def test_sigpy_cupy(self):
import sigpy as sp
assert Device(0) == sp.Device(0)
device = Device(0)
assert device.spdevice == sp.Device(0)
def __init__(self,
ksp,
calib_width=24,
thresh=0.01,
kernel_width=6,
crop=0.8,
max_iter=100,
device=sp.cpu_device,
output_eigenvalue=False,
show_pbar=True):
self.device = sp.Device(device)
self.output_eigenvalue = output_eigenvalue
self.crop = crop
img_ndim = ksp.ndim - 1
num_coils = len(ksp)
with sp.get_device(ksp):
# Get calibration region
calib_shape = [num_coils] + [calib_width] * img_ndim
calib = sp.resize(ksp, calib_shape)
calib = sp.to_device(calib, device)
xp = self.device.xp
with self.device:
# Get calibration matrix
kernel_shape = [num_coils] + [kernel_width] * img_ndim
kernel_strides = [1] * (img_ndim + 1)
mat = sp.array_to_blocks(calib, kernel_shape, kernel_strides)
mat = mat.reshape([-1, sp.prod(kernel_shape)])
# Perform SVD on calibration matrix
_, S, VH = xp.linalg.svd(mat, full_matrices=False)
VH = VH[S > thresh * S.max(), :]
# Get kernels
num_kernels = len(VH)
kernels = VH.reshape([num_kernels] + kernel_shape)
img_shape = ksp.shape[1:]
# Get covariance matrix in image domain
AHA = xp.zeros(img_shape[::-1] + (num_coils, num_coils),
dtype=ksp.dtype)
for kernel in kernels:
img_kernel = sp.ifft(sp.resize(kernel, ksp.shape),
axes=range(-img_ndim, 0))
aH = xp.expand_dims(img_kernel.T, axis=-1)
a = xp.conj(aH.swapaxes(-1, -2))
AHA += aH @ a
AHA *= (sp.prod(img_shape) / kernel_width**img_ndim)
self.mps = xp.ones(ksp.shape[::-1] + (1, ), dtype=ksp.dtype)
alg = sp.alg.PowerMethod(
lambda x: AHA @ x,
self.mps,
norm_func=lambda x: xp.sum(
xp.abs(x)**2, axis=-2, keepdims=True)**0.5,
max_iter=max_iter)
super().__init__(alg, show_pbar=show_pbar)
def pipe_menon_dcf(coord,
device=sp.cpu_device,
max_iter=30,
n=128,
beta=8,
width=4,
show_pbar=True):
r"""Compute Pipe Menon density compensation factor.
Perform the following iteration:
.. math::
w = \frac{w}{|G^H G w|}
with :math:`G` as the gridding operator.
Args:
coord (array): k-space coordinates.
device (Device): computing device.
max_iter (int): number of iterations.
n (int): Kaiser-Bessel sampling numbers for gridding operator.
beta (float): Kaiser-Bessel kernel parameter.
width (float): Kaiser-Bessel kernel width.
show_pbar (bool): show progress bar.
Returns:
array: density compensation factor.
References:
Pipe, James G., and Padmanabhan Menon.
Sampling Density Compensation in MRI:
Rationale and an Iterative Numerical Solution.
Magnetic Resonance in Medicine 41, no. 1 (1999): 179–86.
"""
device = sp.Device(device)
xp = device.xp
with device:
w = xp.ones(coord.shape[:-1], dtype=coord.dtype)
img_shape = sp.estimate_shape(coord)
# Get kernel
x = xp.arange(n, dtype=coord.dtype) / n
kernel = xp.i0(beta * (1 - x**2)**0.5).astype(coord.dtype)
kernel /= kernel.max()
G = sp.linop.Gridding(img_shape, coord, width, kernel)
with tqdm(total=max_iter, disable=not show_pbar) as pbar:
for it in range(max_iter):
GHGw = G.H * G * w
w /= xp.abs(GHGw)
resid = xp.abs(GHGw - 1).max().item()
pbar.set_postfix(resid='{0:.2E}'.format(resid))
pbar.update()
return w
def __init__(self, input, output, batch_size, mu,
lamda=0,
max_iter=100, max_inner_iter=100, device=sp.cpu_device,
checkpoint_path=None):
dtype = output.dtype
num_data = len(output)
num_batches = num_data // batch_size
self.device = device
self.lamda = lamda
