def test_1dphase(self, level=1):
x = np.arange(32.)
phs = np.angle(np.exp(1.j * x))
uw_phs = util.unwrap1D(phs)
assert_array_almost_equal(x, uw_phs, decimal=14)
wr_phs = util.normalize_angle(uw_phs)
assert_array_almost_equal(wr_phs, phs, decimal=14)
def run(self, image):
# can't perform segmentation correction on a non-segmented image!
if image.nseg < 2:
self.log("Image is non-segmented, nothing to do.")
return
pe_per_seg = image.n_pe_true/image.nseg
# phase angle of inverse fft'd ref navs and image navs
#ref_nav_phs = angle(ifft(image.ref_nav_data[0], shift=True))
#nav_phs = angle(ifft(image.nav_data, shift=True))
ref_nav_phs = N.angle(ifft(image.ref_nav_data[0]))
nav_phs = N.angle(ifft(image.nav_data))
# phase difference between ref navs and image navs
phsdiff = normalize_angle(ref_nav_phs - nav_phs)
# weight phase difference by the phase encode timing during each segment
pe_times = (image.pe_times[image.nav_per_seg:]/image.echo_time)[:,N.newaxis]
theta = N.empty(image.shape, N.float64)
theta[:,:,:pe_per_seg] = phsdiff[:,:,N.newaxis,0]*pe_times
theta[:,:,pe_per_seg:] = phsdiff[:,:,N.newaxis,1]*pe_times
# Apply the phase correction.
apply_phase_correction(image[:], N.exp(-1.j*theta))
def test_1dphase(self, level=1):
x = np.arange(32.)
phs = np.angle(np.exp(1.j*x))
uw_phs = util.unwrap1D(phs)
assert_array_almost_equal(x, uw_phs, decimal=14)
wr_phs = util.normalize_angle(uw_phs)
assert_array_almost_equal(wr_phs, phs, decimal=14)
def run(self, image):
# can't perform segmentation correction on a non-segmented image!
if image.nseg < 2:
self.log("Image is non-segmented, nothing to do.")
return
pe_per_seg = image.n_pe_true / image.nseg
# phase angle of inverse fft'd ref navs and image navs
#ref_nav_phs = angle(ifft(image.ref_nav_data[0], shift=True))
#nav_phs = angle(ifft(image.nav_data, shift=True))
ref_nav_phs = N.angle(ifft(image.ref_nav_data[0]))
nav_phs = N.angle(ifft(image.nav_data))
# phase difference between ref navs and image navs
phsdiff = normalize_angle(ref_nav_phs - nav_phs)
# weight phase difference by the phase encode timing during each segment
pe_times = (image.pe_times[image.nav_per_seg:] /
image.echo_time)[:, N.newaxis]
theta = N.empty(image.shape, N.float64)
theta[:, :, :pe_per_seg] = phsdiff[:, :, N.newaxis, 0] * pe_times
theta[:, :, pe_per_seg:] = phsdiff[:, :, N.newaxis, 1] * pe_times
# Apply the phase correction.
apply_phase_correction(image[:], N.exp(-1.j * theta))
def test_simple2d(self, level=1):
grid = outer(ones(64), arange(-32,32)) + \
1.j * outer(arange(-32,32), ones(64))
pgrid = abs(grid)
wr_grid = normalize_angle(pgrid)
uw_grid = unwrap2D(wr_grid)
uw_grid += (pgrid[32,32] - uw_grid[32,32])
assert_array_almost_equal(pgrid, uw_grid, decimal=5)
def test_simple2d(self, level=1):
grid = outer(ones(64), arange(-32,32)) + \
1.j * outer(arange(-32,32), ones(64))
pgrid = abs(grid)
wr_grid = normalize_angle(pgrid)
uw_grid = unwrap2D(wr_grid)
uw_grid += (pgrid[32, 32] - uw_grid[32, 32])
assert_array_almost_equal(pgrid, uw_grid, decimal=5)
def test_simple3d(self):
grid = indices((64,64,64))
grid[0] -= 32
grid[1] -= 32
grid[2] -= 32
# get distance of each point in the grid from 0
grid = power(power(grid, 2.0).sum(axis=0), 0.5)
wr_grid = normalize_angle(grid)
uw_grid = unwrap3D(wr_grid)
uw_grid += (grid[32,32,32] - uw_grid[32,32,32])
assert_array_almost_equal(grid, uw_grid, decimal=5)
def test_simple3d(self):
grid = indices((64, 64, 64))
grid[0] -= 32
grid[1] -= 32
grid[2] -= 32
# get distance of each point in the grid from 0
grid = power(power(grid, 2.0).sum(axis=0), 0.5)
wr_grid = normalize_angle(grid)
uw_grid = unwrap3D(wr_grid)
uw_grid += (grid[32, 32, 32] - uw_grid[32, 32, 32])
assert_array_almost_equal(grid, uw_grid, decimal=5)