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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 | |