def create_ct_foam_phantom(shape=501, seed=0, gen_new=False):
""""""
if gen_new:
foam_ct_phantom.FoamPhantom.generate('large_foam_phantom.h5',
seed,
nspheres_per_unit=10000)
# (nx, ny, nx) for phatom volume geometry
shape = shape if isinstance(shape, tuple) else (shape, ) * 3
phantom = foam_ct_phantom.FoamPhantom('large_foam_phantom.h5')
geom = foam_ct_phantom.VolumeGeometry(*shape, voxsize=3 / shape[0])
phantom.generate_volume('test_phantom.h5', geom)
# [z,y,x] axis order
phantom_volume = foam_ct_phantom.load_volume('test_phantom.h5')
return phantom_volume
startz=1.5,
cutoff=1e-2)
infiltration_phantom = foam_ct_phantom.InfiltrationFoamPhantom(
'test_infiltration.h5')
vol_geom = foam_ct_phantom.VolumeGeometry(256, 256, 1, 3 / 256)
infiltration_phantom.generate_volume('test_infiltration_vol_start.h5',
vol_geom,
time=0)
infiltration_phantom.generate_volume('test_infiltration_vol_end.h5',
vol_geom,
time=1)
vol0 = foam_ct_phantom.load_volume('test_infiltration_vol_start.h5')
vol1 = foam_ct_phantom.load_volume('test_infiltration_vol_end.h5')
pl.imshow(vol0[0])
pl.figure()
pl.imshow(vol1[0])
pl.show()
proj_geom = foam_ct_phantom.ParallelGeometry(
256, 256, np.linspace(0, 4 * np.pi, 128, False), 3 / 256)
infiltration_phantom.generate_projections('test_infiltration_projs.h5',
proj_geom)
projs = foam_ct_phantom.load_projections('test_infiltration_projs.h5')
pl.imshow(projs[0])
pl.figure()
def build_foam_phantom_dataset(folder_path,
n_phantoms,
spheres_per_unit=10000,
GPU_ID=0):
# Choose to reset dataset path or not
if os.path.exists(folder_path):
print("Path already exists, delete?")
choice = input()
if choice.lower()[0] == 'y':
shutil.rmtree(folder_path)
os.makedirs(folder_path)
else:
print("Will overwrite files in folder")
shape = (501, ) * 3
n_rad_slices = 360
temp_dir = '_temp_phatoms/'
if not os.path.exists(temp_dir):
os.mkdir(temp_dir)
scanner_params = FleX_ray_scanner()
orbit_elevation = [-15, 0, 15]
theta_range = np.linspace(0, np.pi, n_rad_slices, endpoint=False)
for i in range(n_phantoms):
foam_ct_phantom.FoamPhantom.generate(
os.path.join(temp_dir, 'foam_phantom.h5'),
seed=i,
nspheres_per_unit=spheres_per_unit)
phantom = foam_ct_phantom.FoamPhantom(
os.path.join(temp_dir, 'foam_phantom.h5'))
geom = foam_ct_phantom.VolumeGeometry(*shape, voxsize=3 / shape[0])
phantom.generate_volume(os.path.join(temp_dir, 'gen_phantom.h5'), geom)
phantom_volume = foam_ct_phantom.load_volume(
os.path.join(temp_dir, 'gen_phantom.h5'))
if not os.path.exists(os.path.join(folder_path, f'phantom{i+1}/')):
os.makedirs(os.path.join(folder_path, f'phantom{i+1}/'))
rad_slices = astra_sim.radial_slice_sampling(phantom_volume,
theta_range)
for j in range(len(rad_slices)):
print(f"\rSaving phantom_n{i+1:0>3d}_s{j+1:0>4d}.tif", end=' ' * 5)
imsave(
os.path.join(folder_path, f'phantom{i+1}/',
f"phantom_true_n{i+1:0>3d}_s{j+1:0>4d}.tif"),
rad_slices[j].astype('float32'))
print('')
# Simulates FDK reconstruction for all 3 orbits
for orbit in [1, 2, 3]:
vecs = astra_sim.create_scan_geometry(
scanner_params, 1200, elevation=orbit_elevation[orbit - 1])
projections = astra_sim.create_CB_projection(phantom_volume,
scanner_params,
proj_vecs=vecs,
gpu_id=GPU_ID)
fdk_phantom_volume = astra_sim.FDK_reconstruction(projections,
scanner_params,
proj_vecs=vecs,
gpu_id=GPU_ID,
rec_shape=(501,
501,
501))
fdk_rad_slices = astra_sim.radial_slice_sampling(
fdk_phantom_volume, theta_range)
for j in range(len(rad_slices)):
print(f"\rSaving phantom_n{i+1:0>3d}_s{j+1:0>4d}.tif",
end=' ' * 5)
imsave(
os.path.join(
folder_path, f'phantom{i+1}/',
f"phantom_fdk_n{i+1:0>3d}_o{orbit:d}_s{j+1:0>4d}.tif"),
fdk_rad_slices[j].astype('float32'))
print('')
# Removes temp phatom files
shutil.rmtree(temp_dir)
"""
import foam_ct_phantom
import numpy as np
import pylab as pl
pl.gray()
random_seed = 12345
def maxsize_func(x, y, z):
return 0.2 - 0.1 * np.abs(z)
