm[marker, frame] = np.sqrt(
random_marker[0:3, marker,
frame].dot(random_marker[0:3, marker, frame]))
np.testing.assert_array_equal(norm, expected_norm)
def test_rt_from_markers():
all_m = Markers.from_random_data()
rt_xy = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 1]),
axis_2=all_m.isel(channel=[0, 2]),
axes_name="xy",
axis_to_recalculate="y",
)
rt_yx = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 2]),
axis_2=all_m.isel(channel=[0, 1]),
axes_name="yx",
axis_to_recalculate="y",
)
rt_xy_x_recalc = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 1]),
axis_2=all_m.isel(channel=[0, 2]),
axes_name="yx",
axis_to_recalculate="x",
)
rt_xy_x_recalc = rt_xy_x_recalc.isel(col=[1, 0, 2, 3])
rt_xy_x_recalc[:, 2, :] = -rt_xy_x_recalc[:, 2, :]
rt_yz = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 1]),
axis_2=all_m.isel(channel=[0, 2]),
axes_name="yz",
axis_to_recalculate="z",
)
rt_zy = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 2]),
axis_2=all_m.isel(channel=[0, 1]),
axes_name="zy",
axis_to_recalculate="z",
)
rt_xy_from_yz = rt_yz.isel(col=[1, 2, 0, 3])
rt_xz = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 1]),
axis_2=all_m.isel(channel=[0, 2]),
axes_name="xz",
axis_to_recalculate="z",
)
rt_zx = Rototrans.from_markers(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 2]),
axis_2=all_m.isel(channel=[0, 1]),
axes_name="zx",
axis_to_recalculate="z",
)
rt_xy_from_zx = rt_xz.isel(col=[0, 2, 1, 3])
rt_xy_from_zx[:, 2, :] = -rt_xy_from_zx[:, 2, :]
np.testing.assert_array_equal(rt_xy, rt_xy_x_recalc)
np.testing.assert_array_equal(rt_xy, rt_yx)
np.testing.assert_array_equal(rt_yz, rt_zy)
np.testing.assert_array_equal(rt_xz, rt_zx)
np.testing.assert_array_equal(rt_xy, rt_xy_from_yz)
np.testing.assert_array_equal(rt_xy, rt_xy_from_zx)
# Produce one that we know the solution
ref_m = Markers(
np.array(((1, 2, 3), (4, 5, 6), (6, 5, 4))).T[:, :, np.newaxis])
rt_xy_from_known_m = Rototrans.from_markers(
origin=ref_m.isel(channel=[0]),
axis_1=ref_m.isel(channel=[0, 1]),
axis_2=ref_m.isel(channel=[0, 2]),
axes_name="xy",
axis_to_recalculate="y",
)
rt_xy_expected = Rototrans(
np.array([
[0.5773502691896257, 0.7071067811865475, -0.408248290463863, 1.0],
[0.5773502691896257, 0.0, 0.816496580927726, 2.0],
[0.5773502691896257, -0.7071067811865475, -0.408248290463863, 3.0],
[0, 0, 0, 1.0],
]))
np.testing.assert_array_equal(rt_xy_from_known_m, rt_xy_expected)
exception_default_params = dict(
origin=all_m.isel(channel=[0]),
axis_1=all_m.isel(channel=[0, 1]),
axis_2=all_m.isel(channel=[0, 2]),
axes_name="xy",
axis_to_recalculate="y",
)
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(origin=all_m.isel(channel=[0, 1]))
})
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(axis_1=all_m.isel(channel=[0]))
})
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(axis_2=all_m.isel(channel=[0]))
})
with pytest.raises(ValueError):
Rototrans.from_markers(
**{
**exception_default_params,
**dict(axis_1=all_m.isel(channel=[0, 1], time=slice(None, 50))),
})
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(axes_name="yyz")
})
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(axes_name="xxz")
})
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(axes_name="zzz")
})
with pytest.raises(ValueError):
Rototrans.from_markers(**{
**exception_default_params,
**dict(axis_to_recalculate="h")
})