def setUpClass(cls):
# Point self to cls so we can use it like in a normal method
self = cls
# Load in test data
self.path = ('mr_utils/test_data/tests/cs/convex/' 'temporal_gd_tv')
self.Coil, self.mask = load_test_data(self.path, ['Coil6', 'mask'])
# For some reason they are the wrong dimensions coming out
# of MATLAB, probably because they are old format
self.Coil = self.Coil.T
self.mask = self.mask.T
# Set the recon parameters
self.weight_fidelity = 1
self.weight_temporal = .01
self.beta_sqrd = 0.0000001
self.niter = 200
# Get an encoding model
self.uft = UFT(self.mask, axes=(0, 1))
# Compute reduced kspace
self.reduced_kspace = self.Coil * self.mask
# Compute prior
self.prior = generate_prior(self.Coil * self.mask, self.uft.inverse_s)
# Compute monotonic sort order
(self.sort_order_real,
self.sort_order_imag) = sort_real_imag_parts(self.prior, axis=-1)
# Compute measured image domain
self.measuredImgDomain = self.uft.inverse_s(self.reduced_kspace)
# Get reduced data, whatever that is
self.reduced_data = np.abs(self.measuredImgDomain)
# Get initial estimates
self.img_est = self.measuredImgDomain.copy()
self.W_img_est = self.measuredImgDomain.copy()
# Construct R and C (rows and columns, I assume)
rows, cols, pages = self.img_est.shape[:]
self.R = np.tile(np.arange(rows), (cols, pages, 1)).transpose(
(2, 0, 1))
self.C = np.tile(np.arange(cols), (rows, pages, 1)).transpose(
(0, 2, 1))
# From R and C get the indices we'll actually use
self.nIdx_real = self.R + self.C * rows + (
self.sort_order_real) * rows * cols
self.nIdx_imag = self.R + self.C * rows + (
self.sort_order_imag) * rows * cols
class TestAMP(unittest.TestCase):
'''Make sure we line up with Stanford results.'''
def setUp(self):
data = load_test_data('mr_utils/test_data/tests/cs/thresholding/amp',
['cdf97', 'mask', 'x0', 'y'])
self.cdf97, self.mask, self.x0, self.y = data[:] #pylint: disable=W0632
self.uft = UFT(self.mask)
self.level = 5
def test_uft(self):
'''Test undersampled fourier encoding.'''
y0 = self.uft.forward_ortho(self.x0)
self.assertTrue(np.allclose(self.y, y0))
@unittest.skip('Currently do not know how to match cdf97 using pywavelets')
def test_wavelet_decomposition(self):
'''Make sure we decompose using the same wavelet transformation.'''
wavelet_transform, locations = cdf97_2d_forward(self.x0, self.level)
# # Check 'em out
# view(np.stack((np.log(np.abs(self.cdf97)),
# np.log(np.abs(wavelet_transform)))))
# view(np.stack((self.cdf97 - wavelet_transform)), log=True)
#
# # Make sure we can go back
inverse = cdf97_2d_inverse(wavelet_transform, locations)
self.assertTrue(np.allclose(self.x0, inverse))
