def map_energy(S):
"""
negated log-posterior
"""
ppm = S.ppm.copy()
ppm[S.mask] = binarize_ppm(ppm[S.mask])
return S.free_energy(ppm=ppm)
def run_vem(data, mask, laplace_init=False):
mu, sigma = moment_matching(data[mask])
S = Segmentation(data, mask=mask, mu=mu, sigma=sigma, beta=0)
S.run(niters=PRE_NITERS)
S = Segmentation(data, mask=mask, mu=S.mu, sigma=S.sigma,
ngb_size=NGB_SIZE, beta=BETA)
e, f, v, vf = [], [], [], []
# Initialize ppm with RW optionally
if laplace_init:
S = run_rw(S)
S.ppm[S.mask] = binarize_ppm(S.ppm[S.mask])
for s in range(len(NITERS)):
# Run VEM for a few iterations
S, es, fs, vs, vfs = _run_vem(S, niters=NITERS[s])
e += es
f += fs
v += vs
vf += vfs
return S, e, f, v, vf
def post_vem(S, update_params=True):
S.ppm[S.mask] = binarize_ppm(S.ppm[S.mask])
e, f = [], []
for it in range(NITERS):
t0 = time()
if update_params:
S.vm_step()
S.ve_step()
dt = time() - t0
print('VEM iteration time: %f' % dt)
f += [S.free_energy()]
ppm = S.ppm.copy()
ppm[S.mask] = binarize_ppm(ppm[S.mask])
e += [S.free_energy(ppm=ppm)]
return S, e, f
def init_laplace(img, mask, mu, sigma):
S = Segmentation(img.get_data(), mask=mask, mu=mu, sigma=sigma,
ngb_size=NGB_SIZE, beta=BETA)
prior, gamma = config_random_walker(S.ext_field(), BETA)
q = random_walker(mask, prior, gamma)
if BINARIZE:
S.ppm[mask] = binarize_ppm(q)
else:
S.ppm[mask] = q
return S
def _run_vem(S, niters):
e, f, v, vf = [], [], [], []
for it in range(niters):
print('VE-step...')
S.ve_step()
print('Compute energies...')
f += [S.free_energy()]
vf += [np.sum(S.ppm[S.mask], 0)]
ppm = S.ppm.copy()
ppm[S.mask] = binarize_ppm(ppm[S.mask])
e += [S.free_energy(ppm=ppm)]
v += [np.sum(ppm[S.mask], 0)]
print('VM-step...')
S.vm_step()
return S, e, f, v, vf