def test_normalisations_real(self):
log = logging.getLogger('TestZern.test_normalisations_real')
n_alpha = 6
L, K = 400, 357
# polar grid
pol = RZern(n_alpha)
fitAlpha = FitZern(pol, L, K)
t1 = time()
pol.make_pol_grid(fitAlpha.rho_j, fitAlpha.theta_i)
t2 = time()
log.debug('make pol grid {:.6f}'.format(t2 - t1))
# cartesian grid
cart = RZern(n_alpha)
dd = np.linspace(-1.0, 1.0, max(L, K))
xx, yy = np.meshgrid(dd, dd)
t1 = time()
cart.make_cart_grid(xx, yy)
t2 = time()
log.debug('make cart grid {:.6f}'.format(t2 - t1))
smap = np.isfinite(cart.eval_grid(np.zeros(cart.nk)))
scale = (1.0 / np.sum(smap))
log.debug('')
log.debug('{} modes, {} x {} grid'.format(n_alpha, L, K))
for i in range(pol.nk):
a = np.zeros(pol.nk)
a[i] = 1.0
Phi_a = cart.eval_grid(a)
for j in range(pol.nk):
b = np.zeros(pol.nk)
b[j] = 1.0
Phi_b = cart.eval_grid(b)
ip = scale * np.sum(Phi_a[smap] * Phi_b[smap])
if i == j:
eip = 1.0
else:
eip = 0.0
iperr = abs(ip - eip)
log.debug('<{:02},{:02}> = {:+e} {:+e}'.format(
i + 1, j + 1, ip, iperr))
self.assertTrue(iperr < self.max_ip_err)
def test_normalisations_real(self):
log = logging.getLogger('TestZern.test_normalisations_real')
n_alpha = 6
L, K = 400, 357
# polar grid
pol = RZern(n_alpha)
fitAlpha = FitZern(pol, L, K)
t1 = time()
pol.make_pol_grid(fitAlpha.rho_j, fitAlpha.theta_i)
t2 = time()
log.debug('make pol grid {:.6f}'.format(t2 - t1))
# cartesian grid
cart = RZern(n_alpha)
dd = np.linspace(-1.0, 1.0, max(L, K))
xx, yy = np.meshgrid(dd, dd)
t1 = time()
cart.make_cart_grid(xx, yy)
t2 = time()
log.debug('make cart grid {:.6f}'.format(t2 - t1))
smap = np.isfinite(cart.eval_grid(np.zeros(cart.nk)))
scale = (1.0/np.sum(smap))
log.debug('')
log.debug('{} modes, {} x {} grid'.format(n_alpha, L, K))
for i in range(pol.nk):
a = np.zeros(pol.nk)
a[i] = 1.0
Phi_a = cart.eval_grid(a)
for j in range(pol.nk):
b = np.zeros(pol.nk)
b[j] = 1.0
Phi_b = cart.eval_grid(b)
ip = scale*np.sum(Phi_a[smap]*Phi_b[smap])
if i == j:
eip = 1.0
else:
eip = 0.0
iperr = abs(ip - eip)
log.debug('<{:02},{:02}> = {:+e} {:+e}'.format(
i + 1, j + 1, ip, iperr))
self.assertTrue(iperr < self.max_ip_err)
def __init__(self, unparsed):
super().__init__()
args = self.do_cmdline(unparsed)
# plot objects
phaseplot = PhasePlot(n=args.n_alpha) # to plot beta and the PSF
betaplot = BetaPlot(args) # to plot the phase
# complex-valued Zernike polynomials for the GPF
ip = FitZern(CZern(args.n_beta), args.fit_L, args.fit_K)
# real-valued Zernike polynomials for the phase
phase_pol = RZern(args.n_alpha)
phase_pol.make_pol_grid(ip.rho_j, ip.theta_i) # make a polar grid
# real-valued Zernike coefficients
alpha = np.zeros(phase_pol.nk)
# set the alpha coefficients randomly
if args.random:
alpha1 = normal(size=alpha.size - 1)
alpha1 = (args.rms / norm(alpha1)) * alpha1
alpha[1:] = alpha1
del alpha1
self.rms = args.rms
self.alpha = alpha
self.phase_pol = phase_pol
self.ip = ip
self.betaplot = betaplot
self.phaseplot = phaseplot
# fit beta coefficients from alpha coefficients
self.alpha2beta()
# make gui
self.make_gui()
def __init__(self, unparsed):
super().__init__()
args = self.do_cmdline(unparsed)
# plot objects
phaseplot = PhasePlot(n=args.n_alpha) # to plot beta and the PSF
betaplot = BetaPlot(args) # to plot the phase
