Syris
Syris is a framework for simulations of X-ray absorption and phase contrast dynamic imaging experiments, like time-resolved radiography, tomography or laminography. It includes X-ray sources, various sample shape creation possibilities, complex refractive index lookup options, motion model and indirect detection model (scintillator combined with a conventional camera). Phase contrast is simulated by the Angular spectrum method, which enables one to include various optical elements in the simulation, e.g. gratings and X-ray lenses.
Compute-intensive algorithms like Fourier transforms, sample shape creation and free-space propagation are implemented by using OpenCL, which enables one to execute the code on graphic cards.
Installation
Download or clone the repository and run
pyhon setup.py install.
Usage
Simulating simple white beam propagation example looks like this:
import matplotlib.pyplot as plt
import numpy as np
import quantities as q
import syris
from syris.physics import propagate
from syris.bodies.simple import make_sphere
from syris.materials import make_henke
syris.init()
energies = np.arange(10, 30) * q.keV
n = 1024
pixel_size = 0.4 * q.um
distance = 2 * q.m
material = make_henke('PMMA', energies)
sample = make_sphere(n, n / 4 * pixel_size, pixel_size, material=material)
image = propagate([sample], (n, n), energies, distance, pixel_size).get()
plt.imshow(image)
plt.show()