def gaussian(sigma=0.5, samples=128):
"""Generate a gaussian mask with a given sigma.
Parameters
----------
sigma : `float`
width parameter of the gaussian, expressed in samples of the output array
samples : `int`
number of samples in square array
Returns
-------
`numpy.ndarray`
mask with gaussian shape
"""
s = sigma
x = m.arange(0, samples, 1, dtype=config.precision)
y = x[:, m.newaxis]
# // is floor division in python
x0 = y0 = samples // 2
return m.exp(-4 * m.log(2) * ((x - x0)**2 + (y - y0)**2) /
(s * samples)**2)
def resample_2d_complex(array, sample_pts, query_pts):
'''Resamples a 2D complex array.
Works by interpolating the magnitude and phase independently and merging the results into a complex value.
Parameters
----------
array : `numpy.ndarray`
complex 2D array
sample_pts : `tuple`
pair of `numpy.ndarray` objects that contain the x and y sample locations,
each array should be 1D
query_pts : `tuple`
points to interpolate onto, also 1D for each array
Returns
-------
`numpy.ndarray`
array resampled onto query_pts via bivariate spline
'''
xq, yq = m.meshgrid(*query_pts)
mag = abs(array)
phase = m.angle(array)
magfunc = interpolate.RegularGridInterpolator(sample_pts, mag)
phasefunc = interpolate.RegularGridInterpolator(sample_pts, phase)
interp_mag = magfunc((yq, xq))
interp_phase = phasefunc((yq, xq))
return interp_mag * m.exp(1j * interp_phase)
def longexposure_otf(nu, Cn, z, f, lambdabar, h_z_by_r=2.91):
"""Compute the long exposure OTF for given parameters.
Parameters
----------
nu : `numpy.ndarray`
spatial frequencies, cy/mm
Cn: `float`
atmospheric structure constant of refractive index, ranges ~ 10^-13 - 10^-17
z : `float`
propagation distance through atmosphere, m
f : `float`
effective focal length of the optical system, mm
lambdabar : `float`
mean wavelength, microns
h_z_by_r : `float`, optional
constant for h[z/r] -- see Eq. 8.5-37 & 8.5-38 in Statistical Optics, J. Goodman, 2nd ed.
Returns
-------
`numpy.ndarray`
the OTF
"""
# homogenize units
nu = nu / 1e3
f = f / 1e3
lambdabar = lambdabar / 1e6
power = 5 / 3
const1 = -m.pi**2 * 2 * h_z_by_r * Cn**2
const2 = z * f**power / (lambdabar**3)
nupow = nu**power
const = const1 * const2
return m.exp(const * nupow)
def resample_2d_complex(array, sample_pts, query_pts):
''' Resamples a 2D complex array by interpolating the magnitude and phase
independently and merging the results into a complex value.
Args:
array (numpy.ndarray): complex 2D array.
sample_pts (tuple): pair of numpy.ndarray objects that contain the x and y sample locations,
each array should be 1D.
query_pts (tuple): points to interpolate onto, also 1D for each array.
Returns:
numpy.ndarray array resampled onto query_pts via bivariate spline
'''
xq, yq = np.meshgrid(*query_pts)
mag = abs(array)
phase = np.angle(array)
magfunc = interpolate.RegularGridInterpolator(sample_pts, mag)
phasefunc = interpolate.RegularGridInterpolator(sample_pts, phase)
interp_mag = magfunc((yq, xq))
interp_phase = phasefunc((yq, xq))
return interp_mag * exp(1j * interp_phase)
def matrix_dft(f, alpha, npix, shift=None, unitary=False):
'''
A technique shamelessly stolen from Andy Kee @ NASA JPL
Is it magic or math?
'''
if np.isscalar(alpha):
ax = ay = alpha
else:
ax = ay = np.asarray(alpha)
f = np.asarray(f)
m, n = f.shape
if np.isscalar(npix):
M = N = npix
else:
M = N = np.asarray(npix)
if shift is None:
sx = sy = 0
else:
sx = sy = np.asarray(shift)
# Y and X are (r,c) coordinates in the (m x n) input plane, f
# V and U are (r,c) coordinates in the (M x N) output plane, F
X = np.arange(n) - floor(n / 2) - sx
Y = np.arange(m) - floor(m / 2) - sy
U = np.arange(N) - floor(N / 2) - sx
V = np.arange(M) - floor(M / 2) - sy
E1 = exp(1j * -2 * np.pi * (ay / m) * np.outer(Y, V).T)
E2 = exp(1j * -2 * np.pi * (ax / m) * np.outer(X, U))
F = E1.dot(f).dot(E2)
if unitary is True:
norm_coef = sqrt((ay * ax) / (m * n * M * N))
return F * norm_coef
else:
return F
def fcn(self):
"""Complex wavefunction associated with the pupil."""
phase = self.change_phase_unit(to='waves', inplace=False)
fcn = m.exp(1j * 2 * m.pi *
phase) # phase implicitly in units of waves, no 2pi/l
# guard against nans in phase
fcn[m.isnan(phase)] = 0
if self.mask_target in ('fcn', 'both'):
fcn *= self._mask
return fcn
def blackbody_spectrum(temperature, wavelengths):
''' Computes the spectral power distribution of a black body at a given
temperature.