# view(self.x0 - inverse)
# view(cdf97_2d_inverse(wavelet_transform, locations))
# Currently failing...
self.assertTrue(np.allclose(wavelet_transform, self.cdf97))
# Undersampling pattern
samp0 = np.zeros((sx, sy, st))
desc = 'Making sampling mask'
num_spokes = 16
offsets = np.random.randint(0, high=st, size=st)
for ii in trange(st, leave=False, desc=desc):
samp0[..., ii] = radial(
(sx, sy), num_spokes, offset=offsets[ii],
extend=True, skinny=False)
# view(samp0)
# Set up the recon
x = imspace_true.copy()
ax = (0, 1)
uft = UFT(samp0, axes=ax, scale=True)
forward = uft.forward_ortho
inverse = uft.inverse_ortho
y = forward(x)
# view(y, log=True)
imspace_u = inverse(y)
# from mr_utils.cs import SpatioTemporalTVSB
# recon, err = SpatioTemporalTVSB(
# samp0, y, betaxy=1/4, betat=1, mu=1, lam=1, gamma=1/2,
# nInner=1, niter=3, x=x)
# view(recon)
w = 50
recon_l1 = ptv.tvgen(
from mr_utils import view
from mr_utils.cs import proximal_GD
from mr_utils.cs.models import UFT
from mr_utils.utils.wavelet import cdf97_2d_forward, cdf97_2d_inverse
from mr_utils.utils.orderings import bulk_up, whittle_down, colwise, rowwise
from mr_utils.utils.sort2d import sort2d
if __name__ == '__main__':
# We need a mask
mask = load_test_data('mr_utils/test_data/tests/recon/reordering',
['mask'])[0]
mask = np.fft.fftshift(mask)
# Get the encoding model
uft = UFT(mask)
# Load in the test data
kspace = load_test_data('mr_utils/test_data/tests/recon/reordering',
['coil1'])[0]
kspace = np.fft.fftshift(kspace)
imspace = uft.inverse(kspace)
# Undersample data to get prior
kspace_u = kspace * mask
imspace_u = uft.inverse(kspace_u)
# Sparsifying transforms
level = 3
wvlt, locations = cdf97_2d_forward(imspace, level)
sparsify = lambda x: cdf97_2d_forward(x, level)[0]
class TestTemporalGDTV(unittest.TestCase):
'''Make sure output of function matches MATLAB output.'''
@classmethod
def setUpClass(cls):
# Point self to cls so we can use it like in a normal method
self = cls
# Load in test data
self.path = ('mr_utils/test_data/tests/cs/convex/' 'temporal_gd_tv')
self.Coil, self.mask = load_test_data(self.path, ['Coil6', 'mask'])
# For some reason they are the wrong dimensions coming out
# of MATLAB, probably because they are old format
self.Coil = self.Coil.T
self.mask = self.mask.T
# Set the recon parameters
self.weight_fidelity = 1
self.weight_temporal = .01
self.beta_sqrd = 0.0000001
self.niter = 200
# Get an encoding model
self.uft = UFT(self.mask, axes=(0, 1))
# Compute reduced kspace
self.reduced_kspace = self.Coil * self.mask
# Compute prior
self.prior = generate_prior(self.Coil * self.mask, self.uft.inverse_s)
# Compute monotonic sort order
(self.sort_order_real,
self.sort_order_imag) = sort_real_imag_parts(self.prior, axis=-1)
# Compute measured image domain
self.measuredImgDomain = self.uft.inverse_s(self.reduced_kspace)
# Get reduced data, whatever that is
self.reduced_data = np.abs(self.measuredImgDomain)
# Get initial estimates
self.img_est = self.measuredImgDomain.copy()
self.W_img_est = self.measuredImgDomain.copy()
# Construct R and C (rows and columns, I assume)
rows, cols, pages = self.img_est.shape[:]
self.R = np.tile(np.arange(rows), (cols, pages, 1)).transpose(
(2, 0, 1))
self.C = np.tile(np.arange(cols), (rows, pages, 1)).transpose(
(0, 2, 1))
# From R and C get the indices we'll actually use
self.nIdx_real = self.R + self.C * rows + (
self.sort_order_real) * rows * cols
self.nIdx_imag = self.R + self.C * rows + (
self.sort_order_imag) * rows * cols
def test_reduced_kspace(self):
'''Verify reduced_kspace variable is the same as MATLAB'''
reduced_kspace_true = load_test_data(self.path, ['reduced_kspace'])
self.assertTrue(np.allclose(self.reduced_kspace, reduced_kspace_true))
def test_generate_prior(self):
'''Verify prior variable is the same as MATLAB'''
prior_true = load_test_data(
self.path,
['prior'],
)
self.assertTrue(np.allclose(self.prior, prior_true))
