def non_uniform_kspace(phantom):
NufftObj = pnft.NUFFT()
Nd = (phantom.shape[0], phantom.shape[1])
Kd = (2 * phantom.shape[0], 2 * phantom.shape[1])
Jd = (6, 6)
om = np.random.randn(15120, 3)
NufftObj.plan(om, Nd, Kd, Jd)
x = NufftObj.forward(phantom)
Data = NufftObj.solve(x, solver='cg', maxiter=50)
k = np.fft.fft2(Data)
k_space = (np.fft.fftshift(k)) / np.sqrt(k)
plt.title('Non-uniform K-Space of The phantom'), plt.xticks(
[]), plt.yticks([])
plt.imshow(20 * np.log(np.abs(k_space)), cmap='gray')
plt.show()
def __init__(self, samples, shape):
""" Initialize the 'NUFFT3' class.
Parameters
----------
samples: np.ndarray((m'*n'*p', 3))
samples' coordinates in the Fourier domain.
shape: tuple of int
shape of the final reconstructed image (m, n, p) (not necessarily
a square matrix).
"""
self.plan = pynufft.NUFFT()
shape_fourier = []
for dim_size in shape:
shape_fourier.append(int(2 * dim_size))
self.plan.plan(samples, tuple(shape), tuple(shape_fourier), (5, 5, 5))
self.shape = shape
self.samples = samples
def get_nufft_obj(trajectory, nimg, nfe, n_kernel=6, device_index=None):
NufftObj = pynufft.NUFFT(device_indx=device_index)
n_size = np.prod(trajectory[0].shape)
traj0_max = np.max(trajectory[0])
traj1_max = np.max(trajectory[1])
traj0 = np.reshape(trajectory[0],
(n_size, )) / traj0_max * np.pi # normalize to -pi..pi
traj1 = np.reshape(trajectory[1],
(n_size, )) / traj1_max * np.pi # normalize to -pi..pi
# Stack real and imag together
om_traj = np.stack([traj0, traj1], axis=-1)
NufftObj.plan(om_traj,
Nd=(nimg, nimg),
Kd=(nfe, nfe),
Jd=(n_kernel, n_kernel))
return NufftObj
def test_init():
import cProfile
import numpy
import matplotlib.pyplot
import copy
cm = matplotlib.cm.gray
# load example image
import pkg_resources
DATA_PATH = pkg_resources.resource_filename('pynufft', 'src/data/')
# PHANTOM_FILE = pkg_resources.resource_filename('pynufft', 'data/phantom_256_256.txt')
import numpy
import matplotlib.pyplot
import scipy
# load example image
# image = numpy.loadtxt(DATA_PATH +'phantom_256_256.txt')
# image = scipy.misc.face(gray=True)
image = scipy.misc.ascent()
image = scipy.misc.imresize(image, (256,256))
image=image.astype(numpy.float)/numpy.max(image[...])
#numpy.save('phantom_256_256',image)
matplotlib.pyplot.subplot(1,3,1)
matplotlib.pyplot.imshow(image, cmap=matplotlib.cm.gray)
matplotlib.pyplot.title("Load Scipy \"ascent\" image")
# matplotlib.pyplot.show()
print('loading image...')