# complex-valued Zernike polynomials for the GPF
ip = FitZern(CZern(args.n_beta), args.fit_L, args.fit_K)
# real-valued Zernike polynomials for the phase
phase_pol = RZern(args.n_alpha)
phase_pol.make_pol_grid(ip.rho_j, ip.theta_i) # make a polar grid
# real-valued Zernike coefficients
alpha = np.zeros(phase_pol.nk)
# set the alpha coefficients randomly
if args.random:
alpha1 = normal(size=alpha.size-1)
alpha1 = (args.rms/norm(alpha1))*alpha1
alpha[1:] = alpha1
del alpha1
self.rms = args.rms
self.alpha = alpha
self.phase_pol = phase_pol
self.ip = ip
self.betaplot = betaplot
self.phaseplot = phaseplot
# fit beta coefficients from alpha coefficients
self.alpha2beta()
# make gui
self.make_gui()
help='Make a random alpha aberration.')
parser.add_argument(
'--fit-L', type=int, default=95, metavar='L',
help='Grid size for the inner products.')
parser.add_argument(
'--fit-K', type=int, default=105, metavar='K',
help='Grid size for the inner products.')
args = parser.parse_args()
# complex-valued Zernike polynomials for the GPF
ip = FitZern(CZern(args.n_beta), args.fit_L, args.fit_K)
# real-valued Zernike polynomials for the phase
phase_pol = RZern(args.n_alpha)
phase_pol.make_pol_grid(ip.rho_j, ip.theta_i) # make a polar grid
# real-valued Zernike coefficients
alpha = np.zeros(phase_pol.nk)
# nm to linear index conversion
nmlist = list(zip(phase_pol.ntab, phase_pol.mtab))
# set an alpha coefficient using the (n, m) indeces
if args.nm[0] != -1 and args.nm[0] != -1:
try:
k = nmlist.index(tuple(args.nm))
alpha[k] = args.rms
except:
print('Cannot find indeces ' + str(args.nm))
print('Possible [n, m] indeces are:')
help='Make a random alpha aberration.')
parser.add_argument(
'--fit-L', type=int, default=95, metavar='L',
help='Grid size for the inner products.')
parser.add_argument(
'--fit-K', type=int, default=105, metavar='K',
help='Grid size for the inner products.')
args = parser.parse_args()
# complex-valued Zernike polynomials for the GPF
ip = FitZern(CZern(args.n_beta), args.fit_L, args.fit_K)
# real-valued Zernike polynomials for the phase
phase_pol = RZern(args.n_alpha)
phase_pol.make_pol_grid(ip.rho_j, ip.theta_i) # make a polar grid
# real-valued Zernike coefficients
alpha = np.zeros(phase_pol.nk)
# nm to linear index conversion
nmlist = list(zip(phase_pol.ntab, phase_pol.mtab))
# set an alpha coefficient using the (n, m) indeces
if args.nm[0] != -1 and args.nm[0] != -1:
try:
k = nmlist.index(tuple(args.nm))
alpha[k] = args.rms
except BaseException:
print('Cannot find indeces ' + str(args.nm))
print('Possible [n, m] indeces are:')
class Config:
def __init__(self):
pass
def make(
self, wavelength, aperture_radius, focal_length, pixel_size,
image_width, image_height,
n_alpha, n_beta,
fit_L, fit_K,
focus_positions):
self.wavelength = wavelength
self.aperture_radius = aperture_radius
self.focal_length = focal_length
self.image_width = image_width
self.image_height = image_height
self.pixel_size = pixel_size
self.n_alpha, self.n_beta = n_alpha, n_beta
self.fit_L, self.fit_K = fit_L, fit_K
self.focus_positions = np.array(focus_positions)
fu = enz.get_field_unit(
wavelength,
aperture_radius, focal_length)
def make_space(w, p, fu):
if w % 2 == 0:
return np.linspace(-(w/2 - 0.5), w/2 - 0.5, w)*p/fu
else:
return np.linspace(-(w - 1)/2, (w - 1)/2, w)*p/fu