def test_monotonic_sort_real_imag_parts(self):
'''Verify sort orders are the same as MATLAB'''
real_true, imag_true = load_test_data(
self.path, ['sort_order_real', 'sort_order_imag'])
# 0-based indexing
real_true -= 1
imag_true -= 1
self.assertTrue(np.alltrue(self.sort_order_real == real_true))
self.assertTrue(np.alltrue(self.sort_order_imag == imag_true))
def test_measuredImgDomain(self):
'''Verify measuredImgDomain variable same as MATLAB'''
mid = load_test_data(self.path, ['measuredImgDomain'])
self.assertTrue(np.allclose(self.measuredImgDomain, mid))
def test_reduced_data(self):
'''Verify reduced_data variable same as MATLAB'''
reduced_data = load_test_data(self.path, ['reduced_data'])
self.assertTrue(np.allclose(self.reduced_data, reduced_data))
def test_R_and_C(self):
'''Verify R, C variables are the same as MATLAB'''
R, C = load_test_data(self.path, ['R', 'C'])
self.assertTrue(np.allclose(self.R, R - 1))
self.assertTrue(np.allclose(self.C, C - 1))
def test_nIdx_real_and_imag(self):
'''Verify nIdx_real/imag variables are the same as MATLAB'''
real, imag = load_test_data(self.path, ['nIdx_real', 'nIdx_imag'])
# print(np.unravel_index(self.nIdx_real, self.prior.shape))
self.assertTrue(np.allclose(self.nIdx_real, real - 1))
self.assertTrue(np.allclose(self.nIdx_imag, imag - 1))
def test_recon(self):
'''See if the full recon matches the MATLAB output'''
recon = GD_temporal_TV(self.prior,
self.reduced_kspace,
self.mask,
self.weight_fidelity,
self.weight_temporal,
self.uft.forward_s,
self.uft.inverse_s,
x=self.Coil)
view(recon)
from mr_utils import view
from mr_utils.cs import GD_TV
from mr_utils.cs.models import UFT
from mr_utils.test_data.phantom import binary_smiley
from mr_utils.sim.traj import cartesian_pe
if __name__ == '__main__':
# Same binary smiley face example
do_reordering = True
N = 1000
x = binary_smiley(N)
k = np.sum(np.abs(np.diff(x)) > 0)
np.random.seed(5)
samp = cartesian_pe(x.shape, undersample=.2, reflines=5)
uft = UFT(samp)
# Make the complex measurement in kspace
# Note this is different than uft.forward, as fftshift must be performed
y = uft.forward_ortho(x)
# Solve inverse problem using gradient descent with TV sparsity constraint
x_hat = GD_TV(y,
forward_fun=uft.forward_ortho,
inverse_fun=uft.inverse_ortho,
alpha=.5,
lam=.022,
do_reordering=do_reordering,
x=x,
ignore_residual=True,
disp=True,
plt.hist(im.imag.flatten(), density=True)
plt.title('Distribution of Imag')
plt.xlabel('Variance: %g' % laplace_sample_var(im.imag.flatten()))
plt.subplot(1, 3, 3)
plt.hist(np.abs(im.flatten()), density=True)
plt.title('Distribution of Mag')
plt.xlabel('Variance: %g' % exp_sample_var(np.abs(im).flatten()))
plt.show()
# Radial sampling pattern for retrospective undersampling
num_spokes = 16
samp = radial(im.shape, num_spokes, skinny=True, extend=True)
samp_percent = np.sum(samp.flatten()) / samp.size * 100
uft = UFT(samp)
kspace_u = np.fft.fft2(im) * samp
imspace_u = np.fft.ifft2(kspace_u)
# view(samp)
# view(imspace_u)
# view(kspace_u)
# Use wavelet transform
lvl = 3
_coeffs, locs = cdf97_2d_forward(im, lvl)
sparsify = lambda x0: cdf97_2d_forward(x0, lvl)[0]
unsparsify = lambda x0: cdf97_2d_inverse(x0, locs)
assert np.allclose(unsparsify(sparsify(im)), im)
# Recon params
ignore_mse = False
from mr_utils.test_data.phantom import binary_smiley
from mr_utils.sim.traj import radial
from mr_utils.cs.models import UFT
from mr_utils.cs import proximal_GD
from mr_utils.utils.wavelet import cdf97_2d_forward, cdf97_2d_inverse
from mr_utils.utils.sort2d import sort2d
if __name__ == '__main__':
# Phantom
N = 2**9
x = binary_smiley(N)
# Sampling mask and encoding model
mask = radial(x.shape, 16, extend=True)
uft = UFT(mask)
# Sample
y = uft.forward_ortho(x)
# Decide how we'll be selective in our updates
percent_to_keep = .04
num_to_keep = int(percent_to_keep * y.size)
def select_n(x_hat, update):
'''Return indices of n largest updates each iteration.'''
