def get_linear_n_regularization_operator(self,
gradient_formulation,
wavelet_name,
dimension=2,
nb_scale=3,
n_coils=1,
n_jobs=1,
verbose=0):
# A helper function to obtain linear and regularization operator
try:
linear_op = WaveletN(
nb_scale=nb_scale,
wavelet_name=wavelet_name,
dim=dimension,
n_coils=n_coils,
n_jobs=n_jobs,
verbose=verbose,
)
except ValueError:
# TODO this is a hack and we need to have a separate WaveletUD2.
# For Undecimated wavelets, the wavelet_name is wavelet_id
linear_op = WaveletUD2(
wavelet_id=wavelet_name,
nb_scale=nb_scale,
n_coils=n_coils,
n_jobs=n_jobs,
verbose=verbose,
)
if gradient_formulation == 'synthesis':
regularizer_op = SparseThreshold(Identity(), 0, thresh_type="soft")
elif gradient_formulation == "analysis":
regularizer_op = SparseThreshold(linear_op, 0, thresh_type="soft")
return linear_op, regularizer_op
class simplex_threshold(object):
""" Simplex Threshold proximity operator
This class stacks the proximity operators Simplex and Threshold
Calls:
* :func:`proxs.Simplex`
"""
def __init__(self,linop, weights,mass=None,pos_en=False):
self.linop = linop
self.weights = weights
self.thresh = SparseThreshold(self.linop, self.weights)
self.simplex = Simplex(mass=mass,pos_en=pos_en)
def update_weights(self, weights):
"""Update weights
This method update the values of the weights
Parameters
----------
weights : np.ndarray
Input array of weights
"""
self.weights = weights
self.thresh = SparseThreshold(self.linop, weights)
def op(self, data, extra_factor=1.0):
return np.array([self.simplex.op(data[0]),self.thresh.op(data[1],extra_factor=extra_factor)])
def set_objective(self, X, y, lmbd):
self.X, self.y, self.lmbd = X, y, lmbd
n_features = self.X.shape[1]
if self.restart_strategy == 'greedy':
min_beta = 1.0
s_greedy = 1.1
p_lazy = 1.0
q_lazy = 1.0
else:
min_beta = None
s_greedy = None
p_lazy = 1 / 30
q_lazy = 1 / 10
self.fb = ForwardBackward(
x=np.zeros(n_features), # this is the coefficient w
grad=GradBasic(
input_data=y,
op=lambda w: self.X@w,
trans_op=lambda res: self.X.T@res,
),
prox=SparseThreshold(Identity(), lmbd),
beta_param=1.0,
min_beta=min_beta,
metric_call_period=None,
restart_strategy=self.restart_strategy,
xi_restart=0.96,
s_greedy=s_greedy,
p_lazy=p_lazy,
q_lazy=q_lazy,
auto_iterate=False,
progress=False,
cost=None,
)
def update_weights(self, weights):
"""Update weights
This method update the values of the weights
Parameters
----------
weights : np.ndarray
Input array of weights
"""
self.weights = weights
self.thresh = SparseThreshold(self.linop, weights)
def reco_wav(kspace,
gradient_op,
mu=1 * 1e-8,
max_iter=10,
nb_scales=4,
wavelet_name='db4'):
# for now this is only working with my fork of pysap-fastMRI
# I will get it changed soon so that we don't need to ask for a specific
# pysap-mri install
from ..wavelets import WaveletDecimated
from mri.numerics.reconstruct import sparse_rec_fista
linear_op = WaveletDecimated(
nb_scale=nb_scales,
wavelet_name=wavelet_name,
padding='periodization',
)
prox_op = LinearCompositionProx(
linear_op=linear_op,
prox_op=SparseThreshold(Identity(), None, thresh_type="soft"),
)
gradient_op.obs_data = kspace
cost_op = None
x_final, _, _, _ = sparse_rec_fista(
gradient_op=gradient_op,
linear_op=Identity(),
prox_op=prox_op,
cost_op=cost_op,
xi_restart=0.96,
s_greedy=1.1,
mu=mu,
restart_strategy='greedy',
pov='analysis',
max_nb_of_iter=max_iter,
metrics=None,
metric_call_period=1,
verbose=0,
progress=False,
)
x_final = np.abs(x_final)