self.batch_size = batch_size
self.input = input
self.output = output
self.checkpoint_path = checkpoint_path
self.device = sp.Device(device)
xp = self.device.xp
with self.device:
self.mat = xp.zeros(input.shape[1:] + output.shape[1:], dtype=dtype)
self.input_t = xp.empty((batch_size, ) + input.shape[1:], dtype=dtype)
self.output_t = xp.empty((batch_size, ) + output.shape[1:], dtype=dtype)
self.t_idx = sp.ShuffledNumbers(num_batches)
self._get_A()
def proxf(mu, x):
return sp.app.LinearLeastSquares(self.A, self.output_t, x=x,
lamda=self.lamda / num_batches,
mu=1 / mu, z=x,
max_iter=max_inner_iter).run()
alg = sp.alg.ProximalPointMethod(proxf, mu, self.mat, max_iter=max_iter)
super().__init__(alg)
def __init__(self,
y,
mps_ker_width=16,
ksp_calib_width=24,
lamda=0,
device=sp.cpu_device,
comm=None,
weights=None,
coord=None,
max_iter=10,
max_inner_iter=10,
normalize=True,
show_pbar=True):
self.y = y
self.mps_ker_width = mps_ker_width
self.ksp_calib_width = ksp_calib_width
self.lamda = lamda
self.weights = weights
self.coord = coord
self.max_iter = max_iter
self.max_inner_iter = max_inner_iter
self.normalize = normalize
self.device = sp.Device(device)
self.comm = comm
self.dtype = y.dtype
self.num_coils = len(y)
if comm is not None:
show_pbar = show_pbar and comm.rank == 0
self._get_data()
self._get_vars()
self._get_alg()
super().__init__(self.alg, show_pbar=show_pbar)
def spdevice(self):
"""sigpy.Device: The equivalent ```sigpy.Device```."""
if not env.sigpy_available():
raise RuntimeError("`sigpy` not installed.")
if self.id >= 0 and self.type != "cuda":
raise RuntimeError(
f"sigpy.Device does not support type {self.type}")
return sp.Device(self.id)
def __init__(self,
ksp,
coord,
dcf,
mps,
T,
lamda,
blk_widths=[32, 64, 128],
alpha=1,
beta=0.5,
sgw=None,
device=sp.cpu_device,
comm=None,
seed=0,
max_epoch=60,
decay_epoch=20,
max_power_iter=5,
show_pbar=True):
self.ksp = ksp
self.coord = coord
self.dcf = dcf
self.mps = mps
self.sgw = sgw
self.blk_widths = blk_widths
self.T = T
self.lamda = lamda
self.alpha = alpha
self.beta = beta
self.device = sp.Device(device)
self.comm = comm
self.seed = seed
self.max_epoch = max_epoch
self.decay_epoch = decay_epoch
self.max_power_iter = max_power_iter
self.show_pbar = show_pbar and (comm is None or comm.rank == 0)
np.random.seed(self.seed)
self.xp = self.device.xp
with self.device:
self.xp.random.seed(self.seed)
self.dtype = self.ksp.dtype
self.C, self.num_tr, self.num_ro = self.ksp.shape
self.tr_per_frame = self.num_tr // self.T
self.img_shape = self.mps.shape[1:]
self.D = len(self.img_shape)
self.J = len(self.blk_widths)
if self.sgw is not None:
self.dcf *= np.expand_dims(self.sgw, -1)
self.B = [self._get_B(j) for j in range(self.J)]
self.G = [self._get_G(j) for j in range(self.J)]
self._normalize()
def jsens_calib(ksp, coord, dcf, ishape, device = sp.Device(-1)):
img_s = nft.nufft_adj([ksp],[coord],[dcf],device = device,ishape = ishape,id_channel =True)
ksp = sp.fft(input=np.asarray(img_s[0]),axes=(1,2,3))
mps = mr.app.JsenseRecon(ksp,
mps_ker_width=12,
ksp_calib_width=32,
lamda=0,
device=device,
comm=sp.Communicator(),
max_iter=10,
max_inner_iter=10).run()
return mps
def check_linop_adjoint(A, dtype=np.float, device=sp.cpu_device):
device = sp.Device(device)
x = sp.randn(A.ishape, dtype=dtype, device=device)
y = sp.randn(A.oshape, dtype=dtype, device=device)