# image[128, 128] = 1.0
Nd = (256, 256) # image space size
Kd = (512, 512) # k-space size
Jd = (6, 6) # interpolation size
# load k-space points
om = numpy.load(DATA_PATH+'om2D.npz')['arr_0']
# create object
# else:
# n_shift=tuple(list(n_shift)+numpy.array(Nd)/2)
import pynufft
nfft = pynufft.NUFFT() # CPU
nfft.plan(om, Nd, Kd, Jd)
# nfft.initialize_gpu()
import scipy.sparse
# scipy.sparse.save_npz('tests/test.npz', nfft.st['p'])
NufftObj = NUFFT()
NufftObj.plan(om, Nd, Kd, Jd)
NufftObj.offload(API='ocl', platform_number= 1 , device_number= 0)
# print('sp close? = ', numpy.allclose( nfft.st['p'].data, NufftObj.st['p'].data, atol=1e-1))
# NufftObj.initialize_gpu()
y = nfft.k2y(nfft.xx2k(nfft.x2xx(image)))
NufftObj.x_Nd = NufftObj.thr.to_device( image.astype(dtype))
gx = NufftObj.thr.copy_array(NufftObj.x_Nd)
print('x close? = ', numpy.allclose(image, NufftObj.x_Nd.get() , atol=1e-4))
NufftObj._x2xx()
# ttt2= NufftObj.thr.copy_array(NufftObj.x_Nd)
print('xx close? = ', numpy.allclose(nfft.x2xx(image), NufftObj.x_Nd.get() , atol=1e-4))
NufftObj._xx2k()
# print(NufftObj.k_Kd.get(queue=NufftObj.queue, async=True).flags)
# print(nfft.xx2k(nfft.x2xx(image)).flags)
k = nfft.xx2k(nfft.x2xx(image))
print('k close? = ', numpy.allclose(nfft.xx2k(nfft.x2xx(image)), NufftObj.k_Kd.get() , atol=1e-3*numpy.linalg.norm(k)))
NufftObj._k2y()
NufftObj._y2k()
y2 = NufftObj.y.get( )
print('y close? = ', numpy.allclose(y, y2 , atol=1e-3*numpy.linalg.norm(y)))
# print(numpy.mean(numpy.abs(nfft.y2k(y)-NufftObj.k_Kd2.get(queue=NufftObj.queue, async=False) )))
print('k2 close? = ', numpy.allclose(nfft.y2k(y2), NufftObj.k_Kd2.get(), atol=1e-3*numpy.linalg.norm(nfft.y2k(y2)) ))
NufftObj._k2xx()
# print('xx close? = ', numpy.allclose(nfft.k2xx(nfft.y2k(y2)), NufftObj.xx_Nd.get(queue=NufftObj.queue, async=False) , atol=0.1))
NufftObj._xx2x()
print('x close? = ', numpy.allclose(nfft.adjoint(y2), NufftObj.x_Nd.get() , atol=1e-3*numpy.linalg.norm(nfft.adjoint(y2))))
image3 = NufftObj.x_Nd.get()
import time
t0 = time.time()
for pp in range(0,10):
# y = nfft.k2y(nfft.xx2k(nfft.x2xx(image)))
# x = nfft.adjoint(y)
y = nfft.forward(image)
# y2 = NufftObj.y.get( NufftObj.queue, async=False)
t_cpu = (time.time() - t0)/10.0
print(t_cpu)
# del nfft
t0= time.time()
for pp in range(0,100):
# pass
# NufftObj.adjoint()
gy=NufftObj.forward(gx)
# NufftObj.thr.synchronize()
t_cl = (time.time() - t0)/100
print(t_cl)
print('gy close? = ', numpy.allclose(y,gy.get(), atol=1e-1))
print("acceleration=", t_cpu/t_cl)
maxiter =100
import time
t0= time.time()
# x2 = nfft.solver(y2, 'cg',maxiter=maxiter)
x2 = nfft.solver(y2, 'L1TVLAD',maxiter=maxiter, rho = 2)
t1 = time.time()-t0
# gy=NufftObj.thr.copy_array(NufftObj.thr.to_device(y2))
t0= time.time()
# x = NufftObj.solver(gy,'dc', maxiter=maxiter)
x = NufftObj.solver(gy,'L1TVLAD', maxiter=maxiter, rho=2)
t2 = time.time() - t0
print(t1, t2)
print('acceleration=', t1/t2 )
# k = x.get()
# x = nfft.k2xx(k)/nfft.st['sn']
# return
matplotlib.pyplot.subplot(1, 3, 2)
matplotlib.pyplot.imshow( x.get().real, cmap= matplotlib.cm.gray)
matplotlib.pyplot.subplot(1, 3,3)
matplotlib.pyplot.imshow(x2.real, cmap= matplotlib.cm.gray)
matplotlib.pyplot.show()
import numpy
# from pynufft import NUFFT
import pynufft
NufftObj = pynufft.NUFFT()
# load the data folder
import pkg_resources
# find the relative path of data folder
DATA_PATH = pkg_resources.resource_filename('pynufft', 'src/data/')
# now load the om locations
om = numpy.load(DATA_PATH + 'om2D.npz')['arr_0']
# om is an Mx2 numpy.ndarray
print(om)
# display om
import matplotlib.pyplot as pyplot
pyplot.plot(om[:, 0], om[:, 1])
pyplot.title('2D trajectory of M points')
pyplot.xlabel('X')
pyplot.ylabel('Y')
pyplot.show()
Nd = (256, 256) # image dimension
Kd = (512, 512) # k-spectrum dimension
Jd = (6, 6) # interpolator size
NufftObj.plan(om, Nd, Kd, Jd)