x_final = crop_center(x_final, 320)
return x_final
def set_objective(self, X, y, lmbd):
self.X, self.y, self.lmbd = X, y, lmbd
n_features = self.X.shape[1]
sigma_bar = 0.96
var_init = np.zeros(n_features)
self.pogm = POGM(
x=var_init, # this is the coefficient w
u=var_init,
y=var_init,
z=var_init,
grad=GradBasic(
op=lambda w: self.X @ w,
trans_op=lambda res: self.X.T @ res,
data=y,
),
prox=SparseThreshold(Identity(), lmbd),
beta_param=1.0,
metric_call_period=None,
sigma_bar=sigma_bar,
auto_iterate=False,
progress=False,
cost=None,
)
def generate_operators(data,
wavelet_name,
samples,
nb_scales=4,
non_cartesian=False,
uniform_data_shape=None,
gradient_space="analysis"):
""" Function that ease the creation of a set of common operators.
.. note:: At the moment, supports only 2D data.
Parameters
----------
data: ndarray
the data to reconstruct: observation are expected in Fourier space.
wavelet_name: str
the wavelet name to be used during the decomposition.
samples: np.ndarray
the mask samples in the Fourier domain.
nb_scales: int, default 4
the number of scales in the wavelet decomposition.
non_cartesian: bool (optional, default False)
if set, use the nfftw rather than the fftw. Expect an 1D input dataset.
uniform_data_shape: uplet (optional, default None)
the shape of the matrix containing the uniform data. Only required
for non-cartesian reconstructions.
gradient_space: str (optional, default 'analysis')
the space where the gradient operator is defined: 'analysis' or
'synthesis'
Returns
-------
gradient_op: instance of class GradBase
the gradient operator.
linear_op: instance of LinearBase
the linear operator: seek the sparsity, ie. a wavelet transform.
prox_op: instance of ProximityParent
the proximal operator.
cost_op: instance of costObj
the cost function used to check for convergence during the
optimization.
"""
# Local imports
from mri.numerics.cost import DualGapCost
from mri.numerics.linear import Wavelet2
from mri.numerics.fourier import FFT2
from mri.numerics.fourier import NFFT
from mri.numerics.gradient import GradAnalysis2
from mri.numerics.gradient import GradSynthesis2
from modopt.opt.proximity import SparseThreshold
# Check input parameters
if gradient_space not in ("analysis", "synthesis"):
raise ValueError(
"Unsupported gradient space '{0}'.".format(gradient_space))
if non_cartesian and data.ndim != 1:
raise ValueError("Expect 1D data with the non-cartesian option.")
elif non_cartesian and uniform_data_shape is None:
raise ValueError("Need to set the 'uniform_data_shape' parameter with "
"the non-cartesian option.")
elif not non_cartesian and data.ndim != 2:
raise ValueError("At the moment, this functuion only supports 2D "
"data.")
# Define the gradient/linear/fourier operators
linear_op = Wavelet2(nb_scale=nb_scales, wavelet_name=wavelet_name)
if non_cartesian:
fourier_op = NFFT(samples=samples, shape=uniform_data_shape)
else:
fourier_op = FFT2(samples=samples, shape=data.shape)
if gradient_space == "synthesis":
gradient_op = GradSynthesis2(data=data,
linear_op=linear_op,
fourier_op=fourier_op)
else:
gradient_op = GradAnalysis2(data=data, fourier_op=fourier_op)
# Define the proximity dual/primal operator
prox_op = SparseThreshold(linear_op, None, thresh_type="soft")
# Define the cost function
if gradient_space == "synthesis":
cost_op = None
else:
cost_op = DualGapCost(linear_op=linear_op,
initial_cost=1e6,
tolerance=1e-4,
cost_interval=1,
test_range=4,
verbose=0,
plot_output=None)
