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"""Implementation of various restoration functions."""
import numpy as np
from scipy.signal import convolve
from .._shared.utils import _supported_float_type
from . import uft
def wiener(image, psf, balance, reg=None, is_real=True, clip=True):
r"""Restore image using Wiener–Hunt deconvolution.
Wiener–Hunt deconvolution is a restoration method which follows a Bayesian
approach [1]_.
Parameters
----------
image : (N1, N2, ..., ND) ndarray
Degraded image.
psf : ndarray
Point spread function (PSF). Assumed to be the impulse
response (input image space) if the data type is real, or the
transfer function (Fourier or frequency space) if the data type is
complex. There is no constraint on the shape of the impulse
response. The transfer function though must be of shape
`(N1, N2, ..., ND)` if `is_real is True`,
`(N1, N2, ..., ND // 2 + 1)` otherwise (see :func:`numpy.fft.rfftn`).
balance : float
Regularization parameter. Denoted by :math:`\lambda`: in the Notes
section below, its value lets you balance data adequacy (improving
frequency restoration) with respect to prior adequacy (reducing
frequency restoration and avoiding noise artifacts). A larger value for
this parameter favors the regularization/prior.
reg : ndarray, optional
Regularization operator. Laplacian by default. It can
be an impulse response or a transfer function, as for the PSF.
Shape constraints are the same as for `psf`.
is_real : bool, optional
True by default. Specify if `psf` and `reg` are provided over just half
the frequency space (thanks to the redundancy of the Fourier transform
for real signals). Applies only if `psf` and/or `reg` are
provided as transfer functions.
See ``uft`` module and :func:`np.fft.rfftn`.
clip : bool, optional
True by default. If True, pixel values of the deconvolved image (which
is the return value) above 1 (resp. below -1) are clipped to 1 (resp.
to -1). Be careful to set `clip=False` if you do not want this clipping
and/or if your data range is not [0, 1] or [-1,1].
Returns
-------
im_deconv : (N1, N2, ..., ND) ndarray
The deconvolved image.
Examples
--------
>>> import skimage as ski
>>> import scipy as sp
>>> img = ski.color.rgb2gray(ski.data.astronaut())
>>> psf = np.ones((5, 5)) / 25
>>> img = sp.signal.convolve2d(img, psf, 'same')
>>> rng = np.random.default_rng()
>>> img += 0.1 * img.std() * rng.standard_normal(img.shape)
>>> deconvolved_img = ski.restoration.wiener(img, psf, 0.1)
Notes
-----
This function applies the Wiener filter to a noisy (degraded)
image by an impulse response (or PSF). If the data model is
.. math:: y = Hx + n
where :math:`n` is noise, :math:`H` the PSF, and :math:`x` the
unknown original image, the Wiener filter is
.. math::
\hat x = F^\dagger \left( |\Lambda_H|^2 + \lambda |\Lambda_D|^2 \right)^{-1}
\Lambda_H^\dagger F y
where :math:`F` and :math:`F^\dagger` are the Fourier and inverse
Fourier transforms respectively, :math:`\Lambda_H` the transfer
function (or the Fourier transform of the PSF, see [2]_),
and :math:`\Lambda_D` the regularization operator, which is a filter
penalizing the restored image frequencies (Laplacian by default, that is,
penalization of high frequencies). The parameter :math:`\lambda` tunes the
balance between data (which tends to increase high frequencies, even those
coming from noise) and regularization/prior (which tends to avoid noise
artifacts).
These methods are then specific to a prior model. Consequently,
the application or the true image nature must correspond to the
prior model. By default, the prior model (Laplacian) introduces
image smoothness or pixel correlation. It can also be interpreted
as high-frequency penalization to compensate for the instability of
the solution with respect to the data (sometimes called noise
amplification or "explosive" solution).
Finally, the use of Fourier space implies a circulant property of
:math:`H`, see [2]_.
References
----------
.. [1] François Orieux, Jean-François Giovannelli, and Thomas
Rodet, "Bayesian estimation of regularization and point
spread function parameters for Wiener–Hunt deconvolution",
J. Opt. Soc. Am. A 27, 1593–1607 (2010)
https://www.osapublishing.org/josaa/abstract.cfm?URI=josaa-27-7-1593
https://hal.archives-ouvertes.fr/hal-00674508
.. [2] B. R. Hunt "A matrix theory proof of the discrete
convolution theorem", IEEE Trans. on Audio and
Electroacoustics, vol. au-19, no. 4, pp. 285–288, dec. 1971
"""
if reg is None:
reg, _ = uft.laplacian(image.ndim, image.shape, is_real=is_real)
if not np.iscomplexobj(reg):
reg = uft.ir2tf(reg, image.shape, is_real=is_real)
float_type = _supported_float_type(image.dtype)
image = image.astype(float_type, copy=False)
psf = psf.real.astype(float_type, copy=False)
reg = reg.real.astype(float_type, copy=False)
if psf.shape != reg.shape:
trans_func = uft.ir2tf(psf, image.shape, is_real=is_real)
else:
trans_func = psf
wiener_filter = np.conj(trans_func) / (
np.abs(trans_func) ** 2 + balance * np.abs(reg) ** 2
)
if is_real:
deconv = uft.uirfftn(wiener_filter * uft.urfftn(image), shape=image.shape)
else:
deconv = uft.uifftn(wiener_filter * uft.ufftn(image))
if clip:
deconv[deconv > 1] = 1
deconv[deconv < -1] = -1
return deconv
def unsupervised_wiener(
image, psf, reg=None, user_params=None, is_real=True, clip=True, *, rng=None
):
"""Unsupervised Wiener-Hunt deconvolution.
