def create_rotating_plaque_phantoms():
"""
A cross-sectional slice through e.g. an artery with a
lump of scatterers moving along the outer perimenter to
simulate a plaque which is moving.
"""
from rotating_plaque import create_phantom
args = Args()
args.x_min = -0.015
args.x_max = 0.015
args.z_min = 0.0
args.z_max = 0.03
args.num_scatterers = 100000
args.z0 = 0.015
args.radius = 5e-3
args.num_cs = 10
args.spline_degree = 3
args.num_plaque_scatterers = 1000
args.inside_ampl = 0.02
args.plaque_radius = 1.6e-3
args.h5_file = os.path.join(out_dir, "rotating_plaque_small.h5")
create_phantom(args)
args.plaque_radius = 2.9e-3
args.h5_file = os.path.join(out_dir, "rotating_plaque_large.h5")
create_phantom(args)
def create_carotid_bifurcation_phantoms():
"""
Create carotid bifurcation phantom (1) without plaque and (2) with plaque
"""
from carotid_bifurcation import create_phantom
args = Args()
args.z0 = 0.025
args.x_min = -0.08
args.x_max = 0.08
args.y_min = -0.03
args.y_max = 0.03
args.z_min = 0.0
args.z_max = 0.05
args.num_scatterers = 5000000
args.small_r = 5e-3
args.large_r = 8.2e-3
args.common_x_max = 13e-3
args.theta = 3.141592*10/180.0
args.visualize = False
args.lumen_ampl = 0.1
args.enable_plaque = False
args.h5_file = os.path.join(out_dir, "carotid_no_plaque.h5")
create_phantom(args)
args.enable_plaque = True
args.h5_file = os.path.join(out_dir, "carotid_plaque.h5")
create_phantom(args)
def create_lv_spline_phantom():
"""
3D left ventricle phantom which contracts according to a realistic
contraction function.
"""
from lv_spline_model import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "lv_spline_model.h5")
args.thickness = 8e-3
args.z_ratio = 0.7
args.x_min = -0.02
args.x_max = 0.02
args.y_min = -0.02
args.y_max = 0.02
args.z_min = 0.008
args.z_max = 0.09
args.num_scatterers_in_box = 400000
args.motion_ampl = 0.25
args.t0 = 0.0
args.t1 = 1.0
args.spline_degree = 2
args.num_cs = 10
args.scale_h5_file = "phantom_data/real_left_ventricle_contraction.h5"
args.lv_max_amplitude = 1.0
args.rotation_scale = 3.0
create_phantom(args)
def create_artery_phantom():
"""
Stack cross-sectional splines and interpolate shape
in between.
"""
from realistic_artery import create_phantom
args = Args()
args.x_min = -0.06
args.x_max = 0.06
args.h5_out = os.path.join(out_dir, "realistic_artery.h5")
args.spline_files = ["phantom_data/artery_crossection_splines/spline_000.txt",
"phantom_data/artery_crossection_splines/spline_001.txt",
"phantom_data/artery_crossection_splines/spline_002.txt",
"phantom_data/artery_crossection_splines/spline_003.txt",
"phantom_data/artery_crossection_splines/spline_004.txt",
"phantom_data/artery_crossection_splines/spline_005.txt",
"phantom_data/artery_crossection_splines/spline_006.txt"]
args.scale = 3e-3
args.num_scatterers = 2000000
args.inside_factor = 0.1
args.outside_factor = 1.0
args.space_factor = 0.5
create_phantom(args)
def create_rotating_cube_phantom():
"""
A rotating 3D cube of scatterers, which is a good example
of complex scatterer tracjectories in 3D.
"""
from rotating_cube import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "rot_cube.h5")
args.x_min = -0.03
args.x_max = 0.03
args.y_min = -0.03
args.y_max = 0.03
args.z_min = -0.0
args.z_max = 0.03
args.z0 = 0.06
args.num_cs = 20
args.spline_degree = 3
args.t0 = 0.0
args.t1 = 1.0
args.num_scatterers = 100000
# velocities are chosen so that the motion has a period of one second
args.x_angular_velocity = 3.14159*2
args.y_angular_velocity = 3.14159*4
args.z_angular_velocity = 3.14159*8
create_phantom(args)
def create_2d_cyst_phantom():
"""
Create a 2D cyst phantom.
"""
from cyst_phantom_2d import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "cyst_2d.h5")
args.density = 500.0
args.cyst_scale = 0.3
create_phantom(args)
def create_spinning_disk_phantom():
from spinning_disc import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "spinning_disc.h5")
args.degree = 2
args.num_cs = 10
args.period = 1.0
args.num_scatterers = 20000
args.z0 = 0.025
args.radius = 2e-2
create_phantom(args)
def create_simple_phantom():
"""
A few scatterers along the positive z-axis.
"""
from simple import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "simple.h5")
args.num_scatterers=12
args.z0 = 0.005
args.z1 = 0.12
create_phantom(args)
def create_contracting_cylinder():
"""
A cylinder which contracts according to a scaling signal
which is a function of time.
"""
from contracting_cylinder_spline import create_phantom
args = Args()
args.h5_out = os.path.join(out_dir, "contracting_cylinder_spline.h5")
args.h5_scale = "phantom_data/real_left_ventricle_contraction.h5"
args.r0 = 1e-2
args.z0 = 0.12
args.num_scatterers = 20000
args.num_control_points = 10
args.spline_degree = 3
create_phantom(args)
def create_random_spline_noise_phantom():
"""
Scatterers moving along random 3D trajectories.
"""
from spline_noise import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "random_spline_noise.h5")
args.num_scatterers = 100000
args.x_min = -0.04
args.x_max = 0.04
args.y_min = -0.04
args.y_max = 0.04
args.z_min = 0.01
args.z_max = 0.08
args.spline_degree = 3
args.num_cs = 20
create_phantom(args)
def create_tissue_flow_phantom():
from tissue_with_flow import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "tissue_with_constant_flow.h5")
args.num_tissue_scatterers = 1000000
args.num_flow_scatterers = 500000
args.box_dim = 0.03
args.radius = 0.008
args.tissue_length = 8e-2
args.flow_ampl_factor = 0.2
args.peak_velocity = 15e-2
args.end_time = 1.0
args.exponent = 20 # approximate constant flow
create_phantom(args)
args.exponent = 2
args.h5_file = os.path.join(out_dir, "tissue_with_parabolic_flow.h5")
create_phantom(args)
def create_harmonic_box_phantom():
"""
A cube of scatterers moving harmonically up and down along
the Z-axis.
"""
from harmonic_box import create_phantom
args = Args()
args.h5_file = os.path.join(out_dir, "harmonic_box.h5")
args.x_min = -0.025
args.x_max = 0.025
args.y_min = -0.025
args.y_max = 0.025
args.thickness = 0.05
args.z0 = 8e-2
args.ampl = 1e-2
args.freq = 1.3
args.num_scatterers = 100000
args.num_control_points = 10
args.t_start = 0.0
args.t_end = 1.0
args.spline_degree =3
create_phantom(args)
