def gaussianArrND(shape=(256, 256), sigma=2., peakVal=None, orig=None, rot=0):
try:
ndim = len(shape)
except TypeError:
shape = [shape]
ndim = 1
sidx = ndim + 2
slices = [Ellipsis] + [slice(0, m) for m in shape]
inds, LD = imgFit.rotateIndicesND(slices, N.float32, rot)
#inds = N.indices(shape, N.float32)
try:
if len(sigma) != ndim:
raise ValueError, 'len(sigma) must be the same as len(shape)'
except TypeError:
sigma = [sigma] * ndim
if orig is None:
c = N.asarray(shape, N.float32) / 2.
else:
c = N.asarray(orig, N.float32)
if peakVal:
k0 = peakVal
else:
k0 = 1. / (N.average(sigma) * ((2 * N.pi)**0.5))
param = [0, k0] + list(c) + list(sigma)
param = N.asarray(param, N.float32)
return imgFit.yGaussianND(param, inds, sidx)
def getSphericalAbbe(arr3D, kmin=2, kmax=60, plot=False):
"""
compare frequency above and below the focus
return amplitude var(above)/var(below)
"""
afz = getFourierZprofile(arr3D)
# get z profile around the reasonable frequency
aa = N.abs(N.average(afz[:, kmin:kmax], axis=1))
# previously it was N.average(N.abs(afz[:,kmin:kmax]), axis=1), but that seems wrong...
# findMax
inds = N.indices(aa.shape, dtype=N.float64)
v, _0, _1, z = U.findMax(aa)
parm, check = imgFit.fitGaussianND(aa, [z], window=len(aa))
if check == 5:
raise RuntimeError, 'Peak not found check=%i' % check
gg = imgFit.yGaussianND(parm, inds, 3)
amg = aa - gg
z0 = parm[2]
mask = (parm[-1] * 3) / 2. # sigma * 3 / 2
ms0 = N.ceil(z0 - mask)
ms1 = N.ceil(z0 + mask)
amg[ms0:ms1] = 0
below = N.var(amg[:ms0])
above = N.var(amg[ms1:])
if plot:
Y.ploty(N.array((aa, gg, amg)))
print 'below: ', below
print 'above: ', above
print ms0, ms1, z0
return above / (above + below) #above / below