# image side space
xspace = make_space(image_width, pixel_size, fu)
yspace = make_space(image_height, pixel_size, fu)
self.xspace, self.yspace = xspace, yspace
# phase
self.phase_grid = RZern(n_alpha)
self.phase_fit = FitZern(self.phase_grid, self.fit_L, self.fit_K)
print('phase: n_alpha = {}, N_alpha = {}'.format(
self.n_alpha, self.phase_grid.nk))
# complex psf
self.cpsf = CPsf(n_beta)
self.gpf_fit = FitZern(self.cpsf.czern, self.fit_L, self.fit_K)
print('cpsf: n_beta = {}, N_beta = {}, N_f = {}'.format(
n_beta, self.cpsf.czern.nk, self.focus_positions.size))
# make phase polar grid
t1 = time.time()
self.phase_grid.make_pol_grid(
self.phase_fit.rho_j,
self.phase_fit.theta_i)
t2 = time.time()
print('make phase pol grid {:.6f}'.format(t2 - t1))
# make gpf polar grid (Zernike approximation)
t1 = time.time()
self.cpsf.czern.make_pol_grid(
self.phase_fit.rho_j,
self.phase_fit.theta_i)
t2 = time.time()
print('make gpf pol grid {:.6f}'.format(t2 - t1))
# make cpsf cart grid
t1 = time.time()
self.cpsf.make_cart_grid(
x_sp=xspace, y_sp=yspace, f_sp=focus_positions)
t2 = time.time()
print('make cpsf cart grid {:.6f}'.format(t2 - t1))
def save(self, filename, prepend=None, libver='latest'):
"""Save object into an HDF5 file."""
f = h5py.File(filename, 'w', libver=libver)
self.save_h5py(f, prepend=prepend)
f.close()
print('saved <{}>'.format(filename))
def save_h5py(self, f, prepend=None):
"""Dump object contents into an opened HDF5 file object."""
prefix = 'Config/'
if prepend is not None:
prefix = prepend + prefix
params = {
'chunks': True,
'shuffle': True,
'fletcher32': True,
'compression': 'gzip',
'compression_opts': 9,
}
f.create_dataset(
prefix + 'wavelength',
data=np.array([self.wavelength], dtype=np.float))
f.create_dataset(
prefix + 'aperture_radius',
data=np.array([self.aperture_radius], dtype=np.float))
f.create_dataset(
prefix + 'focal_length',
data=np.array([self.focal_length], dtype=np.float))
f.create_dataset(
prefix + 'image_width',
data=np.array([self.image_width], dtype=np.int))
f.create_dataset(
prefix + 'image_height',
data=np.array([self.image_height], dtype=np.int))
f.create_dataset(
prefix + 'pixel_size',
data=np.array([self.pixel_size], dtype=np.float))
f.create_dataset(
prefix + 'n_alpha',
data=np.array([self.n_alpha], dtype=np.int))
f.create_dataset(
prefix + 'n_beta',
data=np.array([self.n_beta], dtype=np.int))
f.create_dataset(
prefix + 'fit_L',
data=np.array([self.fit_L], dtype=np.int))
f.create_dataset(
prefix + 'fit_K',
data=np.array([self.fit_K], dtype=np.int))
params['data'] = self.focus_positions
f.create_dataset(prefix + 'focus_positions', **params)
params['data'] = self.xspace
f.create_dataset(prefix + 'xspace', **params)
params['data'] = self.yspace
f.create_dataset(prefix + 'yspace', **params)
self.phase_fit.save_h5py(f, prepend=prefix+'phase_fit/')
self.cpsf.save_h5py(f, prepend=prefix+'cpsf/')
self.gpf_fit.save_h5py(f, prepend=prefix+'gpf_fit/')
@classmethod
def load(cls, filename, prepend=None):
"""Load object from an HDF5 file."""
f = h5py.File(filename, 'r')
print('load <{}>'.format(filename))
z = cls.load_h5py(f, prepend=prepend)
f.close()
return z
@classmethod
def load_h5py(cls, f, prepend=None):
"""Load object contents from an opened HDF5 file object."""