return gradient_op, linear_op, prox_op, cost_op
#############################################################################
# FISTA optimization
# ------------------
#
# We now want to refine the zero order solution using a FISTA optimization.
# The cost function is set to Proximity Cost + Gradient Cost
# Setup the operators
linear_op = WaveletN(
wavelet_name="sym8",
nb_scales=4,
dim=3,
padding_mode="periodization",
)
regularizer_op = SparseThreshold(Identity(), 2 * 1e-11, thresh_type="soft")
# Setup Reconstructor
reconstructor = SingleChannelReconstructor(
fourier_op=fourier_op,
linear_op=linear_op,
regularizer_op=regularizer_op,
gradient_formulation='synthesis',
verbose=1,
)
# Start Reconstruction
x_final, costs, metrics = reconstructor.reconstruct(
kspace_data=kspace_data,
optimization_alg='fista',
num_iterations=200,
)
image_rec = pysap.Image(data=np.abs(x_final))
def __init__(self,linop, weights,mass=None,pos_en=False):
self.linop = linop
self.weights = weights
self.thresh = SparseThreshold(self.linop, self.weights)
self.simplex = Simplex(mass=mass,pos_en=pos_en)
base_ssim = ssim(image_rec0, image)
print('The Base SSIM is : ' + str(base_ssim))
#############################################################################
# FISTA optimization
# ------------------
#
# We now want to refine the zero order solution using a FISTA optimization.
# The cost function is set to Proximity Cost + Gradient Cost
# Setup the operators
linear_op = WaveletN(
wavelet_name='sym8',
nb_scale=4,
)
regularizer_op = SparseThreshold(Identity(), 1.5e-8, thresh_type="soft")
# Setup Reconstructor
reconstructor = SelfCalibrationReconstructor(
fourier_op=fourier_op,
linear_op=linear_op,
regularizer_op=regularizer_op,
gradient_formulation='synthesis',
kspace_portion=0.01,
verbose=1,
)
x_final, costs, metrics = reconstructor.reconstruct(
kspace_data=kspace_obs,
optimization_alg='fista',
num_iterations=10,
)
image_rec = pysap.Image(data=x_final)
def sparse_deconv_condatvu(data, psf, n_iter=300, n_reweights=1):
"""Sparse Deconvolution with Condat-Vu
Parameters
----------
data : np.ndarray
Input data, 2D image
psf : np.ndarray
Input PSF, 2D image
n_iter : int, optional
Maximum number of iterations
n_reweights : int, optional
Number of reweightings
Returns
-------
np.ndarray deconvolved image
"""
# Print the algorithm set-up
print(condatvu_logo())
# Define the wavelet filters
filters = (get_cospy_filters(
data.shape, transform_name='LinearWaveletTransformATrousAlgorithm'))
# Set the reweighting scheme
reweight = cwbReweight(get_weights(data, psf, filters))
# Set the initial variable values
primal = np.ones(data.shape)
dual = np.ones(filters.shape)
# Set the gradient operators
grad_op = GradBasic(data, lambda x: psf_convolve(x, psf),
lambda x: psf_convolve(x, psf, psf_rot=True))
# Set the linear operator
linear_op = WaveletConvolve2(filters)
# Set the proximity operators
prox_op = Positivity()
prox_dual_op = SparseThreshold(linear_op, reweight.weights)
# Set the cost function
cost_op = costObj([grad_op, prox_op, prox_dual_op],
tolerance=1e-6,
cost_interval=1,
plot_output=True,
verbose=False)
# Set the optimisation algorithm
alg = Condat(primal,
dual,
grad_op,
prox_op,
prox_dual_op,
linear_op,
cost_op,
rho=0.8,
sigma=0.5,
tau=0.5,
auto_iterate=False)
# Run the algorithm
alg.iterate(max_iter=n_iter)
# Implement reweigting
for rw_num in range(n_reweights):
print(' - Reweighting: {}'.format(rw_num + 1))
reweight.reweight(linear_op.op(alg.x_final))
alg.iterate(max_iter=n_iter)
# Return the final result
return alg.x_final
def sparse_rec_fista(data, wavelet_name, samples, mu, nb_scales=4,
lambda_init=1.0, max_nb_of_iter=300, atol=1e-4,
non_cartesian=False, uniform_data_shape=None, verbose=0):
""" The FISTA sparse reconstruction without reweightings.