xp = device.xp
with device:
lhs = xp.vdot(A * x, y)
rhs = xp.vdot(x, A.H * y)
xp.testing.assert_allclose(lhs, rhs, atol=1e-5, rtol=1e-5)
def nufft1(img,
traj,
device=sp.Device(-1),
smap=None,
dcf=None,
batch=40000,
id_channel=False):
xp = device.xp
N_phase = img.shape[0]
ksp = []
for num_ph in range(N_phase):
img_t = img[num_ph]
coord_t = traj[num_ph]
if dcf is not None:
dcf_t = dcf[num_ph]
img_shape = sp.estimate_shape(coord_t)
num_tr, num_ro, ndim = coord_t.shape
if id_channel is True:
num_coils = img_t.shape[0]
else:
if smap is None:
smap = np.array([1])
num_coils = 1
else:
num_coils = smap.shape[0]
with device:
ksp_t = np.zeros((num_coils, num_tr, num_ro), dtype=np.complex64)
for c in range(num_coils):
if id_channel is True:
img_tc = sp.to_device(img_t[c, ...], device)
else:
img_tc = sp.to_device(img_t * smap[c, ...], device)
for seg in range((num_tr - 1) // batch + 1):
coord_tt = sp.to_device(
coord_t[seg * batch:np.minimum((seg + 1) *
batch, num_tr), ...],
device)
ksp_tt = sp.nufft(img_tc, coord_tt)
if dcf is not None:
dcf_tt = sp.to_device(
dcf_t[seg * batch:np.minimum((seg + 1) *
batch, num_tr), ...],
device)
ksp_tt = dcf_tt * ksp_tt
ksp_t[c, seg * batch:np.minimum((seg + 1) * batch, num_tr),
...] = sp.to_device(ksp_tt)
ksp.append(ksp_t)
return np.asarray(ksp)
def process_slice(kspace, args, calib_method='jsense'):
# get data dimensions
nky, nkz, nechoes, ncoils = kspace.shape
# ESPIRiT parameters
nmaps = args.num_emaps
calib_size = args.ncalib
crop_value = args.crop_value
if args.device is -1:
device = sp.cpu_device
else:
device = sp.Device(args.device)
# compute sensitivity maps (BART)
#cmd = f'ecalib -d 0 -S -m {nmaps} -c {crop_value} -r {calib_size}'
#maps = bart.bart(1, cmd, kspace[:,:,0,None,:])
#maps = np.reshape(maps, (nky, nkz, 1, ncoils, nmaps))
# compute sensitivity maps (SigPy)
ksp = np.transpose(kspace[:, :, 0, :], [2, 1, 0])
if calib_method is 'espirit':
maps = app.EspiritCalib(ksp,
calib_width=calib_size,
crop=crop_value,
device=device,
show_pbar=False).run()
elif calib_method is 'jsense':
maps = app.JsenseRecon(ksp,
mps_ker_width=6,
ksp_calib_width=calib_size,
device=device,
show_pbar=False).run()
else:
raise ValueError('%s calibration method not implemented...' %
calib_method)
maps = np.reshape(np.transpose(maps, [2, 1, 0]),
(nky, nkz, 1, ncoils, nmaps))
# Convert everything to tensors
kspace_tensor = cplx.to_tensor(kspace).unsqueeze(0)
maps_tensor = cplx.to_tensor(maps).unsqueeze(0)
# Do coil combination using sensitivity maps (PyTorch)
A = T.SenseModel(maps_tensor)
im_tensor = A(kspace_tensor, adjoint=True)
# Convert tensor back to numpy array
image = cplx.to_numpy(im_tensor.squeeze(0))
return image, maps
def autofov(ksp, coord, dcf, num_ro=100, device=sp.cpu_device, thresh=0.1):
"""Automatic estimation of FOV.
FOV is estimated by thresholding a low resolution gridded image.
coord will be modified in-place.
Args:
ksp (array): k-space measurements of shape (C, num_tr, num_ro, D).
where C is the number of channels,
num_tr is the number of TRs, num_ro is the readout points,
and D is the number of spatial dimensions.
coord (array): k-space coordinates of shape (num_tr, num_ro, D).
dcf (array): density compensation factor of shape (num_tr, num_ro).
num_ro (int): number of read-out points.
device (Device): computing device.
thresh (float): threshold between 0 and 1.