sc = cls()
prefix = 'Config/'
if prepend is not None:
prefix = prepend + prefix
sc.wavelength = float(f[prefix + 'wavelength'].value[0])
sc.aperture_radius = float(f[prefix + 'aperture_radius'].value[0])
sc.focal_length = float(f[prefix + 'focal_length'].value[0])
sc.image_width = int(f[prefix + 'image_width'].value[0])
sc.image_height = int(f[prefix + 'image_height'].value[0])
sc.pixel_size = float(f[prefix + 'pixel_size'].value[0])
sc.n_alpha = int(f[prefix + 'n_alpha'].value[0])
sc.n_beta = int(f[prefix + 'n_beta'].value[0])
sc.fit_L = int(f[prefix + 'fit_L'].value[0])
sc.fit_K = int(f[prefix + 'fit_K'].value[0])
sc.focus_positions = f[prefix + 'focus_positions'].value
sc.xspace = f[prefix + 'xspace'].value
sc.yspace = f[prefix + 'yspace'].value
sc.phase_fit = FitZern.load_h5py(f, prepend=prefix+'phase_fit/')
sc.phase_grid = sc.phase_fit.z
sc.cpsf = CPsf.load_h5py(f, prepend=prefix+'cpsf/')
sc.gpf_fit = FitZern.load_h5py(f, prepend=prefix+'gpf_fit/')
sc.gpf_fit.z = sc.cpsf.czern
print('phase: n_alpha = {}, N_alpha = {}'.format(
sc.n_alpha, sc.phase_grid.nk))
print('cpsf: n_beta = {}, N_beta = {}, N_f = {}'.format(
sc.n_beta, sc.cpsf.czern.nk, sc.focus_positions.size))
return sc
class Config:
def __init__(self):
pass
def make(self, wavelength, aperture_radius, focal_length, pixel_size,
image_width, image_height, n_alpha, n_beta, fit_L, fit_K,
focus_positions):
self.wavelength = wavelength
self.aperture_radius = aperture_radius
self.focal_length = focal_length
self.image_width = image_width
self.image_height = image_height
self.pixel_size = pixel_size
self.n_alpha, self.n_beta = n_alpha, n_beta
self.fit_L, self.fit_K = fit_L, fit_K
self.focus_positions = np.array(focus_positions)
fu = enz.get_field_unit(wavelength, aperture_radius, focal_length)
def make_space(w, p, fu):
if w % 2 == 0:
return np.linspace(-(w / 2 - 0.5), w / 2 - 0.5, w) * p / fu
else:
return np.linspace(-(w - 1) / 2, (w - 1) / 2, w) * p / fu
# image side space
xspace = make_space(image_width, pixel_size, fu)
yspace = make_space(image_height, pixel_size, fu)
self.xspace, self.yspace = xspace, yspace
# phase
self.phase_grid = RZern(n_alpha)
self.phase_fit = FitZern(self.phase_grid, self.fit_L, self.fit_K)
print('phase: n_alpha = {}, N_alpha = {}'.format(
self.n_alpha, self.phase_grid.nk))
# complex psf
self.cpsf = CPsf(n_beta)
self.gpf_fit = FitZern(self.cpsf.czern, self.fit_L, self.fit_K)
print('cpsf: n_beta = {}, N_beta = {}, N_f = {}'.format(
n_beta, self.cpsf.czern.nk, self.focus_positions.size))
# make phase polar grid
t1 = time.time()
self.phase_grid.make_pol_grid(self.phase_fit.rho_j,
self.phase_fit.theta_i)
t2 = time.time()
print('make phase pol grid {:.6f}'.format(t2 - t1))
# make gpf polar grid (Zernike approximation)
t1 = time.time()
self.cpsf.czern.make_pol_grid(self.phase_fit.rho_j,
self.phase_fit.theta_i)
t2 = time.time()
print('make gpf pol grid {:.6f}'.format(t2 - t1))
# make cpsf cart grid
t1 = time.time()
self.cpsf.make_cart_grid(x_sp=xspace,
y_sp=yspace,
f_sp=focus_positions)
t2 = time.time()
print('make cpsf cart grid {:.6f}'.format(t2 - t1))
def save(self, filename, prepend=None, libver='latest'):
"""Save object into an HDF5 file."""