.. note:: At the moment, supports only 2D data.
Parameters
----------
data: ndarray
the data to reconstruct (observation are expected in the Fourier
space).
wavelet_name: str
the wavelet name to be used during the decomposition.
samples: np.ndarray
the mask samples in the Fourier domain.
mu: float
coefficient of regularization.
nb_scales: int, default 4
the number of scales in the wavelet decomposition.
lambda_init: float, (default 1.0)
initial value for the FISTA step.
max_nb_of_iter: int (optional, default 300)
the maximum number of iterations in the Condat-Vu proximal-dual
splitting algorithm.
atol: float (optional, default 1e-4)
tolerance threshold for convergence.
non_cartesian: bool (optional, default False)
if set, use the nfftw rather than the fftw. Expect an 1D input dataset.
uniform_data_shape: uplet (optional, default None)
the shape of the matrix containing the uniform data. Only required
for non-cartesian reconstructions.
verbose: int (optional, default 0)
the verbosity level.
Returns
-------
x_final: ndarray
the estimated FISTA solution.
transform: a WaveletTransformBase derived instance
the wavelet transformation instance.
"""
# Check inputs
start = time.clock()
if non_cartesian and data.ndim != 1:
raise ValueError("Expect 1D data with the non-cartesian option.")
elif non_cartesian and uniform_data_shape is None:
raise ValueError("Need to set the 'uniform_data_shape' parameter with "
"the non-cartesian option.")
elif not non_cartesian and data.ndim != 2:
raise ValueError("At the moment, this functuion only supports 2D "
"data.")
# Define the gradient/linear/fourier operators
linear_op = Wavelet2(
nb_scale=nb_scales,
wavelet_name=wavelet_name)
if non_cartesian:
fourier_op = NFFT2(
samples=samples,
shape=uniform_data_shape)
else:
fourier_op = FFT2(
samples=samples,
shape=data.shape)
gradient_op = GradSynthesis2(
data=data,
linear_op=linear_op,
fourier_op=fourier_op)
# Define the initial primal and dual solutions
x_init = np.zeros(fourier_op.shape, dtype=np.complex)
alpha = linear_op.op(x_init)
alpha[...] = 0.0
# Welcome message
if verbose > 0:
print(fista_logo())
print(" - mu: ", mu)
print(" - lipschitz constant: ", gradient_op.spec_rad)
print(" - data: ", data.shape)
print(" - wavelet: ", wavelet_name, "-", nb_scales)
print(" - max iterations: ", max_nb_of_iter)
print(" - image variable shape: ", x_init.shape)
print(" - alpha variable shape: ", alpha.shape)
print("-" * 40)
# Define the proximity dual operator
weights = copy.deepcopy(alpha)
weights[...] = mu
prox_op = SparseThreshold(linear_op, weights, thresh_type="soft")
# Define the optimizer
cost_op = None
opt = ForwardBackward(
x=alpha,
grad=gradient_op,
prox=prox_op,
cost=cost_op,
auto_iterate=False)
# Perform the reconstruction
end = time.clock()
if verbose > 0:
print("Starting optimization...")
opt.iterate(max_iter=max_nb_of_iter)
if verbose > 0:
# cost_op.plot_cost()
# print(" - final iteration number: ", cost_op._iteration)
# print(" - final log10 cost value: ", np.log10(cost_op.cost))
print(" - converged: ", opt.converge)
print("Done.")
print("Execution time: ", end - start, " seconds")
print("-" * 40)
x_final = linear_op.adj_op(opt.x_final)
return x_final, linear_op.transform
def sparse_rec_condatvu(data, wavelet_name, samples, nb_scales=4,
std_est=None, std_est_method=None, std_thr=2.,
mu=1e-6, tau=None, sigma=None, relaxation_factor=1.0,
nb_of_reweights=1, max_nb_of_iter=150,
add_positivity=False, atol=1e-4, non_cartesian=False,
uniform_data_shape=None, verbose=0):
""" The Condat-Vu sparse reconstruction with reweightings.
