obj3D_2 = {
'Obj': Objects3D.CUBOID,
'C0': 1.00,
'x0': 0.1,
'y0': 0.2,
'z0': 0.0,
'a': 0.15,
'b': 0.35,
'c': 0.6,
'phi1': -60.0
}
print("Building 3D object using TomoPhantom software")
myObjects = [obj3D_1, obj3D_2] # dictionary of objects
Object3D = TomoP3D.Object(N3D_size, myObjects)
sliceSel = int(0.5 * N3D_size)
#plt.gray()
plt.figure()
plt.subplot(131)
plt.imshow(Object3D[sliceSel, :, :], vmin=0, vmax=1)
plt.title('3D Object, axial view')
plt.subplot(132)
plt.imshow(Object3D[:, sliceSel, :], vmin=0, vmax=1)
plt.title('3D Object, coronal view')
plt.subplot(133)
plt.imshow(Object3D[:, :, sliceSel], vmin=0, vmax=1)
plt.title('3D Object, sagittal view')
N3D_size = 256
obj3D = {
'Obj': Objects3D.GAUSSIAN,
'C0': 1.00,
'x0': -0.25,
'y0': 0.1,
'z0': 0.0,
'a': 0.2,
'b': 0.35,
'c': 0.7,
'phi1': 30.0,
'phi2': 60.0,
'phi3': -25.0
}
Object3D = TomoP3D.Object(N3D_size, [obj3D])
sliceSel = int(0.5 * N3D_size)
#plt.gray()
plt.figure(7)
plt.subplot(121)
plt.imshow(Object3D[sliceSel, :, :], vmin=0, vmax=1)
plt.title('3D Phantom, axial view')
plt.subplot(122)
plt.imshow(Object3D[:, sliceSel, :], vmin=0, vmax=1)
plt.title('3D Phantom, coronal view')
plt.show()
#%%
'Obj': Objects3D.ELLIPSOID,
'C0': 1.00,
'x0': -0.5,
'y0': -0.5,
'z0': z_coord_steps[i],
'a': 0.18,
'b': 0.07,
'c': 0.13,
'phi1': 0.0,
'phi2': 0.0,
'phi3': 0.0
}
myObjects = [obj3D1, obj3D2, obj3D3, obj3D4] # dictionary of objects
object3D = TomoP3D.Object(ObjSize, myObjects)
"""
sliceSel = 200
#plt.gray()
plt.figure()
plt.subplot(121)
plt.imshow(Object3D[sliceSel,:,:],vmin=0, vmax=1)
plt.title('3D Phantom, axial view')
plt.subplot(122)
plt.imshow(Object3D[:,sliceSel,:],vmin=0, vmax=1)
plt.title('3D Phantom, coronal view')
plt.show()
"""
# obtain projections using ASTRA-toolbox
Atools = AstraTools3D(DetRows, DetColumns, angles_rad,
print("append", end1 - start)
while (nop.append_for(np.random.uniform(low=-1, high=1, size=3)) < M):
pass
end2 = time.time()
print("append_for", end2 - end1)
#%%
gaussians = [{
'Obj': tp3.Objects3D.PARABOLOID,
'C0': 1.,
'x0': float(nop.apoints[loc][0]),
'y0': float(nop.apoints[loc][1]),
'z0': float(nop.apoints[loc][2]),
'a': .2,
'b': .1,
'c': .15,
'phi1': np.random.uniform(low=0, high=360),
'phi2': np.random.uniform(low=0, high=360),
'phi3': np.random.uniform(low=0, high=360)
} for loc in range(len(nop.apoints))]
vol = tp3.Object(128, gaussians)
plt.imshow(vol[0])
plt.show()
writer = vtk.vtkMetaImageWriter()
conv = Converter.numpy2vtkImporter(vol)
conv.Update()
writer.SetInputData(conv.GetOutput())
writer.SetFileName("dvc_phantom0.mha")
writer.Write()
phi_max = 180.0
phi1 = random.uniform(phi_min, phi_max)
el3 = {
'Obj': Objects3D.CUBOID,
'C0': C_0,
'x0': x0_rand,
'y0': y0_rand,
'z0': z0_rand,
'a': a_el3,
'b': b_el3,
