def _pupil(self, F, r, theta):
from PYME.misc import zernike
ang = 0
for i, c in self.zernikeCoeffs.items():
ang = ang + c * zernike.zernike(i, r, theta)
return F * np.exp(-1j * ang)
def GenSAPRIPSF(zs, dx=5, strength=1.0, SA=0, X=None, Y=None, lamb=700, n=1.51, NA = 1.47):
from PYME.misc import zernike
Xk = X.ctypes.data
if not Xk in fps.keys():
fpset = GenWidefieldAP(dx, X, Y, lamb=lamb, n=n, NA = NA)
fps[Xk] = fpset
else:
fpset = fps[Xk]
X, Y, R, FP, F, u, v = fpset #GenWidefieldAP(dx, X, Y)
r = R/R[abs(F)>0].max()
F = F * exp(-1j*sign(X)*10*strength*v)
theta = angle(X + 1j*Y)
ang = SA*zernike.zernike(8, r, theta)
F = F*exp(-1j*ang)
#clf()
#imshow(angle(F))
ps = concatenate([FP.propagate(F, z)[:,:,None] for z in zs], 2)
return abs(ps**2)
def GenZernikeDAPSF(zs,
zernikeCoeffs={},
field_x=0,
field_y=0,
apertureNA=1.5,
apertureZGradient=0,
**kwargs):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = clipped_widefield_pupil_and_propagator(
field_x=field_x,
field_y=field_y,
apertureNA=apertureNA,
apertureZGradient=apertureZGradient,
**kwargs)
theta = np.angle(X + 1j * Y)
r = R / R[abs(F) > 0].max()
ang = 0
for i, c in zernikeCoeffs.items():
ang = ang + c * zernike.zernike(i, r, theta)
F = F * np.exp(-1j * ang)
return PSF_from_pupil_and_propagator(X,
Y,
R,
FP,
u,
v,
pupil=F,
zs=zs,
**kwargs)
def GenSAAstigPSF(zs, dx=5, strength=1.0, SA=0, X=None, Y=None, lamb=700, n=1.51, NA = 1.47):
from PYME.misc import zernike
if X == None:
Xk = 'none'
else:
Xk = X.ctypes.data
if not Xk in fps.keys():
fpset = GenWidefieldAP(dx, X, Y, lamb=lamb, n=n, NA = NA)
X, Y, R, FP, F, u, v = fpset
r = R/R[abs(F)>0].max()
theta = angle(X + 1j*Y)
z8 = zernike.zernike(8, r, theta)
a_s = (v**2 - 0.5*R**2)
fps[Xk] = (fpset, z8, a_s)
else:
fpset, z8, a_s = fps[Xk]
X, Y, R, FP, F, u, v = fpset #GenWidefieldAP(dx, X, Y)
#F = F * exp(-1j*(strength*a_s + SA*z8))
pf = -(strength*a_s + SA*z8)
F = F *(cos(pf) + j*sin(pf))
#clf()
#imshow(angle(F))
ps = concatenate([FP.propagate(F, z)[:,:,None] for z in zs], 2)
return abs(ps**2)
def GenZernikeDonutPSF(zs, zernikeCoeffs={}, spiral_amp=1.0, **kwargs):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = widefield_pupil_and_propagator(**kwargs)
kwargs.pop('X', None)
kwargs.pop('Y', None)
theta = np.angle(X + 1j * Y)
r = R / R[abs(F) > 0].max()
ang = 0
for i, c in zernikeCoeffs.items():
ang = ang + c * zernike.zernike(i, r, theta)
ang = ang + spiral_amp * theta
F = F * np.exp(-1j * ang)
return PSF_from_pupil_and_propagator(X,
Y,
R,
FP,
u,
v,
pupil=F,
zs=zs,
**kwargs)
def GenSAPSF(zs, strength=1.0, **kwargs):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = widefield_pupil_and_propagator(**kwargs)
r = R/R[abs(F)>0].max()
theta = np.angle(X + 1j*Y)
z8 = zernike.zernike(8, r, theta)
F = F * np.exp(-1j*strength*z8)
return PSF_from_pupil_and_propagator(X, Y, R, FP, u, v, pupil=F, zs=zs, **kwargs)
def GenSAAstigPSF(zs, strength=1.0, SA=0, **kwargs):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = widefield_pupil_and_propagator(**kwargs)
r = R/R[abs(F)>0].max()
theta = np.angle(X + 1j*Y)
z8 = zernike.zernike(8, r, theta)
a_s = (v**2 - 0.5*R**2)
pf = -(strength*a_s + SA*z8)
F = F *(np.cos(pf) + j*np.sin(pf))
return PSF_from_pupil_and_propagator(X, Y, R, FP, u, v, pupil=F, zs=zs, **kwargs)
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)
def GenZernikePSF(zs, zernikeCoeffs = [], **kwargs):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = widefield_pupil_and_propagator(**kwargs)
theta = np.angle(X + 1j*Y)
r = R/R[abs(F)>0].max()
ang = 0
for i, c in enumerate(zernikeCoeffs):
ang = ang + c*zernike.zernike(i, r, theta)
pupil = F.astype('d')*np.exp(-1j*ang)
return PSF_from_pupil_and_propagator(X, Y, R, FP, u, v, pupil=pupil, zs=zs, **kwargs)
def GenSABesselPSF(zs, dx=5, rad=.95, strength=1.0, X=None, Y=None, lamb=700, n=1.51, NA = 1.47):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = GenWidefieldAP(dx, X, Y, lamb=lamb, n=n, NA = NA)