"""
device = sp.Device(device)
xp = device.xp
with device:
kspc = ksp[:, :, :num_ro]
coordc = coord[:, :num_ro, :]
dcfc = dcf[:, :num_ro]
coordc2 = sp.to_device(coordc * 2, device)
num_coils = len(kspc)
imgc_shape = np.array(sp.estimate_shape(coordc))
imgc2_shape = sp.estimate_shape(coordc2)
imgc2_center = [i // 2 for i in imgc2_shape]
imgc2 = sp.nufft_adjoint(sp.to_device(dcfc * kspc, device), coordc2,
[num_coils] + imgc2_shape)
imgc2 = xp.sum(xp.abs(imgc2)**2, axis=0)**0.5
if imgc2.ndim == 3:
imgc2_cor = imgc2[:, imgc2.shape[1] // 2, :]
thresh *= imgc2_cor.max()
else:
thresh *= imgc2.max()
boxc = imgc2 > thresh
boxc = sp.to_device(boxc)
boxc_idx = np.nonzero(boxc)
boxc_shape = np.array([
int(np.abs(boxc_idx[i] - imgc2_center[i]).max()) * 2
for i in range(imgc2.ndim)
])
img_scale = boxc_shape / imgc_shape
coord *= img_scale
def _get_params(self):
self.device = sp.Device(self.device)
self.dtype = self.y.dtype
self.num_data = len(self.y)
self.filt_width = self.L.shape[-1]
self.num_filters = self.L.shape[self.multi_channel]
self.data_ndim = self.y.ndim - self.multi_channel - 1
if self.mode == 'full':
self.R_shape = [self.num_data, self.num_filters] + [i - self.filt_width + 1
for i in self.y.shape[-self.data_ndim:]]
else:
self.R_shape = [self.num_data, self.num_filters] + [i + self.filt_width - 1
for i in self.y.shape[-self.data_ndim:]]
def interp(I, M_field, device=sp.Device(-1), k_id=1, deblur=True):
# b spline interpolation
N = 64
if k_id is 0:
kernel = [(3 * (x / N)**3 - 6 * (x / N)**2 + 4) / 6
for x in range(0, N)] + [(2 - x / N)**3 / 6
for x in range(N, 2 * N)]
dkernel = np.array([-.2, 1.4, -.2])
k_wid = 4
else:
kernel = [1 - x / (2 * N) for x in range(0, 2 * N)]
dkernel = np.array([0, 1, 0])
deblur = False
k_wid = 2
kernel = np.asarray(kernel)
c_device = sp.get_device(I)
ndim = M_field.shape[-1]
# 2d/3d
if ndim is 3:
dkernel = dkernel[:, None, None] * dkernel[None, :,
None] * dkernel[None,
None, :]
Nx, Ny, Nz = I.shape
my, mx, mz = np.meshgrid(np.arange(Ny), np.arange(Nx), np.arange(Nz))
m = np.stack((mx, my, mz), axis=-1)
M_field = M_field + m
else:
dkernel = dkernel[:, None] * dkernel[None, :]
Nx, Ny = I.shape
my, mx = np.meshgrid(np.arange(Ny), np.arange(Nx))
m = np.stack((mx, my, mz), axis=-1)
M_field = M_field + m
# TODO remove out of range values
# image warp
g_device = device
I = sp.to_device(input=I, device=g_device)
I = sp.interp.interpolate(I, k_wid, kernel, M_field.astype(np.float64))
# deconv
if deblur is True:
sp.conv.convolve(I, dkernel)
I = sp.to_device(input=I, device=c_device)
return I
def __init__(self,
ksp,
coord,
dcf,
mps,
resp,
B,
lamda=1e-6,
alpha=1,
beta=0.5,
max_power_iter=10,
max_iter=300,
device=sp.cpu_device,
margin=10,
coil_batch_size=None,
comm=None,
show_pbar=True,
**kwargs):
self.B = B
self.C = len(mps)
self.mps = mps
self.device = sp.Device(device)
self.xp = device.xp
self.alpha = alpha
self.beta = beta
self.lamda = lamda
self.max_iter = max_iter
self.max_power_iter = max_power_iter
self.comm = comm
if comm is not None:
self.show_pbar = show_pbar and comm.rank == 0
self.img_shape = list(mps.shape[1:])
bins = np.percentile(resp, np.linspace(0 + margin, 100 - margin,
B + 1))
self.bksp = []
self.bcoord = []
self.bdcf = []
for b in range(B):
idx = (resp >= bins[b]) & (resp < bins[b + 1])
self.bksp.append(sp.to_device(ksp[:, idx], self.device))
self.bcoord.append(sp.to_device(coord[idx], self.device))
self.bdcf.append(sp.to_device(dcf[idx], self.device))
self._normalize()
def gridding_recon(ksp, coord, dcf, T=1, device=sp.cpu_device):
""" Gridding reconstruction.
Args:
ksp (array): k-space measurements of shape (C, num_tr, num_ro, D).
where C is the number of channels,
num_tr is the number of TRs, num_ro is the readout points,
and D is the number of spatial dimensions.
coord (array): k-space coordinates of shape (num_tr, num_ro, D).
dcf (array): density compensation factor of shape (num_tr, num_ro).
mps (array): sensitivity maps of shape (C, N_D, ..., N_1).
where (N_D, ..., N_1) represents the image shape.
T (int): number of frames.
Returns:
img (array): image of shape (T, N_D, ..., N_1).
