def _apodization_function(R, NA, n, apodization='sine', ns=None):
from PYME.misc import snells
t_ = np.arcsin(np.minimum(R, 1))
if apodization is None:
M = 1.0 * (R < (NA / n)) # NA/lambda
elif apodization == 'sine':
M = 1.0 * (R < (NA / n)) * np.sqrt(np.cos(t_))
elif apodization == 'empirical':
r_ = np.minimum(R, 1)
M = 1.0 * (R < (NA / n)) * (1 - 0.65 * t_) * (1 - np.exp(-10 * ((NA / n) - r_)))
else:
M = 1.0 * (R < (NA / n)) # NA/lambda
r = R / R[abs(M) > 0].max()
if (ns is None) or (ns == n):
T = 1.0 * M
else:
#find angles
t_t = np.minimum(r * np.arcsin(NA / n), np.pi / 2)
#corresponding angle in sample with mismatch
t_i = snells.theta_t(t_t, n, ns)
#Transmission at interface (average of S and P)
T = 0.5 * (snells.Ts(t_i, ns, n) + snells.Tp(t_i, ns, n))
#concentration of high np.angle rays:
T = T * 1.0 / (n * np.cos(t_t) / np.sqrt(ns * 2 - (n * np.sin(t_t)) ** 2))
return M*T
def GenZernikeDAPSF(zs, dx = 5, X=None, Y=None, zernikeCoeffs = {}, lamb=700, n=1.51, NA = 1.47, ns=1.51,field_x=0, field_y=0, apertureNA=1.5, apertureZGradient = 0, apodizisation=None, vect=True):
from PYME.misc import zernike, snells
X, Y, R, FP, F, u, v = GenWidefieldAPA(dx, X = X, Y=Y, lamb=lamb, n = n, NA = NA, field_x=field_x, field_y=field_y, apertureNA=apertureNA, apertureZGradient = apertureZGradient, apodizisation=apodizisation)
theta = angle(X + 1j*Y)
r = R/R[abs(F)>0].max()
if ns == n:
T = 1.0*F
else:
#find angles
t_t = np.minimum(r*arcsin(NA/n), np.pi/2)
#corresponding angle in sample with mismatch
t_i = snells.theta_t(t_t, n, ns)
#Transmission at interface (average of S and P)
T = 0.5*(snells.Ts(t_i, ns, n) + snells.Tp(t_i, ns, n))
#concentration of high angle rays:
T = T*F/(n*np.cos(t_t)/np.sqrt(ns*2 - (n*np.sin(t_t))**2))
#imshow(T*(-t_i + snells.theta_t(t_t+.001, n, ns)))
#imshow(F)
#colorbar()
#figure()
#imshow(T, clim=(.8, 1.2))
#colorbar()
#figure()
#imshow(T*(-t_i + snells.theta_t(t_t+.01, n, ns)))
#imshow(t_i - t_t)
ang = 0
for i, c in zernikeCoeffs.items():
ang = ang + c*zernike.zernike(i, r, theta)
#clf()
#imshow(angle(exp(1j*ang)))
F = T*exp(-1j*ang)
#figure()
#imshow(angle(F))
if vect:
return PsfFromPupilVectFP(X,Y,R, FP, u,v, n, F, zs)
else:
return PsfFromPupilFP(X,Y,R, FP, u,v, n, F, zs)