.. note:: At the moment, supports only 2D data.
Parameters
----------
data: ndarray
the data to reconstruct: observation are expected in Fourier space.
wavelet_name: str
the wavelet name to be used during the decomposition.
samples: np.ndarray
the mask samples in the Fourier domain.
nb_scales: int, default 4
the number of scales in the wavelet decomposition.
std_est: float, default None
the noise std estimate.
If None use the MAD as a consistent estimator for the std.
std_est_method: str, default None
if the standard deviation is not set, estimate this parameter using
the mad routine in the image ('primal') or in the sparse wavelet
decomposition ('dual') domain.
std_thr: float, default 2.
use this treshold expressed as a number of sigma in the residual
proximity operator during the thresholding.
mu: float, default 1e-6
regularization hyperparameter.
tau, sigma: float, default None
parameters of the Condat-Vu proximal-dual splitting algorithm.
If None estimates these parameters.
relaxation_factor: float, default 0.5
parameter of the Condat-Vu proximal-dual splitting algorithm.
If 1, no relaxation.
nb_of_reweights: int, default 1
the number of reweightings.
max_nb_of_iter: int, default 150
the maximum number of iterations in the Condat-Vu proximal-dual
splitting algorithm.
add_positivity: bool, default False
by setting this option, set the proximity operator to identity or
positive.
atol: float, default 1e-4
tolerance threshold for convergence.
non_cartesian: bool (optional, default False)
if set, use the nfftw rather than the fftw. Expect an 1D input dataset.
uniform_data_shape: uplet (optional, default None)
the shape of the matrix containing the uniform data. Only required
for non-cartesian reconstructions.
verbose: int, default 0
the verbosity level.
Returns
-------
x_final: ndarray
the estimated CONDAT-VU solution.
transform: a WaveletTransformBase derived instance
the wavelet transformation instance.
"""
# Check inputs
start = time.clock()
if non_cartesian and data.ndim != 1:
raise ValueError("Expect 1D data with the non-cartesian option.")
elif non_cartesian and uniform_data_shape is None:
raise ValueError("Need to set the 'uniform_data_shape' parameter with "
"the non-cartesian option.")
elif not non_cartesian and data.ndim != 2:
raise ValueError("At the moment, this functuion only supports 2D "
"data.")
if std_est_method not in (None, "primal", "dual"):
raise ValueError(
"Unrecognize std estimation method '{0}'.".format(std_est_method))
# Define the gradient/linear/fourier operators
linear_op = Wavelet2(
nb_scale=nb_scales,
wavelet_name=wavelet_name)
if non_cartesian:
data_shape = uniform_data_shape
fourier_op = NFFT2(
samples=samples,
shape=uniform_data_shape)
else:
data_shape = data.shape
fourier_op = FFT2(
samples=samples,
shape=data.shape)
gradient_op = GradAnalysis2(
data=data,
fourier_op=fourier_op)
# Define the initial primal and dual solutions
x_init = np.zeros(fourier_op.shape, dtype=np.complex)
weights = linear_op.op(x_init)
# Define the weights used during the thresholding in the dual domain,
# the reweighting strategy, and the prox dual operator
# Case1: estimate the noise std in the image domain
if std_est_method == "primal":
if std_est is None:
std_est = sigma_mad(gradient_op.MtX(data))
weights[...] = std_thr * std_est
reweight_op = cwbReweight(weights)
prox_dual_op = SparseThreshold(linear_op, reweight_op.weights,
thresh_type="soft")
# Case2: estimate the noise std in the sparse wavelet domain
elif std_est_method == "dual":
if std_est is None:
std_est = 0.0
weights[...] = std_thr * std_est
reweight_op = mReweight(weights, linear_op, thresh_factor=std_thr)
prox_dual_op = SparseThreshold(linear_op, weights=reweight_op.weights,
thresh_type="soft")
# Case3: manual regularization mode, no reweighting
else:
weights[...] = mu
reweight_op = None
prox_dual_op = SparseThreshold(linear_op, weights, thresh_type="soft")