Args:
temperature (`float`): body temp, in Kelvin.
wavelengths (`numpy.ndarray`): array of wavelengths, in nanometers.
Returns:
numpy.ndarray: spectral power distribution in units of W/m^2/nm
'''
wavelengths = wavelengths.astype(config.precision) / 1e9
return (2 * h * c ** 2) / (wavelengths ** 5) * \
1 / (exp((h * c) / (wavelengths * k * temperature) - 1))
def _phase_to_wavefunction(self):
"""Compute the wavefunction from the phase.
Returns
-------
`Pupil`
this pupil instance
"""
phase = self.change_phase_unit(to='waves', inplace=False)
self.fcn = m.exp(1j * 2 * m.pi *
phase) # phase implicitly in units of waves, no 2pi/l
# guard against nans in phase
self.fcn[m.isnan(phase)] = 0
return self
def gaussian(sigma=0.5, samples=128):
''' Generates a gaussian mask with a given sigma
Args:
sigma (`float`): width parameter of the gaussian, expressed in radii of
the output array.
samples (`int`): number of samples in square array.
Returns:
`numpy.ndarray`: mask with gaussian shape.
'''
s = sigma
x = np.arange(0, samples, 1, float)
y = x[:, np.newaxis]
# // is floor division in python
x0 = y0 = samples // 2
return exp(-4 * log(2) * ((x - x0**2) + (y - y0)**2) / (s * samples)**2)
def merge_pupils(pupil1, pupil2):
'''Merges the phase from two pupils and returns a new :class:`Pupil` instance
Args:
pupil1 (:class:`Pupil`): first pupil
pupil2 (:class:`Pupil`): second pupil
Returns
:class:`Pupil`: New pupil with merged phase
'''
if pupil1.sample_spacing != pupil2.sample_spacing or pupil1.samples != pupil2.samples:
raise ValueError('Pupils must be identically sampled')
# create a new pupil and copy Pupil1's dictionary into it
retpupil = pupil1.clone()
retpupil.phase = pupil1.phase + pupil2.phase
retpupil.fcn = exp(1j * 2 * pi / retpupil.wavelength * retpupil.phase)
retpupil.clip()
return retpupil
def total_integrated_scatter(self, wavelength, incident_angle=0):
"""Calculate the total integrated scatter (TIS) for an angle or angles.
Parameters
----------
wavelength : `float`
wavelength of light in microns.
incident_angle : `float` or `numpy.ndarray`
incident angle(s) of light.
Returns
-------
`float` or `numpy.ndarray`
TIS value.
"""
if self.spatial_unit != 'μm':
raise ValueError('Use microns for spatial unit when evaluating TIS.')
upper_limit = 1 / wavelength
kernel = 4 * m.pi * m.cos(m.radians(incident_angle))
kernel *= self.bandlimited_rms(upper_limit, None) / wavelength
return 1 - m.exp(-kernel**2)
def synthesize_surface_from_psd(psd, nu_x, nu_y):
"""Synthesize a surface height map from PSD data.
Parameters
----------
psd : `numpy.ndarray`
PSD data, units nm²/(cy/mm)²
nu_x : `numpy.ndarray`
x spatial frequency, cy/mm
nu_y : `numpy.ndarray`
y spatial frequency, cy_mm
"""
# generate a random phase to be matched to the PSD
randnums = m.rand(*psd.shape)
randfft = m.fft2(randnums)
phase = m.angle(randfft)
# calculate the output window
# the 0th element of nu_y has the greatest frequency in magnitude because of
# the convention to put the nyquist sample at -fs instead of +fs for even-size arrays
fs = -2 * nu_y[0]
dx = dy = 1 / fs
ny, nx = psd.shape
x, y = m.arange(nx) * dx, m.arange(ny) * dy
# calculate the area of the output window, "S2" in GH_FFT notation
A = x[-1] * y[-1]
# use ifft to compute the PSD
signal = m.exp(1j * phase) * m.sqrt(A * psd)
coef = 1 / dx / dy
out = m.ifftshift(m.ifft2(m.fftshift(signal))) * coef
out = out.real
return x, y, out
def _phase_to_wavefunction(self):
''' Computes the wavefunction from the phase
'''
self.fcn = exp(1j * 2 * pi / self.wavelength * self.phase)
return self
