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from pycpd import DeformableRegistration, RigidRegistration
import numpy as np
import time
from scipy.interpolate import Rbf
import warnings
def cpd_non_rigid_transform_pt(pt, Y, G, W):
from scipy.interpolate import LinearNDInterpolator
interp = LinearNDInterpolator(points=Y, values=np.dot(G, W), fill_value=0.)
return interp(pt)
def radial_basis_function(pts, vals, function='thin-plate'):
# The Rbf function does not handle n-D hyper-surfaces, so we need an interpolator per displacements. Actually it does mode='N-D'
pts_unique, idxs = np.unique(pts, return_index=True, axis=0) # Prevent singular matrices
ill_conditioned = False
with warnings.catch_warnings(record=True) as caught_warns:
warnings.simplefilter('always')
dx = Rbf(pts_unique[:, 0], pts_unique[:, 1], pts_unique[:, 2], vals[idxs][:, 0], function=function)
dy = Rbf(pts_unique[:, 0], pts_unique[:, 1], pts_unique[:, 2], vals[idxs][:, 1], function=function)
dz = Rbf(pts_unique[:, 0], pts_unique[:, 1], pts_unique[:, 2], vals[idxs][:, 2], function=function)
for w in caught_warns:
print(w)
ill_conditioned = ill_conditioned or 'ill-conditioned matrix' in str(w).lower()
return lambda int_pt: np.asarray([dx(*int_pt), dy(*int_pt), dz(*int_pt)]), ill_conditioned
def deform_registration(fix_pts, mov_pts, callback_fnc=None, time_it=False, max_iterations=100, tolerance=1e-8, alpha=None, beta=None):
deform_reg = DeformableRegistration(**{'Y': mov_pts, 'X': fix_pts},
alpha=alpha, beta=beta, tolerance=tolerance, max_iterations=max_iterations)
start_t = time.time()
trf_mov_pts, deform_p = deform_reg.register(callback_fnc)
end_t = time.time()
if time_it:
return end_t - start_t, deform_reg
else:
return trf_mov_pts, deform_p, deform_reg
def rigid_registration(fix_pts, mov_pts, callback_fnc=None, time_it=False):
rigid_reg = RigidRegistration(**{'Y': mov_pts, 'X': fix_pts})
start_t = time.time()
trf_mov_pts, trf_p = rigid_reg.register(callback_fnc)
end_t = time.time()
if time_it:
return end_t - start_t, rigid_reg
else:
return trf_mov_pts, trf_p, rigid_reg
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