def test_rodrigues_to_dcm():
RES = np.array([[0.50017235, -0.80049871, 0.33019604],
[0.80739289, 0.56894174, 0.15627544],
[-0.3129606, 0.18843328, 0.9308859]])
R = gtr._rodrigues_to_dcm(TEST_UVEC, TEST_ANGLE)
# assess rotation matrix properties:
# detR = +=1
nt.assert_almost_equal(np.linalg.det(R), 1.)
# R.T = R^-1
nt.assert_true(np.allclose(np.linalg.inv(R), R.transpose()))
# check against calculated matrix
nt.assert_true(np.allclose(R, RES))
# check if opposite sign generates inverse
Rinv = gtr._rodrigues_to_dcm(TEST_UVEC, -TEST_ANGLE)
nt.assert_true(np.allclose(np.dot(Rinv, R), np.identity(3)))
# check basic rotations with a range of angles
for angle in np.linspace(0., 2. * np.pi, 10):
Rx = gtr._rodrigues_to_dcm(np.array([1., 0., 0.]), angle)
Ry = gtr._rodrigues_to_dcm(np.array([0., 1., 0.]), angle)
Rz = gtr._rodrigues_to_dcm(np.array([0., 0., 1.]), angle)
nt.assert_true(np.allclose(Rx, _Rx(angle)))
nt.assert_true(np.allclose(Ry, _Ry(angle)))
nt.assert_true(np.allclose(Rz, _Rz(angle)))
def test_rodrigues_to_dcm():
RES = np.array([[0.50017235, -0.80049871, 0.33019604],
[0.80739289, 0.56894174, 0.15627544],
[-0.3129606, 0.18843328, 0.9308859]])
R = gtr._rodrigues_to_dcm(TEST_UVEC, TEST_ANGLE)
# assess rotation matrix properties:
# detR = +=1
assert_almost_equal(np.linalg.det(R), 1.)
# R.T = R^-1
assert np.allclose(np.linalg.inv(R), R.transpose())
# check against calculated matrix
assert np.allclose(R, RES)
# check if opposite sign generates inverse
Rinv = gtr._rodrigues_to_dcm(TEST_UVEC, -TEST_ANGLE)
assert np.allclose(np.dot(Rinv, R), np.identity(3))
# check basic rotations with a range of angles
for angle in np.linspace(0., 2. * np.pi, 10):
Rx = gtr._rodrigues_to_dcm(np.array([1., 0., 0.]), angle)
Ry = gtr._rodrigues_to_dcm(np.array([0., 1., 0.]), angle)
Rz = gtr._rodrigues_to_dcm(np.array([0., 0., 1.]), angle)
assert np.allclose(Rx, _Rx(angle))
assert np.allclose(Ry, _Ry(angle))
assert np.allclose(Rz, _Rz(angle))
def test_pivot_rotate_point():
point = [1, 2, 3]
new_orig = np.array([10. , 45., 50.])
t = gtr.Translation(new_orig)
t_inv = gtr.Translation(new_orig * -1)
R = gtr._rodrigues_to_dcm(TEST_UVEC, np.pi)
# change origin, rotate 180
p1 = gtr.PivotRotation(R, new_orig)(point)
# do the steps manually
p2 = t_inv(point)
p2 = gtr.Rotation(R)(p2)
p2 = t(p2)
nt.assert_equal(p1.tolist(), p2.tolist())
def test_pivot_rotate_point():
point = [1, 2, 3]
new_orig = np.array([10., 45., 50.])
t = gtr.Translation(new_orig)
t_inv = gtr.Translation(new_orig * -1)
R = gtr._rodrigues_to_dcm(TEST_UVEC, np.pi)
# change origin, rotate 180
p1 = gtr.PivotRotation(R, new_orig)(point)
# do the steps manually
p2 = t_inv(point)
p2 = gtr.Rotation(R)(p2)
p2 = t(p2)
assert p1.tolist() == p2.tolist()
def test_pivot_rotate_points():
points = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12]])
new_orig = np.array([10., 45., 50.])
t = gtr.Translation(new_orig)
t_inv = gtr.Translation(new_orig * -1)
R = gtr._rodrigues_to_dcm(TEST_UVEC, np.pi)
# change origin, rotate 180
p1 = gtr.PivotRotation(R, new_orig)(points)
# do the steps manually
p2 = t_inv(points)
p2 = gtr.Rotation(R)(p2)
p2 = t(p2)
nt.assert_true(np.all(p1 == p2))
def test_pivot_rotate_points():
points = np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9],
[10, 11, 12]])
new_orig = np.array([10. , 45., 50.])
t = gtr.Translation(new_orig)
t_inv = gtr.Translation(new_orig * -1)
R = gtr._rodrigues_to_dcm(TEST_UVEC, np.pi)
# change origin, rotate 180
p1 = gtr.PivotRotation(R, new_orig)(points)
# do the steps manually
p2 = t_inv(points)
p2 = gtr.Rotation(R)(p2)
p2 = t(p2)
nt.assert_true(np.all(p1 == p2))
def test_rotate_neurite_h5():
nrn_a = load_neuron(H5_NRN_PATH)
nrt_a = nrn_a.neurites[0]
nrt_b = gtr.rotate(nrt_a, [0,0,1], math.pi/2.0)
rot = gtr._rodrigues_to_dcm([0,0,1], math.pi/2.0)
_check_fst_neurite_rotate(nrt_a, nrt_b, rot)
def test_rotate_neuron_swc():
nrn_a = load_neuron(SWC_NRN_PATH)
nrn_b = gtr.rotate(nrn_a, [0,0,1], math.pi/2.0)
rot = gtr._rodrigues_to_dcm([0,0,1], math.pi/2.0)
_check_fst_nrn_rotate(nrn_a, nrn_b, rot)
def test_rotate_neuron_h5():
nrn_a = load_neuron(H5_NRN_PATH)
nrn_b = gtr.rotate(nrn_a, [0, 0, 1], math.pi/2.0)
rot = gtr._rodrigues_to_dcm([0, 0, 1], math.pi/2.0)
_check_fst_nrn_rotate(nrn_a, nrn_b, rot)
def test_rotate_neurite_swc():
nrn_a = load_neuron(SWC_NRN_PATH)
nrt_a = nrn_a.neurites[0]
nrt_b = gtr.rotate(nrt_a, [0,0,1], math.pi/2.0)
rot = gtr._rodrigues_to_dcm([0,0,1], math.pi/2.0)
_check_fst_neurite_rotate(nrt_a, nrt_b, rot)