"""
device = sp.Device(device)
xp = device.xp
num_coils, num_tr, num_ro = ksp.shape
tr_per_frame = num_tr // T
img_shape = sp.estimate_shape(coord)
with device:
img = []
for t in range(T):
tr_start = t * tr_per_frame
tr_end = (t + 1) * tr_per_frame
coord_t = sp.to_device(coord[tr_start:tr_end], device)
dcf_t = sp.to_device(dcf[tr_start:tr_end], device)
img_t = 0
for c in range(num_coils):
logging.info(f'Reconstructing time {t}, coil {c}')
ksp_tc = sp.to_device(ksp[c, tr_start:tr_end, :], device)
img_t += xp.abs(
sp.nufft_adjoint(ksp_tc * dcf_t, coord_t, img_shape))**2
img_t = img_t**0.5
img.append(sp.to_device(img_t))
img = np.stack(img)
return img
def _get_params(self):
self.device = sp.Device(self.device)
self.dtype = self.y.dtype
self.data_ndim = self.y.ndim - self.multi_channel - 1
if self.checkpoint_path is not None:
self.checkpoint_path = pathlib.Path(self.checkpoint_path)
self.checkpoint_path.mkdir(parents=True, exist_ok=True)
self.batch_size = min(len(self.y), self.batch_size)
self.num_batches = len(self.y) // self.batch_size
self.L_shape = [self.num_filters] + [self.filt_width] * self.data_ndim
if self.multi_channel:
self.L_shape = [self.y.shape[1]] + self.L_shape
if self.mode == 'full':
self.R_t_shape = [self.batch_size, self.num_filters] + [i - self.filt_width + 1
for i in self.y.shape[-self.data_ndim:]]
else:
self.R_t_shape = [self.batch_size, self.num_filters] + [i + self.filt_width - 1
for i in self.y.shape[-self.data_ndim:]]
def init_bloch_vector(shape=None, dtype=np.complex, device=sp.cpu_device):
"""Initialize magnetization in Bloch vector representation.
Args:
shape (tuple): batch shape.
dtype (Dtype): data type.
device (Device): device.
Returns:
array: magnetization array.
"""
device = sp.Device(device)
xp = device.xp
with device:
if shape is None:
shape = []
m = xp.zeros(list(shape) + [3], dtype=dtype)
m[..., 2] = 1
return m
def init_density_matrix(shape=None, dtype=np.complex, device=sp.cpu_device):
"""Initialize magnetization in density matrix representation.
Args:
shape (tuple): batch shape.
dtype (Dtype): data type.
device (Device): device.
Returns:
array: magnetization array.
"""
device = sp.Device(device)
xp = device.xp
with device:
if shape is None:
shape = []
p = xp.zeros(list(shape) + [2, 2], dtype=dtype)
p[..., 0, 0] = 1
return p
def NFTs(ishape, coord, device = sp.Device(-1)):
n_Channel = ishape[0]
oshape = list((n_Channel,)) + list(coord.shape[:-1])
NFT = sp.linop.NUFFT(ishape[1:], coord=coord)
NFTs = Diags([DLD(NFT,device=device) for i in range(n_Channel)],oshape,ishape)
# B1 = sp.linop.ToDevice(NFT.ishape,idevice=sp.Device(-1),odevice=device)
# B2 = sp.linop.ToDevice(NFT.oshape,idevice=sp.Device(-1),odevice=device)
# NFTs = Diags([B2.H*NFT*B1 for i in range(n_Channel)],oshape,ishape)
# i_vec_len = 1
# for tmp in ishape:
# i_vec_len = i_vec_len * tmp
# o_vec_len = 1
# for tmp in oshape:
# o_vec_len = o_vec_len * tmp
# NFTs = sp.linop.Diag([B2.H*NFT*B1 for i in range(n_Channel)])
# R1 = sp.linop.Reshape(oshape=(o_vec_len,),ishape=oshape)
# R2 = sp.linop.Reshape(oshape=(i_vec_len,),ishape=ishape)
# NFTs = R1.H*NFTs*R2
return NFTs
def DLD(Linop, device = sp.Device(-1)):
B1 = sp.linop.ToDevice(Linop.ishape,idevice=sp.Device(-1),odevice=device)
B2 = sp.linop.ToDevice(Linop.oshape,idevice=sp.Device(-1),odevice=device)
Linop = B2.H*Linop*B1
return Linop
def __init__(self, rdr, tbl, mps, psf, phi, spr='W', cft=True, \
lmb=1e-5, mit=30, alp=0.25, tol=1e-3, dev=-1):
self.cpu = -1
self.max_dims = 8
self.device = sp.Device(dev)
self.xp = self.device.xp
self.center = cft
with self.device:
self.rdr = self.xp.array(rdr).astype(self.xp.int32)
self.tbl = self.xp.array(tbl)
self.tbl = self.tbl / self.xp.max(self.xp.abs(self.tbl))
self.mps = self.xp.array(self._broadcast_check(mps))
self.psf = self.xp.array(self._broadcast_check(psf))
self.phi = self.xp.array(self._broadcast_check(phi))
self.lmb = lmb # Lambda.