return np.unravel_index(
np.argpartition(np.abs(x_hat - update).flatten(),
-num_to_keep)[-num_to_keep:], x_hat.shape)
idx = np.arange(y.size).reshape(y.shape)
from mr_utils.utils.wavelet import cdf97_2d_forward, cdf97_2d_inverse
from mr_utils.sim.traj import radial
from mr_utils.cs.models import UFT
from mr_utils.cs import proximal_GD
from mr_utils import view
if __name__ == '__main__':
# Get a phantom
N = 64
x = binary_smiley(N)
# Do some sampling
num_spokes = 12
mask = radial(x.shape, num_spokes)
uft = UFT(mask)
y = uft.forward_ortho(x)
# Sparsifying transforms
level = 3
wvlt, locations = cdf97_2d_forward(x, level)
sparsify = lambda x0: cdf97_2d_forward(x0, level)[0]
unsparsify = lambda x0: cdf97_2d_inverse(x0, locations)
# Do the recon
alpha = .15
disp = True
ignore = False
maxiter = 200
x_c = proximal_GD(y,
forward_fun=uft.forward_ortho,
def setUp(self):
data = load_test_data('mr_utils/test_data/tests/cs/thresholding/amp',
['cdf97', 'mask', 'x0', 'y'])
self.cdf97, self.mask, self.x0, self.y = data[:] #pylint: disable=W0632
self.uft = UFT(self.mask)
self.level = 5
num_spokes = 16
run = ['monosort', 'lagrangian'] # none is always run to get prior
# Need a reasonable numerical phantom
x = np.rot90(modified_shepp_logan((N, N, N))[:, :, int(N / 2)])
# view(x)
# Sparsifying transform
level = 3
wvlt, locations = cdf97_2d_forward(x, level)
sparsify = lambda x: cdf97_2d_forward(x, level)[0]
unsparsify = lambda x: cdf97_2d_inverse(x, locations)
# Do radial golden-angle sampling
mask = radial(x.shape, num_spokes, skinny=True, extend=False)
uft = UFT(mask)
kspace_u = uft.forward_ortho(x)
view(kspace_u, fft=True)
# # We need to find the best alpha for the no ordering recon
# pGD = partial(
# proximal_GD, y=kspace_u, forward_fun=uft.forward_ortho,
# inverse_fun=uft.inverse_ortho, sparsify=sparsify,
# unsparsify=unsparsify, mode='soft', thresh_sep=True,
# selective=None, x=x, ignore_residual=False, disp=False,
# maxiter=500)
# obj = lambda alpha0: compare_mse(
# np.abs(x), np.abs(pGD(alpha=alpha0)))
# alpha0 = 0.05
# res = minimize(obj, alpha0)
# print(res)
import matplotlib.pyplot as plt
from skimage.measure import compare_mse
from mr_utils.cs import IHT_TV
from mr_utils.cs.models import UFT
from mr_utils.test_data.phantom import binary_smiley
from mr_utils.sim.traj import cartesian_pe
if __name__ == '__main__':
do_reordering = True
N = 1000
x = binary_smiley(N)
k = np.sum(np.abs(np.diff(x)) > 0)
np.random.seed(5)
samp = cartesian_pe(x.shape, undersample=.01, reflines=5)
uft = UFT(samp) # acquisiton model
# Show sampling pattern
plt.imshow(samp, cmap='gray')
plt.title('Sampling Pattern')
plt.show()
# Simulate acquisiton
kspace_u = uft.forward_ortho(x)
imspace_u = uft.inverse_ortho(kspace_u)
# Look at the aliased acquired signal
plt.imshow(np.abs(imspace_u), cmap='gray')
plt.title('Acquired')
plt.show()