Return the deconvolution with a Wiener-Hunt approach, where the
hyperparameters are automatically estimated. The algorithm is a
stochastic iterative process (Gibbs sampler) described in the
reference below. See also ``wiener`` function.
Parameters
----------
image : (M, N) ndarray
The input degraded image.
psf : ndarray
The impulse response (input image's space) or the transfer
function (Fourier space). Both are accepted. The transfer
function is automatically recognized as being complex
(``np.iscomplexobj(psf)``).
reg : ndarray, optional
The regularisation operator. The Laplacian by default. It can
be an impulse response or a transfer function, as for the psf.
user_params : dict, optional
Dictionary of parameters for the Gibbs sampler. Accepted keys are:
threshold : float
The stopping criterion: the norm of the difference between to
successive approximated solution (empirical mean of object
samples, see Notes section). 1e-4 by default.
burnin : int
The number of sample to ignore to start computation of the
mean. 15 by default.
min_num_iter : int
The minimum number of iterations. 30 by default.
max_num_iter : int
The maximum number of iterations if ``threshold`` is not
satisfied. 200 by default.
callback : callable
A user provided callable to which is passed, if the function
exists, the current image sample for whatever purpose. The user
can store the sample, or compute other moments than the
mean. It has no influence on the algorithm execution and is
only for inspection.
clip : bool, optional
True by default. If true, pixel values of the result above 1 or
under -1 are thresholded for skimage pipeline compatibility.
rng : {`numpy.random.Generator`, int}, optional
Pseudo-random number generator.
By default, a PCG64 generator is used (see :func:`numpy.random.default_rng`).
If `rng` is an int, it is used to seed the generator.
.. versionadded:: 0.19
Returns
-------
x_postmean : (M, N) ndarray
The deconvolved image (the posterior mean).
chains : dict
The keys ``noise`` and ``prior`` contain the chain list of
noise and prior precision respectively.
Examples
--------
>>> from skimage import color, data, restoration
>>> img = color.rgb2gray(data.astronaut())
>>> from scipy.signal import convolve2d
>>> psf = np.ones((5, 5)) / 25
>>> img = convolve2d(img, psf, 'same')
>>> rng = np.random.default_rng()
>>> img += 0.1 * img.std() * rng.standard_normal(img.shape)
>>> deconvolved_img = restoration.unsupervised_wiener(img, psf)
Notes
-----
The estimated image is design as the posterior mean of a
probability law (from a Bayesian analysis). The mean is defined as
a sum over all the possible images weighted by their respective
probability. Given the size of the problem, the exact sum is not
tractable. This algorithm use of MCMC to draw image under the
posterior law. The practical idea is to only draw highly probable
images since they have the biggest contribution to the mean. At the
opposite, the less probable images are drawn less often since
their contribution is low. Finally, the empirical mean of these
samples give us an estimation of the mean, and an exact
computation with an infinite sample set.
References
----------
.. [1] François Orieux, Jean-François Giovannelli, and Thomas
Rodet, "Bayesian estimation of regularization and point
spread function parameters for Wiener-Hunt deconvolution",
J. Opt. Soc. Am. A 27, 1593-1607 (2010)
https://www.osapublishing.org/josaa/abstract.cfm?URI=josaa-27-7-1593
https://hal.archives-ouvertes.fr/hal-00674508
"""
params = {
'threshold': 1e-4,
'max_num_iter': 200,
'min_num_iter': 30,
'burnin': 15,
'callback': None,
}
params.update(user_params or {})
if reg is None:
reg, _ = uft.laplacian(image.ndim, image.shape, is_real=is_real)
if not np.iscomplexobj(reg):
reg = uft.ir2tf(reg, image.shape, is_real=is_real)
float_type = _supported_float_type(image.dtype)
image = image.astype(float_type, copy=False)
psf = psf.real.astype(float_type, copy=False)
reg = reg.real.astype(float_type, copy=False)
if psf.shape != reg.shape:
trans_fct = uft.ir2tf(psf, image.shape, is_real=is_real)
else:
trans_fct = psf
# The mean of the object
x_postmean = np.zeros(trans_fct.shape, dtype=float_type)
# The previous computed mean in the iterative loop
prev_x_postmean = np.zeros(trans_fct.shape, dtype=float_type)
# Difference between two successive mean
delta = np.nan
# Initial state of the chain
gn_chain, gx_chain = [1], [1]
# The correlation of the object in Fourier space (if size is big,
# this can reduce computation time in the loop)
areg2 = np.abs(reg) ** 2
atf2 = np.abs(trans_fct) ** 2
# The Fourier transform may change the image.size attribute, so we
# store it.
if is_real:
data_spectrum = uft.urfft2(image)
else:
data_spectrum = uft.ufft2(image)
rng = np.random.default_rng(rng)
# Gibbs sampling
for iteration in range(params['max_num_iter']):