self.mit = mit # Max-Iter
self.alp = alp # Step size.
self.tol = tol # Tolerance.
self.wx = self.psf.shape[7]
self.sx = self.mps.shape[7]
self.sy = self.mps.shape[6]
self.sz = self.mps.shape[5]
self.nc = self.mps.shape[4]
self.md = self.mps.shape[3]
self.tf = self.phi.shape[2]
self.tk = self.phi.shape[1]
self.net_acceleration = (self.tf * self.sy *
self.sz) / self.rdr.shape[0]
assert (self.md == 1
) # Until multiple ESPIRiT maps is implemented.
self.S = None
if (spr == 'W'):
wavelet_axes = tuple(
[k for k in range(5, 8) if self.mps.shape[k] > 1])
self.S = sp.linop.Wavelet(
[1, self.tk, 1, self.md, 1, self.sz, self.sy, self.sx],
axes=wavelet_axes)
elif (spr == 'T'):
self.S = sp.linop.FiniteDifference(
[1, self.tk, 1, self.md, 1, self.sz, self.sy, self.sx],
axes=(5, 6, 7))
else:
self.S = sp.linop.Identity(
[1, self.tk, 1, self.md, 1, self.sz, self.sy, self.sx])
self.E = sp.linop.Multiply(
[1, self.tk, 1, self.md, 1, self.sz, self.sy, self.sx],
self.mps)
self.R = sp.linop.Resize([1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx], \
[1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.sx])
self.Fx = sp.linop.FFT([1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx], axes=(7,), \
center=self.center)
self.Psf = sp.linop.Multiply(
[1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx],
self.psf)
self.Fyz = sp.linop.FFT([1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx], axes=(5, 6), \
center=self.center)
self.K = None
self._construct_kernel()
self.K = sp.linop.Reshape( [ 1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx], \
[ self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx]) * \
sp.linop.Sum( [self.tk, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx], axes=(1,)) * \
sp.linop.Multiply([ 1, self.tk, 1, 1, self.nc, self.sz, self.sy, self.wx], self.kernel)
self._construct_AHb()
self.res = 0 * self.AHb
self.AHA = self.S * self.E.H * self.R.H * self.Fx.H * self.Psf.H * self.Fyz.H * self.K * \
self.Fyz * self.Psf * self.Fx * self.R * self.E * self.S.H
self.mxevl = sp.app.MaxEig(self.AHA, self.xp.complex64,
device=dev).run()
self.alp = self.alp / self.mxevl
self.gradf = lambda x: self.AHA(x) - self.AHb
self.proxg = sp.prox.L1Reg(self.res.shape, lmb)
alg = sp.alg.GradientMethod(self.gradf,
self.res,
self.alp,
proxg=self.proxg,
accelerate=True,
tol=self.tol,
max_iter=self.mit)
super().__init__(alg)
def use_device(self, device):
self.device = sp.Device(device)
def nufft_adj1(data,
traj,
dcf,
device=sp.Device(-1),
smap=None,
batch=40000,
id_channel=False,
ishape=None):
xp = device.xp
N_phase = data.shape[0]
img = []
for num_ph in range(N_phase):
ksp_t = data[num_ph]
coord_t = traj[num_ph]
dcf_t = dcf[num_ph]
if smap is not None:
img_shape = list(smap.shape[-3:])
elif ishape is not None:
img_shape = ishape
else:
img_shape = sp.estimate_shape(coord_t)
num_coils, num_tr, num_ro = ksp_t.shape
ndim = coord_t.shape[-1]
if id_channel is True:
img_t = np.zeros((num_coils, ) + tuple(img_shape),
dtype=np.complex64)
else:
img_t = 0
with device:
for c in range(num_coils):
img_tt = 0
for seg in range((num_tr - 1) // batch + 1):
ksp_ttc = sp.to_device(
ksp_t[c, seg * batch:np.minimum((seg + 1) *
batch, num_tr), ...],
device)
coord_tt = sp.to_device(
coord_t[seg * batch:np.minimum((seg + 1) *
batch, num_tr), ...],
device)
dcf_tt = sp.to_device(
dcf_t[seg * batch:np.minimum((seg + 1) *
batch, num_tr), ...],
device)
img_tt += sp.nufft_adjoint(ksp_ttc * dcf_tt, coord_tt,
img_shape)
# TODO smap
if id_channel is True:
img_t[c, ...] = sp.to_device(img_tt)
else:
if smap is None:
img_t += xp.abs(img_tt)**2
else:
img_t += sp.to_device(
img_tt *
xp.conj(sp.to_device(smap[c, ...], device)))
img_t = sp.to_device(img_t)
img.append(img_t)
return np.asarray(img)
def circulant_precond(mps,
weights=None,
coord=None,
lamda=0,
device=sp.cpu_device):
r"""Compute circulant preconditioner.
