def test_simple():
"""Simple test for backproject"""
count = mp.Value("i")
max_count = mp.Value("i")
sino = np.random.random((10, 30))
radontea.backproject(sinogram=sino,
angles=np.arange(len(sino)),
count=count,
max_count=max_count)
assert count.value == 11
assert count.value == max_count.value
def test_2d_backproject():
sino, angles = create_test_sino(A=100, N=100)
r = radontea.backproject(sino, angles, padding=True)
# np.savetxt('outfile.txt', np.array(r).flatten().view(float), fmt="%.8f")
reffile = pathlib.Path(__file__).parent / "data" / "2d_backproject.txt"
ref = np.loadtxt(str(reffile))
assert np.allclose(np.array(r).flatten().view(float), ref)
def test_2d_backproject():
sino, angles = create_test_sino(A=100, N=100)
r = radontea.backproject(sino, angles, padding=True)
# np.savetxt('outfile.txt', np.array(r).flatten().view(float), fmt="%.8f")
reffile = pathlib.Path(__file__).parent / "data" / "2d_backproject.txt"
ref = np.loadtxt(str(reffile))
assert np.allclose(np.array(r).flatten().view(float), ref)
def test_2d_backproject():
myname = sys._getframe().f_code.co_name
print("running ", myname)
sino, angles = create_test_sino(A=100, N=100)
r = radontea.backproject(sino, angles, padding=True)
r2 = radontea._Back.backproject(sino, angles, padding=True)
# np.savetxt('outfile.txt', np.array(r).flatten().view(float), fmt="%.8f")
assert np.allclose(r, r2)
assert np.allclose(np.array(r).flatten().view(float), results[myname])
from matplotlib import pylab as plt
import numpy as np
import radontea
from radontea.logo import get_original
N = 55 # image size
A = 13 # number of sinogram angles
ITA = 10 # number of iterations a
ITB = 100 # number of iterations b
angles = np.linspace(0, np.pi, A)
im = get_original(N)
sino = radontea.radon_parallel(im, angles)
fbp = radontea.backproject(sino, angles)
fintp = radontea.fourier_map(sino, angles).real
sarta = radontea.sart(sino, angles, iterations=ITA)
sartb = radontea.sart(sino, angles, iterations=ITB)
im2 = (im >= (im.max() / 5)) * 255
sino2 = radontea.radon_parallel(im2, angles)
fbp2 = radontea.backproject(sino2, angles)
fintp2 = radontea.fourier_map(sino2, angles).real
sarta2 = radontea.sart(sino2, angles, iterations=ITA)
sartb2 = radontea.sart(sino2, angles, iterations=ITB)
plt.figure(figsize=(8, 22))
pltkw = {"vmin": -20,
"vmax": 280}
from matplotlib import pylab as plt
import numpy as np
import radontea
from radontea.logo import get_original
N = 55 # image size
A = 13 # number of sinogram angles
ITA = 10 # number of iterations a
ITB = 100 # number of iterations b
angles = np.linspace(0, np.pi, A)
im = get_original(N)
sino = radontea.radon_parallel(im, angles)
fbp = radontea.backproject(sino, angles)
fintp = radontea.fourier_map(sino, angles).real
sarta = radontea.sart(sino, angles, iterations=ITA)
sartb = radontea.sart(sino, angles, iterations=ITB)
im2 = (im >= (im.max() / 5)) * 255
sino2 = radontea.radon_parallel(im2, angles)
fbp2 = radontea.backproject(sino2, angles)
fintp2 = radontea.fourier_map(sino2, angles).real
sarta2 = radontea.sart(sino2, angles, iterations=ITA)
sartb2 = radontea.sart(sino2, angles, iterations=ITB)
plt.figure(figsize=(8, 22))
pltkw = {"vmin": -20, "vmax": 280}
plt.subplot(6, 2, 1, title="original image")
import jobmanager as jm
jm.decorators.decorate_module_ProgressBar(rt,