# Sample of Eq. 27 p(circX^k | gn^k-1, gx^k-1, y).
# weighting (correlation in direct space)
precision = gn_chain[-1] * atf2 + gx_chain[-1] * areg2 # Eq. 29
# Note: Use astype instead of dtype argument to standard_normal to get
# similar random values across precisions, as needed for
# reference data used by test_unsupervised_wiener.
_rand1 = rng.standard_normal(data_spectrum.shape)
_rand1 = _rand1.astype(float_type, copy=False)
_rand2 = rng.standard_normal(data_spectrum.shape)
_rand2 = _rand2.astype(float_type, copy=False)
excursion = np.sqrt(0.5 / precision) * (_rand1 + 1j * _rand2)
# mean Eq. 30 (RLS for fixed gn, gamma0 and gamma1 ...)
wiener_filter = gn_chain[-1] * np.conj(trans_fct) / precision
# sample of X in Fourier space
x_sample = wiener_filter * data_spectrum + excursion
if params['callback']:
params['callback'](x_sample)
# sample of Eq. 31 p(gn | x^k, gx^k, y)
gn_chain.append(
rng.gamma(
image.size / 2,
2 / uft.image_quad_norm(data_spectrum - x_sample * trans_fct),
)
)
# sample of Eq. 31 p(gx | x^k, gn^k-1, y)
gx_chain.append(
rng.gamma((image.size - 1) / 2, 2 / uft.image_quad_norm(x_sample * reg))
)
# current empirical average
if iteration > params['burnin']:
x_postmean = prev_x_postmean + x_sample
if iteration > (params['burnin'] + 1):
current = x_postmean / (iteration - params['burnin'])
previous = prev_x_postmean / (iteration - params['burnin'] - 1)
delta = (
np.sum(np.abs(current - previous))
/ np.sum(np.abs(x_postmean))
/ (iteration - params['burnin'])
)
prev_x_postmean = x_postmean
# stop of the algorithm
if (iteration > params['min_num_iter']) and (delta < params['threshold']):
break
# Empirical average \approx POSTMEAN Eq. 44
x_postmean = x_postmean / (iteration - params['burnin'])
if is_real:
x_postmean = uft.uirfft2(x_postmean, shape=image.shape)
else:
x_postmean = uft.uifft2(x_postmean)
if clip:
x_postmean[x_postmean > 1] = 1
x_postmean[x_postmean < -1] = -1
return (x_postmean, {'noise': gn_chain, 'prior': gx_chain})
def richardson_lucy(image, psf, num_iter=50, clip=True, filter_epsilon=None):
"""Richardson-Lucy deconvolution.
Parameters
----------
image : ([P, ]M, N) ndarray
Input degraded image (can be n-dimensional). If you keep the
default `clip=True` parameter, you may want to normalize
the image so that its values fall in the [-1, 1] interval to avoid
information loss.
psf : ndarray
The point spread function.
num_iter : int, optional
Number of iterations. This parameter plays the role of
regularisation.
clip : bool, optional
True by default. If true, pixel value of the result above 1 or
under -1 are thresholded for skimage pipeline compatibility.
filter_epsilon : float, optional
Value below which intermediate results become 0 to avoid division
by small numbers.
Returns
-------
im_deconv : ndarray
The deconvolved image.
Examples
--------
>>> from skimage import img_as_float, data, restoration
>>> camera = img_as_float(data.camera())
>>> from scipy.signal import convolve2d
>>> psf = np.ones((5, 5)) / 25
>>> camera = convolve2d(camera, psf, 'same')
>>> rng = np.random.default_rng()
>>> camera += 0.1 * camera.std() * rng.standard_normal(camera.shape)
>>> deconvolved = restoration.richardson_lucy(camera, psf, 5)
References
----------
.. [1] https://en.wikipedia.org/wiki/Richardson%E2%80%93Lucy_deconvolution
"""
float_type = _supported_float_type(image.dtype)
image = image.astype(float_type, copy=False)
psf = psf.astype(float_type, copy=False)
im_deconv = np.full(image.shape, 0.5, dtype=float_type)
psf_mirror = np.flip(psf)
# Small regularization parameter used to avoid 0 divisions
eps = 1e-12
for _ in range(num_iter):
conv = convolve(im_deconv, psf, mode='same') + eps
if filter_epsilon:
relative_blur = np.where(conv < filter_epsilon, 0, image / conv)
else:
relative_blur = image / conv
im_deconv *= convolve(relative_blur, psf_mirror, mode='same')
if clip:
im_deconv[im_deconv > 1] = 1
im_deconv[im_deconv < -1] = -1
return im_deconv