Considers the optimization problem:
.. math::
\min_P \| A^H A - F P F^H \|_2^2
where A is the Sense operator,
and F is a unitary Fourier transform operator.
Args:
mps (array): sensitivity maps of shape [num_coils] + image shape.
weights (array): k-space weights.
coord (array): k-space coordinates of shape [...] + [ndim].
lamda (float): regularization.
Returns:
array: circulant preconditioner of image shape.
"""
if coord is not None:
coord = sp.to_device(coord, device)
if weights is not None:
weights = sp.to_device(weights, device)
dtype = mps.dtype
device = sp.Device(device)
xp = device.xp
mps_shape = list(mps.shape)
img_shape = mps_shape[1:]
img2_shape = [i * 2 for i in img_shape]
ndim = len(img_shape)
scale = sp.prod(img2_shape)**1.5 / sp.prod(img_shape)**2
with device:
idx = (slice(None, None, 2), ) * ndim
if coord is None:
ones = xp.zeros(img2_shape, dtype=dtype)
if weights is None:
ones[idx] = 1
else:
ones[idx] = weights**0.5
psf = sp.ifft(ones)
else:
coord2 = coord * 2
ones = xp.ones(coord.shape[:-1], dtype=dtype)
if weights is not None:
ones *= weights**0.5
psf = sp.nufft_adjoint(ones, coord2, img2_shape)
p_inv = 0
for mps_i in mps:
mps_i = sp.to_device(mps_i, device)
xcorr_fourier = xp.abs(sp.fft(xp.conj(mps_i), img2_shape))**2
xcorr = sp.ifft(xcorr_fourier)
xcorr *= psf
p_inv_i = sp.fft(xcorr)
p_inv_i = p_inv_i[idx]
p_inv_i *= scale
if weights is not None:
p_inv_i *= weights**0.5
p_inv += p_inv_i
p_inv += lamda
p_inv[p_inv == 0] = 1
p = 1 / p_inv
return p.astype(dtype)
np.int(np.max(traj[..., 1]) - np.min(traj[..., 1])),
np.int(np.max(traj[..., 2]) - np.min(traj[..., 2])))
## calibration
print('Calibration...')
ksp = np.reshape(np.transpose(data, (2, 1, 0, 3, 4, 5)),
(nCoil, nphase * npe, nfe))
dcf2 = np.reshape(np.transpose(dcf**2, (2, 1, 0, 3, 4, 5)),
(nphase * npe, nfe))
coord = np.reshape(np.transpose(traj, (2, 1, 0, 3, 4, 5)),
(nphase * npe, nfe, 3))
mps = ext.jsens_calib(ksp,
coord,
dcf2,
device=sp.Device(device),
ishape=tshape)
S = sp.linop.Multiply(tshape, mps)
imgL = cfl.read_cfl(fname + '_mrL')
imgL = np.squeeze(imgL)
## registration
print('Registration...')
M_fields = []
iM_fields = []
if reg_flag is 1:
for i in range(nphase):
M_field, iM_field = reg.ANTsReg(np.abs(imgL[n_ref]),
np.abs(imgL[i]))
M_fields.append(M_field)
traj = traj[...,:nf_e,:]
data = data[...,:nf_e,:]
dcf = dcf[...,:nf_e,:]
nphase,nEcalib,nCoil,npe,nfe,_ = data.shape
tshape = (np.int(np.max(traj[...,0])-np.min(traj[...,0]))
,np.int(np.max(traj[...,1])-np.min(traj[...,1]))
,np.int(np.max(traj[...,2])-np.min(traj[...,2])))
## calibration
print('Calibration...')
ksp = np.reshape(np.transpose(data,(2,1,0,3,4,5)),(nCoil,nphase*npe,nfe))
dcf2 = np.reshape(np.transpose(dcf**2,(2,1,0,3,4,5)),(nphase*npe,nfe))
coord = np.reshape(np.transpose(traj,(2,1,0,3,4,5)),(nphase*npe,nfe,3))
mps = ext.jsens_calib(ksp,coord,dcf2,device = sp.Device(device),ishape = tshape)
S = sp.linop.Multiply(tshape, mps)
imgL = cfl.read_cfl(fname+'_mrL')
imgL = np.squeeze(imgL)
## registration
print('Registration...')
