def test_reorient_vectors():
with clear_and_catch_warnings():
bvec = np.arange(12).reshape((3, 4))
assert_array_equal(reorient_vectors(bvec, 'ras', 'ras'), bvec)
assert_array_equal(reorient_vectors(bvec, 'ras', 'lpi'), -bvec)
result = bvec[[1, 2, 0]]
assert_array_equal(reorient_vectors(bvec, 'ras', 'asr'), result)
bvec = result
result = bvec[[1, 0, 2]] * [[-1], [1], [-1]]
assert_array_equal(reorient_vectors(bvec, 'asr', 'ial'), result)
result = bvec[[1, 0, 2]] * [[-1], [1], [1]]
assert_array_equal(reorient_vectors(bvec, 'asr', 'iar'), result)
assert_raises(ValueError, reorient_vectors, bvec, 'ras', 'ra')
bvec = np.arange(12).reshape((3, 4))
bvec = bvec.T
assert_array_equal(reorient_vectors(bvec, 'ras', 'ras', axis=1), bvec)
assert_array_equal(reorient_vectors(bvec, 'ras', 'lpi', axis=1), -bvec)
result = bvec[:, [1, 2, 0]]
assert_array_equal(reorient_vectors(bvec, 'ras', 'asr', axis=1),
result)
bvec = result
result = bvec[:, [1, 0, 2]] * [-1, 1, -1]
assert_array_equal(reorient_vectors(bvec, 'asr', 'ial', axis=1),
result)
result = bvec[:, [1, 0, 2]] * [-1, 1, 1]
assert_array_equal(reorient_vectors(bvec, 'asr', 'iar', axis=1),
result)
def test_reorient_vectors():
bvec = np.arange(12).reshape((3, 4))
assert_array_equal(reorient_vectors(bvec, 'ras', 'ras'), bvec)
assert_array_equal(reorient_vectors(bvec, 'ras', 'lpi'), -bvec)
result = bvec[[1, 2, 0]]
assert_array_equal(reorient_vectors(bvec, 'ras', 'asr'), result)
bvec = result
result = bvec[[1, 0, 2]] * [[-1], [1], [-1]]
assert_array_equal(reorient_vectors(bvec, 'asr', 'ial'), result)
result = bvec[[1, 0, 2]] * [[-1], [1], [1]]
assert_array_equal(reorient_vectors(bvec, 'asr', 'iar'), result)
assert_raises(ValueError, reorient_vectors, bvec, 'ras', 'ra')
def test_reorient_vectors():
bvec = np.arange(12).reshape((3,4))
assert_array_equal(reorient_vectors(bvec, 'ras', 'ras'), bvec)
assert_array_equal(reorient_vectors(bvec, 'ras', 'lpi'), -bvec)
result = bvec[[1,2,0]]
assert_array_equal(reorient_vectors(bvec, 'ras', 'asr'), result)
bvec = result
result = bvec[[1,0,2]]*[[-1],[1],[-1]]
assert_array_equal(reorient_vectors(bvec, 'asr', 'ial'), result)
result = bvec[[1,0,2]]*[[-1],[1],[1]]
assert_array_equal(reorient_vectors(bvec, 'asr', 'iar'), result)
assert_raises(ValueError, reorient_vectors, bvec, 'ras', 'ra')
def reorient_dwi_imgs(input_dwi, input_bval, input_bvec, output_dwi, output_bval, output_bvec, new_x, new_y, new_z, new_r, new_a, new_s):
os.system('fslswapdim ' + input_dwi + ' ' + new_x + ' ' + new_y + ' ' + new_z + ' ' + output_dwi)
#Now reorient the bvecs
bvals, bvecs = read_bvals_bvecs(input_bval, input_bvec)
new_orient = new_r+new_a+new_s
r_bvecs = reorient_vectors(bvecs, 'ras', new_orient, axis=1)
N = len(bvals)
fmt = ' %e' * N + '\n'
open(output_bval, 'wt').write(fmt % tuple(bvals))
bvf = open(output_bvec, 'wt')
for dim_vals in r_bvecs.T:
bvf.write(fmt % tuple(dim_vals))
bvf.close()