decorator=jm.decorators.ProgressBarOverrideCount,
interval=.1)
except:
pass
if __name__ == "__main__":
A = 70 # number of angles
N = 128 # detector size x
M = 24 # detector size y (number of slices)
# generate random data
sino0 = np.random.random((A,N)) # for 2d example
sino = np.random.random((A,M,N)) # for 3d example
sino[:,0,:] = sino0
angles = np.linspace(0,np.pi,A) # for both
a = time.time()
data0 = rt.backproject(sino0, angles)
print("time on 1 core: {} s".format((time.time() - a)*M))
a = time.time()
data = rt._Back_3D.backproject(sino, angles)
print("time on {} cores: {} s".format(cpu_count(), time.time() - a))
assert np.sum(data0==data[:,0,:]) == N**2, "2D and 3D results don't match"
t_ImageInterp[t_Sudut] = t_XValueInterp
## Interpolasi Sudut
t_YIndex = np.arange(t_ImageInterp.shape[0])
t_YIndexInterp = np.linspace(0, t_ImagePartial.shape[0] - 1, A)
for t_SensorPos in range(t_ImageInterp.shape[1]):
t_YValueInterp = np.interp(t_YIndexInterp, t_YIndex,
t_ImageInterp[:, t_SensorPos])
# print(t_YValueInterp, ' len=', len(t_YValueInterp))
t_ImageInterp[:, t_SensorPos] = t_YValueInterp
print(t_ImagePartial.shape)
t_SinoPartial = radontea.radon_parallel(t_ImagePartial, t_Angles)
t_Sino = radontea.radon_parallel(t_ImageInterp, t_Angles)
print('Sinogram shape = ', t_Sino.shape)
t_FilterBackProjection = radontea.backproject(t_Sino, t_Angles)
t_SART = radontea.sart(t_Sino, t_Angles, iterations=15)
# t_Reconstruction = iradon(t_Sino, filter="ramp" ,interpolation="linear", circle=True)#, theta=t_Angles)
# t_Reconstruction = iradon_sart(t_Sino, theta=t_Angles, relaxation=0.01)
fig, axes = plt.subplots(2, 2)
ax = axes.ravel()
ax[0].set_title("Original")
# ax[0].imshow(image, cmap=plt.cm.Greys_r)
# ax[0].imshow(t_ImageNoised[::7], cmap="jet")
ax[0].imshow(t_SinoPartial[::10], cmap="jet")
ax[1].imshow(t_Sino, cmap="jet")
ax[2].imshow(t_FilterBackProjection, cmap="jet")
ax[3].imshow(t_SART, cmap="jet")
def backpropagate_sinogram(
sinogram,
angles,
approx,
res,
nm,
ld=0,
):
"""Backpropagate a 2D or 3D sinogram
Parameters
----------
sinogram: complex ndarray
The scattered field data
angles: 1d ndarray
The angles at which the sinogram data were recorded
approx: str
Approximation to use, one of ["radon", "born", "rytov"]
res: float
Size of vacuum wavelength in pixels
nm: float
Refractive index of surrounding medium
ld: float
Reconstruction distance. Values !=0 only make sense for the
Born approximation (which itself is not very usable).
See the ODTbrain documentation for more information.
Returns
-------
ri: ndarray
The 2D or 3D reconstructed refractive index
"""
sshape = len(sinogram.shape)
assert sshape in [2, 3], "sinogram must have dimension 2 or 3"
uSin = sinogram
assert approx in ["radon", "born", "rytov"]
if approx == "rytov":
uSin = odt.sinogram_as_rytov(uSin)
elif approx == "radon":
uSin = odt.sinogram_as_radon(uSin)
if approx in ["born", "rytov"]:
# Perform reconstruction with ODT
if sshape == 2:
f = odt.backpropagate_2d(uSin,
angles=angles,
res=res,
nm=nm,
lD=ld)
else:
f = odt.backpropagate_3d(uSin,
angles=angles,
res=res,
nm=nm,
lD=ld)
ri = odt.odt_to_ri(f, res, nm)
else:
# Perform reconstruction with OPT
# works in 2d and 3d
f = rt.backproject(uSin, angles=angles)
ri = odt.opt_to_ri(f, res, nm)
return ri