3D optimization with zero dose constraint

Walkthrough

Create a TargetGeometry from a .stl file by specifying the stlfilename and resolution i.e. the number of slices in the z-axis. When a zero dose constraint is desired, use the bodies kwarg to specify which bodies are to be printed (i.e. a dictionary specifying which bodies are to be printed and which are the zero dose constraint/s). In this case, the body to printed is body 1 and the body which is the zero dose constraint is body 2.

import vamtoolbox as vam
import numpy as np

target_geo = vam.geometry.TargetGeometry(stlfilename=vam.resources.load("ring.stl"),resolution=200,bodies={'print':[1],'zero_dose':[2]})

Finally, show the target with the show() method and use the show_bodies kwarg to show the insert bodies in a green color.

target_geo.show(show_bodies=True)

Create the ProjectionGeometry object. First, the angles array is created by using numpy.linspace to create 1D array of evenly spaced angles at which to perform projection.

num_angles = 360
angles = np.linspace(0, 360 - 360 / num_angles, num_angles)
proj_geo = vam.geometry.ProjectionGeometry(angles,ray_type='parallel',CUDA=True)

Create an vamtoolbox.optimize.Options object and run optimization. The Options object holds the parameters used by the optimize() function.

optimizer_params = vam.optimize.Options(method='OSMO',n_iter=45,d_h=0.85,d_l=0.6,filter='hamming',verbose='plot')
opt_sino, opt_recon, error = vam.optimize.optimize(target_geo, proj_geo,optimizer_params)
opt_recon.show()
opt_sino.show()

Tip

Hover the mouse pointer over either slice and scroll to slice through the 3D voxel array at different z and x indices.

Example file

examples/3Dzerodoseconstraint.py

import vamtoolbox as vam
import numpy as np

target_geo = vam.geometry.TargetGeometry(stlfilename=vam.resources.load("ring.stl"),resolution=200,bodies={'print':[1],'zero_dose':[2]})
target_geo.show(show_bodies=True)

num_angles = 360
angles = np.linspace(0, 360 - 360 / num_angles, num_angles)
proj_geo = vam.geometry.ProjectionGeometry(angles,ray_type='parallel',CUDA=True)

optimizer_params = vam.optimize.Options(method='OSMO',n_iter=45,d_h=0.85,d_l=0.6,filter='hamming',verbose='plot')
opt_sino, opt_recon, error = vam.optimize.optimize(target_geo, proj_geo,optimizer_params)
opt_recon.show()
opt_sino.show()