r = R/R[abs(F)>0].max()
theta = angle(X + 1j*Y)
z8 = zernike.zernike(8, r, theta)
F = F * (r > rad)*exp(-1j*strength*z8)
#clf()
#imshow(angle(F))
ps = concatenate([FP.propagate(F, z)[:,:,None] for z in zs], 2)
return abs(ps**2)
def GenZernikePSF(zs, dx = 5, zernikeCoeffs = []):
from PYME.misc import zernike
X, Y, R, FP, F, u, v = GenWidefieldAP(dx)
theta = angle(X + 1j*Y)
r = R/R[abs(F)>0].max()
ang = 0
for i, c in enumerate(zernikeCoeffs):
ang = ang + c*zernike.zernike(i, r, theta)
clf()
imshow(angle(exp(1j*ang)))
F = F.astype('d')*exp(-1j*ang)
figure()
imshow(angle(F))
ps = concatenate([FP.propagate(F, z)[:,:,None] for z in zs], 2)
return abs(ps**2)
def GenZernikePSF(zs, dx = 5, zernikeCoeffs = []):
from PYME.misc import zernike
X, Y, R, FP, F = GenWidefieldAP(dx)
theta = angle(X + 1j*Y)
r = R/R[F].max()
ang = 0
for i, c in enumerate(zernikeCoeffs):
ang = ang + c*zernike.zernike(i, r, theta)
clf()
imshow(angle(exp(1j*ang)))
F = F.astype('d')*exp(-1j*ang)
figure()
imshow(angle(F))
ps = concatenate([FP.propagate(F, z)[:,:,None] for z in zs], 2)
return abs(ps**2)
def Gen4PiPSF(zs,phi=0, zernikeCoeffs=[{},{}], **kwargs):
from PYME.misc import zernike
X, Y, R, FP, pupil, u, v = widefield_pupil_and_propagator(**kwargs)
dphi = phi
kwargs.pop('X', None)
kwargs.pop('Y', None)
NA = kwargs.get('NA', 1.47)
n = kwargs.get('n', 1.51)
output_shape = kwargs.get('output_shape', None)
beadsize = kwargs.get('beadsize', 0)
vectorial = kwargs.get('vectorial', False)
pupil = pupil * _apodization_function(R, NA, n, kwargs.get('apodization', None))
if beadsize > 0:
pupil = pupil * get_bead_pupil(X, Y, beadsize)
theta = np.angle(X + 1j * Y)
r = R / R[abs(pupil) > 0].max()
ang_u = 0
ang_l = 0
zerns_upper, zerns_lower = zernikeCoeffs
#print zernikeCoeffs, zerns_upper, zerns_lower
for i, c in zerns_upper.items():
ang_u = ang_u + c * zernike.zernike(i, r, theta)
for i, c in zerns_lower.items():
ang_l = ang_l + c * zernike.zernike(i, r, theta)
pupil_upper = pupil * np.exp(-1j * ang_u)
pupil_lower = pupil * np.exp(-1j * ang_l)
#pupil_upper = pupil
#pupil_lower = pupil
if vectorial:
if vectorial is True:
#use circular pol by default
a = 1
b = -1j
else:
#vectorial is a tuple of polarization components
a, b = vectorial
phi = np.angle(u + 1j * v)
theta = np.arcsin(np.minimum(R, 1))
ct = np.cos(theta)
st = np.sin(theta)
cp = np.cos(phi)
sp = np.sin(phi)
psf = []
for z in zs:
#ax
fac = a*(ct * cp ** 2 + sp ** 2)
ps_u = FP.propagate(pupil_upper * fac, z)
ps_l = FP.propagate(pupil_lower * fac, -z)*np.exp(1j*dphi)
ps_x = ps_u + ps_l
#p = abs(ps ** 2)
#ay
fac = a*(ct - 1) * cp * sp
ps_u = FP.propagate(pupil_upper * fac, z)
ps_l = FP.propagate(pupil_lower * fac, -z) * np.exp(1j * dphi)
ps_y = ps_u + ps_l
#p += abs(ps ** 2)
#bx
fac = b*(ct - 1) * cp * sp
ps_u = FP.propagate(pupil_upper * fac, z)
ps_l = FP.propagate(pupil_lower * fac, -z) * np.exp(1j * dphi)
ps_x += (ps_u + ps_l)
p = abs(ps_x ** 2)
#by
fac = b*(ct * sp ** 2 + cp ** 2)
ps_u = FP.propagate(pupil_upper * fac, z)
ps_l = FP.propagate(pupil_lower * fac, -z) * np.exp(1j * dphi)
ps_y += (ps_u + ps_l)
p += abs(ps_y ** 2)
#az
fac = -a*st * cp
ps_u = FP.propagate(pupil_upper * fac, z)
ps_l = FP.propagate(pupil_lower * fac, -z) * np.exp(1j * dphi)
ps_z = ps_u + ps_l
#p += abs(ps ** 2)
fac = -b*(st * sp)
ps_u = FP.propagate(pupil_upper * fac, z)
ps_l = FP.propagate(pupil_lower * fac, -z) * np.exp(1j * dphi)
ps_z += (ps_u + ps_l)
p += abs(ps_z ** 2)
psf.append(p[:,:,None])
p = np.concatenate(psf, 2)
else:
###########
# Default scalar case
ps_u = np.concatenate([FP.propagate(pupil_upper, z)[:, :, None] for z in zs], 2)
ps_l = np.concatenate([FP.propagate(pupil_lower, -z)[:, :, None] * np.exp(1j * dphi) for z in zs], 2)
ps = ps_u + ps_l
p = abs(ps ** 2)
if output_shape is None:
return p
else:
sx = output_shape[0]
sy = output_shape[1]
ox = np.ceil((X.shape[0] - sx) / 2.0)
oy = np.ceil((X.shape[1] - sy) / 2.0)
ex = ox + sx
ey = oy + sy
return p[ox:ex, oy:ey, :]