nb_of_reweights = 0
# Define the Condat Vu optimizer: define the tau and sigma in the
# Condat-Vu proximal-dual splitting algorithm if not already provided.
# Check also that the combination of values will lead to convergence.
norm = linear_op.l2norm(data_shape)
lipschitz_cst = gradient_op.spec_rad
if sigma is None:
sigma = 0.5
if tau is None:
# to avoid numerics troubles with the convergence bound
eps = 1.0e-8
# due to the convergence bound
tau = 1.0 / (lipschitz_cst/2 + sigma * norm**2 + eps)
convergence_test = (
1.0 / tau - sigma * norm ** 2 >= lipschitz_cst / 2.0)
# Define initial primal and dual solutions
primal = np.zeros(data_shape, dtype=np.complex)
dual = linear_op.op(primal)
dual[...] = 0.0
# Welcome message
if verbose > 0:
print(condatvu_logo())
print(" - mu: ", mu)
print(" - lipschitz constant: ", gradient_op.spec_rad)
print(" - tau: ", tau)
print(" - sigma: ", sigma)
print(" - rho: ", relaxation_factor)
print(" - std: ", std_est)
print(" - 1/tau - sigma||L||^2 >= beta/2: ", convergence_test)
print(" - data: ", data.shape)
print(" - wavelet: ", wavelet_name, "-", nb_scales)
print(" - max iterations: ", max_nb_of_iter)
print(" - number of reweights: ", nb_of_reweights)
print(" - primal variable shape: ", primal.shape)
print(" - dual variable shape: ", dual.shape)
print("-" * 40)
# Define the proximity operator
if add_positivity:
prox_op = Positive()
else:
prox_op = Identity()
# Define the cost function
cost_op = DualGapCost(
linear_op=linear_op,
initial_cost=1e6,
tolerance=1e-4,
cost_interval=1,
test_range=4,
verbose=0,
plot_output=None)
# Define the optimizer
opt = Condat(
x=primal,
y=dual,
grad=gradient_op,
prox=prox_op,
prox_dual=prox_dual_op,
linear=linear_op,
cost=cost_op,
rho=relaxation_factor,
sigma=sigma,
tau=tau,
rho_update=None,
sigma_update=None,
tau_update=None,
auto_iterate=False)
# Perform the first reconstruction
if verbose > 0:
print("Starting optimization...")
opt.iterate(max_iter=max_nb_of_iter)
# Loop through the number of reweightings
for reweight_index in range(nb_of_reweights):
# Generate the new weights following reweighting prescription
if std_est_method == "primal":
reweight_op.reweight(linear_op.op(opt._x_new))
else:
std_est = reweight_op.reweight(opt._x_new)
# Welcome message
if verbose > 0:
print(" - reweight: ", reweight_index + 1)
print(" - std: ", std_est)
# Update the weights in the dual proximity operator
prox_dual_op.weights = reweight_op.weights
# Perform optimisation with new weights
opt.iterate(max_iter=max_nb_of_iter)
# Goodbye message
end = time.clock()
if verbose > 0:
print(" - final iteration number: ", cost_op._iteration)
print(" - final cost value: ", cost_op.cost)
print(" - converged: ", opt.converge)
print("Done.")
print("Execution time: ", end - start, " seconds")
print("-" * 40)
# Get the final solution
x_final = opt.x_final
linear_op.transform.analysis_data = unflatten(
opt.y_final, linear_op.coeffs_shape)
return x_final, linear_op.transform