# Note that nspheres_per_unit is set to a low value to reduce the computation time here.
# The default value is 100000.
foam_ct_phantom.FoamPhantom.generate('test_uniform.h5',
random_seed,
nspheres_per_unit=1000,
maxsize=maxsize_func)
geom = foam_ct_phantom.VolumeGeometry(1, 256, 256, 3 / 256)
phantom = foam_ct_phantom.FoamPhantom('test_uniform.h5')
phantom.generate_volume('test_uniform_midslice.h5', geom)
vol = foam_ct_phantom.load_volume('test_uniform_midslice.h5')
pl.imshow(vol[..., 0])
pl.show()
import pylab as pl
pl.gray()
random_seed = 9876
foam_ct_phantom.ExpandingFoamPhantom.generate('test_expand.h5',
'test_phantom.h5', random_seed)
expanding_phantom = foam_ct_phantom.ExpandingFoamPhantom('test_expand.h5')
vol_geom = foam_ct_phantom.VolumeGeometry(256, 256, 1, 3 / 256)
expanding_phantom.generate_volume('test_expand_vol_start.h5', vol_geom, time=0)
expanding_phantom.generate_volume('test_expand_vol_end.h5', vol_geom, time=1)
vol0 = foam_ct_phantom.load_volume('test_expand_vol_start.h5')
vol1 = foam_ct_phantom.load_volume('test_expand_vol_end.h5')
pl.imshow(vol0[0])
pl.figure()
pl.imshow(vol1[0])
pl.show()
proj_geom = foam_ct_phantom.ParallelGeometry(
256, 128, np.linspace(0, 4 * np.pi, 128, False), 3 / 256)
expanding_phantom.generate_projections('test_expand_projs.h5', proj_geom)
projs = foam_ct_phantom.load_projections('test_expand_projs.h5')
pl.imshow(projs[0])
pl.figure()
pl.imshow(projs[-1])
import pylab as pl
pl.gray()
random_seed = 9876
foam_ct_phantom.MovingFoamPhantom.generate('test_moving.h5', 'test_phantom.h5',
random_seed, -0.75, 0.75)
moving_phantom = foam_ct_phantom.MovingFoamPhantom('test_moving.h5')
vol_geom = foam_ct_phantom.VolumeGeometry(256, 256, 1, 3 / 256)
moving_phantom.generate_volume('test_moving_vol_start.h5', vol_geom, time=0)
moving_phantom.generate_volume('test_moving_vol_end.h5', vol_geom, time=1)
vol0 = foam_ct_phantom.load_volume('test_moving_vol_start.h5')
vol1 = foam_ct_phantom.load_volume('test_moving_vol_end.h5')
pl.imshow(vol0[0])
pl.figure()
pl.imshow(vol1[0])
pl.show()
proj_geom = foam_ct_phantom.ParallelGeometry(
256, 128, np.linspace(0, 4 * np.pi, 128, False), 3 / 256)
moving_phantom.generate_projections('test_moving_projs.h5', proj_geom)
projs = foam_ct_phantom.load_projections('test_moving_projs.h5')
pl.imshow(projs[0])
pl.figure()
pl.imshow(projs[-1])