def test_symmetrise_data_y_axis():
cube_id = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11],
[12, 13, 14, 15]],
[[16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27],
[28, 29, 30, 31]]])
cube_sym_y2_be_T = np.array([[[0, 1, 1, 0], [4, 5, 5, 4], [8, 9, 9, 8],
[12, 13, 13, 12]],
[[16, 17, 17, 16], [20, 21, 21, 20],
[24, 25, 25, 24], [28, 29, 29, 28]]])
cube_sym_y2_ab_T = np.array([[[3, 2, 2, 3], [7, 6, 6, 7], [11, 10, 10, 11],
[15, 14, 14, 15]],
[[19, 18, 18, 19], [23, 22, 22, 23],
[27, 26, 26, 27], [31, 30, 30, 31]]])
cube_sym_y3_be_F = np.array([[[0, 1, 2, 2, 1, 0], [4, 5, 6, 6, 5, 4],
[8, 9, 10, 10, 9, 8],
[12, 13, 14, 14, 13, 12]],
[[16, 17, 18, 18, 17, 16],
[20, 21, 22, 22, 21, 20],
[24, 25, 26, 26, 25, 24],
[28, 29, 30, 30, 29, 28]]])
cube_sym_y3_be_T = np.array([[[0, 1, 2, 2], [4, 5, 6, 6], [8, 9, 10, 10],
[12, 13, 14, 14]],
[[16, 17, 18, 18], [20, 21, 22, 22],
[24, 25, 26, 26], [28, 29, 30, 30]]])
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='y',
plane_intercept=2,
side_to_copy='below',
keep_in_data_dimensions_boundaries=True),
cube_sym_y2_be_T)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='y',
plane_intercept=2,
side_to_copy='above',
keep_in_data_dimensions_boundaries=True),
cube_sym_y2_ab_T)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='y',
plane_intercept=3,
side_to_copy='below',
keep_in_data_dimensions_boundaries=False),
cube_sym_y3_be_F)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='y',
plane_intercept=3,
side_to_copy='below',
keep_in_data_dimensions_boundaries=True),
cube_sym_y3_be_T)
def test_symmetrise_data_x_axis():
cube_id = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11],
[12, 13, 14, 15]],
[[16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27],
[28, 29, 30, 31]]])
cube_sym_x2_be_T = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [4, 5, 6, 7],
[0, 1, 2, 3]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[20, 21, 22, 23], [16, 17, 18, 19]]])
cube_sym_x2_ab_T = np.array([[[12, 13, 14, 15], [8, 9, 10, 11],
[8, 9, 10, 11], [12, 13, 14, 15]],
[[28, 29, 30, 31], [24, 25, 26, 27],
[24, 25, 26, 27], [28, 29, 30, 31]]])
cube_sym_x3_be_F = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11],
[8, 9, 10, 11], [4, 5, 6, 7], [0, 1, 2, 3]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [24, 25, 26, 27],
[20, 21, 22, 23], [16, 17, 18, 19]]])
cube_sym_x3_be_T = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11],
[8, 9, 10, 11]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [24, 25, 26, 27]]])
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='x',
plane_intercept=2,
side_to_copy='below',
keep_in_data_dimensions_boundaries=True),
cube_sym_x2_be_T)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='x',
plane_intercept=2,
side_to_copy='above',
keep_in_data_dimensions_boundaries=True),
cube_sym_x2_ab_T)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='x',
plane_intercept=3,
side_to_copy='below',
keep_in_data_dimensions_boundaries=False),
cube_sym_x3_be_F)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='x',
plane_intercept=3,
side_to_copy='below',
keep_in_data_dimensions_boundaries=True),
cube_sym_x3_be_T)
def test_symmetrise_data_z_axis():
cube_id = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11],
[12, 13, 14, 15]],
[[16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27],
[28, 29, 30, 31]],
[[32, 33, 34, 35], [36, 37, 38, 39], [40, 41, 42, 43],
[44, 45, 46, 47]]])
cube_sym_z2_be_T = np.array([[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11],
[12, 13, 14, 15]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [28, 29, 30, 31]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [28, 29, 30, 31]]])
cube_sym_z1_ab_T = np.array([[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [28, 29, 30, 31]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [28, 29, 30, 31]],
[[32, 33, 34, 35], [36, 37, 38, 39],
[40, 41, 42, 43], [44, 45, 46, 47]]])
cube_sym_z1_ab_F = np.array([[[32, 33, 34, 35], [36, 37, 38, 39],
[40, 41, 42, 43], [44, 45, 46, 47]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [28, 29, 30, 31]],
[[16, 17, 18, 19], [20, 21, 22, 23],
[24, 25, 26, 27], [28, 29, 30, 31]],
[[32, 33, 34, 35], [36, 37, 38, 39],
[40, 41, 42, 43], [44, 45, 46, 47]]])
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='z',
plane_intercept=2,
side_to_copy='below',
keep_in_data_dimensions_boundaries=True),
cube_sym_z2_be_T)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='z',
plane_intercept=1,
side_to_copy='above',
keep_in_data_dimensions_boundaries=True),
cube_sym_z1_ab_T)
assert_array_equal(
symmetrise_data(cube_id,
axis_direction='z',
plane_intercept=1,
side_to_copy='above',
keep_in_data_dimensions_boundaries=False),
cube_sym_z1_ab_F)
def symmetrise_axial(self, filename_in, filename_out=None, axis='x', plane_intercept=10,
side_to_copy='below', keep_in_data_dimensions=True):
pfi_in, pfi_out = get_pfi_in_pfi_out(filename_in, filename_out, self.pfo_in, self.pfo_out)
im_segm = nib.load(pfi_in)
data_labels = im_segm.get_data()
data_symmetrised = symmetrise_data(data_labels,
axis_direction=axis,
plane_intercept=plane_intercept,
side_to_copy=side_to_copy,
keep_in_data_dimensions_boundaries=keep_in_data_dimensions)
im_symmetrised = set_new_data(im_segm, data_symmetrised)
nib.save(im_symmetrised, pfi_out)
print('Symmetrised axis {0}, plane_intercept {1}, image of {2} saved in {3}.'.format(axis, plane_intercept, pfi_in, pfi_out))
return pfi_out
def test_symmetrise_data_error_input_axis_direction():
with assert_raises(IOError):
symmetrise_data(np.ones([5, 5, 5]), axis_direction='s')
def test_symmetrise_data_error_input_side_to_copy():
with assert_raises(IOError):
symmetrise_data(np.ones([5, 5, 5]), side_to_copy='spam')
def test_symmetrise_data_error_input_ndim():
with assert_raises(IOError):
symmetrise_data(np.ones([5, 5, 5, 5]))