def test_simulated_phantom_2d(self):
# Create the target field map
dim = 64
min_df, max_df = -500, 500
fx = np.linspace(min_df, max_df, dim)
fy = np.zeros(dim)
field_map, _ = np.meshgrid(fx, fy)
# field_map = 100*np.random.normal(0,1,(dim,dim))
# view(field_map)
# Simulate phase-cycled bSSFP acquisitons
# Seems to be better with higher flip angle!
# For some reason worse with higher TR
args = {
'TR': 5e-3,
'alpha': np.pi / 3,
'dims': (dim, dim),
'FOV': ((-1, 1), (-1, 1)),
'radius': .75,
'field_map': field_map
}
pc_vals = [0, np.pi / 2, np.pi, 3 * np.pi / 2]
pcs = np.zeros((len(pc_vals), dim, dim), dtype='complex')
for ii, pc in enumerate(pc_vals):
pcs[ii, ...] = bssfp_2d_cylinder(**args, phase_cyc=pc)
# view(pcs)
# Estimate field map using GS to ESM
gsfm = gs_field_map(
*[x.squeeze() for x in np.split(pcs, len(pc_vals))],
TR=args['TR'],
gs_recon_opts={'second_pass': False})
# TODO: Interestingly, the second pass solution fails... Why is this?
# Now do sims for GRE for a sanity check
TE1 = args['TR'] / 2
TE2 = TE1 - args['TR'] / 2
PD, T1s, T2s = cylinder_2d(dims=args['dims'],
FOV=args['FOV'],
radius=args['radius'])
m1 = gre_sim(T1s,
T2s,
TR=args['TR'],
TE=TE1,
alpha=args['alpha'],
field_map=args['field_map'],
dphi=0,
M0=PD,
tol=1e-4)
m2 = gre_sim(T1s,
T2s,
TR=args['TR'],
TE=TE2,
alpha=args['alpha'],
field_map=args['field_map'],
dphi=0,
M0=PD,
tol=1e-4)
grefm = dual_echo_gre(m1, m2, TE1, TE2)
# Phase wrap the real field map so we prove equivalence up to phase
# unwrapping...
dTE = np.abs(TE1 - TE2)
field_map_pw = np.mod(field_map - 1 /
(2 * dTE), 1 / dTE) - 1 / (2 * dTE)
# Make sure we're getting the same thing when wrapped
idx = np.where(np.abs(grefm) > 0)
self.assertTrue(np.allclose(grefm[idx], field_map_pw[idx]))
idx = np.where(np.abs(gsfm) > 0)
self.assertTrue(np.allclose(gsfm[idx], field_map_pw[idx]))
# Just for fun, try phase unwrapping...
mask = np.zeros(gsfm.shape).astype(bool)
mask[idx] = True
# scale between [-pi,pi], do unwrap, scale back up
scale_fac = np.pi / np.max(np.abs(gsfm)) * np.sign(np.max(gsfm))
val = unwrap_phase(mask * gsfm * scale_fac) / scale_fac
# For some reason the edges are off by about pi, so let's clip it...
val = val[:, 19:-19]
field_map_clipped = field_map[:, 19:-19]
idx = np.where(np.abs(val) > 0)
self.assertTrue(np.allclose(field_map_clipped[idx], val[idx]))
for jj, pc in enumerate(pc_vals):
bssfp_acqs[jj, ..., ii] = bssfp_acq(T1s,
T2s,
PD,
tv_field_map[..., ii],
alpha=bssfp_alpha,
TR=bssfp_TR,
phase_cyc=pc)
# view(bssfp_acqs[0,...],movie_axis=-1)
# view(np.concatenate((gre_acqs,bssfp_acqs[0,...])),movie_axis=-1)
# Now get field maps
recon_fm = np.zeros(tv_field_map.shape)
for ii in trange(time_pts, leave=False, desc='GSFM'):
recon_fm[..., ii] = gs_field_map(*[
x.squeeze() for x in np.split(bssfp_acqs[..., ii], len(pc_vals))
],
TR=bssfp_TR)
# recon_fm[0,0,:] = 1 # ref pixel
# view(recon_fm,movie_axis=-1)
# view(np.stack((recon_fm[31,16,:],tv_field_map[31,16,:])))
# Compare to just getting field map 4 times
avg_field_map = np.zeros(tv_field_map.shape)
for ii in trange(len(pc_vals), desc='AvgFM', leave=False):
avg_field_map += np.random.normal(0, sigma, tv_field_map.shape)
avg_field_map[idx, :] += hrf0
avg_field_map /= len(pc_vals)
if plots:
plt.plot(hrf0, label='HDR')
plt.plot(recon_fm[31, 16, :], label='Recon FM')
'TR': 5e-3,
'alpha': np.pi / 3,
'dims': (dim, dim),
'FOV': ((-1, 1), (-1, 1)),
'radius': .75,
'field_map': field_map
}
pc_vals = [0, np.pi / 2, np.pi, 3 * np.pi / 2]
pcs = np.zeros((len(pc_vals), dim, dim), dtype='complex')
for ii, pc in enumerate(pc_vals):
pcs[ii, ...] = bssfp_2d_cylinder(**args, phase_cyc=pc)
view(pcs)
# Estimate field map using GS to ESM
gsfm = gs_field_map(*[x.squeeze() for x in np.split(
pcs, len(pc_vals))], \
TR=args['TR'], gs_recon_opts={'second_pass': False})
# TODO: Interestingly, the second pass solution fails... Why is this?
view(gsfm)
# Now do sims for GRE for a sanity check
TE1 = args['TR'] / 2
TE2 = TE1 - args['TR'] / 2
PD, T1s, T2s = cylinder_2d(dims=args['dims'],
FOV=args['FOV'],
radius=args['radius'])
m1 = gre_sim(T1s,
T2s,
TR=args['TR'],
TE=TE1,
alpha=args['alpha'],