M_fields = []
iM_fields = []
if reg_flag is 1:
for i in range(nphase):
M_field, iM_field = reg.ANTsReg(np.abs(imgL[n_ref]), np.abs(imgL[i]))
M_fields.append(M_field)
iM_fields.append(iM_field)
M_fields = np.asarray(M_fields)
def use_device(self, device):
self.device = sp.Device(device)
self.L = [sp.to_device(L_j, self.device) for L_j in self.L]
self.R = [sp.to_device(R_j, self.device) for R_j in self.R]
import sigpy as sp
import sigpy.mri as mr
import sigpy.plot as pl
import matplotlib.pyplot as plt
import numpy as np
# Set parameters and load dataset
max_iter = 30
max_cg_iter = 5
lamda = 0.001
ksp_file = 'data/liver/ksp.npy'
coord_file = 'data/liver/coord.npy'
device = sp.Device(-1)
xp = device.xp
device.use()
# Load datasets.
ksp = xp.load(ksp_file)
coord = xp.load(coord_file)
print(f'K-space shape: {ksp.shape}')
print(f'K-space dtype: {ksp.dtype}')
print(f'K-space (min, max): ({np.abs(ksp).min()}, {np.abs(ksp).max()})')
print(f'Coord shape: {coord.shape}') # (na, ns, 2)
print(f'Coord shape: {coord.dtype}')
print(f'Coord (min, max): ({coord.min()}, {coord.max()})')
plt.ion()
def Demons(If,
Im,
level,
device=-1,
rho=0.7,
sigmas_f=[2, 2, 2, 3],
sigmas_e=[2, 2, 2, 2],
sigmas_s=[.5, .5, 1, 1],
iters=[40, 40, 40, 20, 20]):
### normalization??
Im = np.abs(Im)
m_scale = np.max(Im)
Im = Im / m_scale
If = np.abs(If)
If = If / m_scale
### registration
M = np.zeros(Im.shape + (3, ))
Mt = np.zeros(Im.shape + (3, ))
for k in range(level):
print('Demons Level:{}'.format(k))
### hyperparameter assignment
scale = 2**(level - k - 1)
sigma_f = sigmas_f[k]
sigma_e = sigmas_e[k]
sigma_s = sigmas_s[k]
iter_each_level = iters[k]
###
Ift = ndimage.zoom(If, zoom=1 / scale, order=2)
Ift = ndimage.gaussian_filter(Ift, sigma=sigma_s, truncate=2.0)
Imt = ndimage.zoom(Im, zoom=1 / scale, order=2)
Imt = ndimage.gaussian_filter(Imt, sigma=sigma_s, truncate=2.0)
Imask = pmask(Imt + Ift, 1e-2)
Isizet = Ift.shape
Mt = M_scale(Mt, Isizet)
uo = np.zeros_like(Mt)
for i in range(iter_each_level):
Imm = interp(Imt, Mt, device=sp.Device(device), k_id=1)
Ifm = interp(Ift, -Mt, device=sp.Device(device), k_id=1)
dI = Ifm - Imm
Is = (Ifm + Imm) / 2
# Is = ndimage.gaussian_filter((Ifm+Imm)/2,sigma=sigma_s,truncate=2.0)
gIx, gIy, gIz = imgrad3d(Is)
gI = np.sqrt(np.abs(gIx**2 + gIy**2 + gIz**2) + 1e-6)
discriminator = gI**2 + np.abs(dI)**2
dI = dI * 3.0
ux = -dI * gIx / discriminator
uy = -dI * gIy / discriminator
uz = -dI * gIz / discriminator
mask = (gI < 1e-4) | (~Imask)
ux[np.isnan(ux) | mask] = 0
uy[np.isnan(uy) | mask] = 0
uz[np.isnan(uz) | mask] = 0
ux = np.maximum(np.minimum(ux, 1), -1)
uy = np.maximum(np.minimum(uy, 1), -1)
uz = np.maximum(np.minimum(uz, 1), -1)
ux = ndimage.gaussian_filter(ux, sigma=sigma_f)
uy = ndimage.gaussian_filter(uy, sigma=sigma_f)
uz = ndimage.gaussian_filter(uz, sigma=sigma_f)
Mt[..., 0] = Mt[..., 0] + rho * ux + (1 - rho) * uo[..., 0]
Mt[..., 1] = Mt[..., 1] + rho * uy + (1 - rho) * uo[..., 1]
Mt[..., 2] = Mt[..., 2] + rho * uz + (1 - rho) * uo[..., 2]
uo[..., 0] = ux
uo[..., 1] = uy
uo[..., 2] = uz
Mt[..., 0] = ndimage.gaussian_filter(Mt[..., 0], sigma=sigma_e)
Mt[..., 1] = ndimage.gaussian_filter(Mt[..., 1], sigma=sigma_e)
Mt[..., 2] = ndimage.gaussian_filter(Mt[..., 2], sigma=sigma_e)
### TODO inverse combination (right now just double)
M = M_scale(Mt * 2, Im.shape)
return M