'c': c_el3,
'phi1': phi1
}
GROUND_TRUTH = TomoP3D.Object(N_size, [el1, el2, el3])
GROUND_TRUTH[GROUND_TRUTH > 0.7] = 0.43336788
GROUND_TRUTH[(GROUND_TRUTH > 0.0) & (GROUND_TRUTH < 0.29999998)] = 0.43336788
sliceSel = (int)(N_size / 2)
plt.figure()
plt.subplot(131)
plt.imshow(GROUND_TRUTH[sliceSel, :, :])
plt.title('Ideal Phantom1')
plt.subplot(132)
plt.imshow(GROUND_TRUTH[:, sliceSel, :])
plt.title('Ideal Phantom2')
plt.subplot(133)
plt.imshow(GROUND_TRUTH[:, :, sliceSel])
plt.title('Ideal Phantom3')
def foam3D(x0min, x0max, y0min, y0max, z0min, z0max, c0min, c0max, ab_min,
ab_max, N_size, tot_objects, object_type):
import numpy as np
import math
import random
#3D functions
from tomophantom import TomoP3D
from tomophantom.TomoP3D import Objects3D
attemptsNo = 2000
# objects accepted: 'ellipsoid', 'paraboloid', 'gaussian', 'mix'
mix_objects = False
if (object_type == 'ellipsoid'):
object_type = Objects3D.ELLIPSOID
elif (object_type == 'paraboloid'):
object_type = Objects3D.PARABOLOID
elif (object_type == 'gaussian'):
object_type = Objects3D.GAUSSIAN
elif (object_type == 'mix'):
mix_objects = True
else:
raise TypeError(
'object_type can be only ellipse, parabola, gaussian or mix')
X0 = np.float32(np.zeros(tot_objects))
Y0 = np.float32(np.zeros(tot_objects))
Z0 = np.float32(np.zeros(tot_objects))
AB = np.float32(np.zeros(tot_objects))
C0_var = np.float32(np.zeros(tot_objects))
for i in range(0, tot_objects):
(x0, y0, z0, c0, ab) = rand_init3D(x0min, x0max, y0min, y0max, z0min,
z0max, c0min, c0max, ab_min, ab_max)
if (i > 0):
breakj = False
for j in range(0, attemptsNo):
if breakj:
(x0, y0, z0, c0,
ab) = rand_init3D(x0min, x0max, y0min, y0max, z0min,
z0max, c0min, c0max, ab_min, ab_max)
breakj = False
else:
for l in range(
0, i
): # checks consistency with previously created objects
dist = math.sqrt((X0[l] - x0)**2 + (Y0[l] - y0)**2 +
(Z0[l] - z0)**2)
if (dist < (ab + AB[l])) or ((abs(x0) + ab)**2 +
(abs(y0) + ab)**2 +
(abs(z0) + ab)**2 > 1.0):
breakj = True
break
if (breakj == False
): # re-initialise if doesn't fit the criteria
X0[i] = x0
Y0[i] = y0
Z0[i] = z0
AB[i] = ab
C0_var[i] = c0
break
if (AB[i] == 0.0):
X0[i] = x0
Y0[i] = y0
AB[i] = 0.0001
C0_var[i] = c0
myObjects = [] # dictionary of objects
for obj in range(0, len(X0)):
if (mix_objects == True):
rand_obj = random.randint(0, 2)
if (rand_obj == 0):
object_type = Objects3D.ELLIPSOID
if (rand_obj == 1):
object_type = Objects3D.PARABOLOID
if (rand_obj == 2):
object_type = Objects3D.GAUSSIAN
curr_obj = {
'Obj': object_type,
'C0': C0_var[obj],
'x0': X0[obj],
'y0': Y0[obj],
'z0': Z0[obj],
'a': AB[obj],
'b': AB[obj],
'c': AB[obj],
'phi1': 0.0
}
myObjects.append(curr_obj)
Object3D = TomoP3D.Object(N_size, myObjects)
return (Object3D, myObjects)