f = h5py.File(filename, 'w', libver=libver)
self.save_h5py(f, prepend=prepend)
f.close()
print('saved <{}>'.format(filename))
def save_h5py(self, f, prepend=None):
"""Dump object contents into an opened HDF5 file object."""
prefix = 'Config/'
if prepend is not None:
prefix = prepend + prefix
params = {
'chunks': True,
'shuffle': True,
'fletcher32': True,
'compression': 'gzip',
'compression_opts': 9,
}
f.create_dataset(prefix + 'wavelength',
data=np.array([self.wavelength], dtype=np.float))
f.create_dataset(prefix + 'aperture_radius',
data=np.array([self.aperture_radius], dtype=np.float))
f.create_dataset(prefix + 'focal_length',
data=np.array([self.focal_length], dtype=np.float))
f.create_dataset(prefix + 'image_width',
data=np.array([self.image_width], dtype=np.int))
f.create_dataset(prefix + 'image_height',
data=np.array([self.image_height], dtype=np.int))
f.create_dataset(prefix + 'pixel_size',
data=np.array([self.pixel_size], dtype=np.float))
f.create_dataset(prefix + 'n_alpha',
data=np.array([self.n_alpha], dtype=np.int))
f.create_dataset(prefix + 'n_beta',
data=np.array([self.n_beta], dtype=np.int))
f.create_dataset(prefix + 'fit_L',
data=np.array([self.fit_L], dtype=np.int))
f.create_dataset(prefix + 'fit_K',
data=np.array([self.fit_K], dtype=np.int))
params['data'] = self.focus_positions
f.create_dataset(prefix + 'focus_positions', **params)
params['data'] = self.xspace
f.create_dataset(prefix + 'xspace', **params)
params['data'] = self.yspace
f.create_dataset(prefix + 'yspace', **params)
self.phase_fit.save_h5py(f, prepend=prefix + 'phase_fit/')
self.cpsf.save_h5py(f, prepend=prefix + 'cpsf/')
self.gpf_fit.save_h5py(f, prepend=prefix + 'gpf_fit/')
@classmethod
def load(cls, filename, prepend=None):
"""Load object from an HDF5 file."""
f = h5py.File(filename, 'r')
print('load <{}>'.format(filename))
z = cls.load_h5py(f, prepend=prepend)
f.close()
return z
@classmethod
def load_h5py(cls, f, prepend=None):
"""Load object contents from an opened HDF5 file object."""
sc = cls()
prefix = 'Config/'
if prepend is not None:
prefix = prepend + prefix
sc.wavelength = float(f[prefix + 'wavelength'].value[0])
sc.aperture_radius = float(f[prefix + 'aperture_radius'].value[0])
sc.focal_length = float(f[prefix + 'focal_length'].value[0])
sc.image_width = int(f[prefix + 'image_width'].value[0])
sc.image_height = int(f[prefix + 'image_height'].value[0])
sc.pixel_size = float(f[prefix + 'pixel_size'].value[0])
sc.n_alpha = int(f[prefix + 'n_alpha'].value[0])
sc.n_beta = int(f[prefix + 'n_beta'].value[0])
sc.fit_L = int(f[prefix + 'fit_L'].value[0])
sc.fit_K = int(f[prefix + 'fit_K'].value[0])
sc.focus_positions = f[prefix + 'focus_positions'].value
sc.xspace = f[prefix + 'xspace'].value
sc.yspace = f[prefix + 'yspace'].value
sc.phase_fit = FitZern.load_h5py(f, prepend=prefix + 'phase_fit/')
sc.phase_grid = sc.phase_fit.z
sc.cpsf = CPsf.load_h5py(f, prepend=prefix + 'cpsf/')
sc.gpf_fit = FitZern.load_h5py(f, prepend=prefix + 'gpf_fit/')
sc.gpf_fit.z = sc.cpsf.czern
print('phase: n_alpha = {}, N_alpha = {}'.format(
sc.n_alpha, sc.phase_grid.nk))
print('cpsf: n_beta = {}, N_beta = {}, N_f = {}'.format(
sc.n_beta, sc.cpsf.czern.nk, sc.focus_positions.size))
return sc
