#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Examples of the geometry classes usage: initialiation of a circular, helical and linear orbits; import ASTRA geometries.
"""
#%% Imports:
from flexdata import geometry
from flexdata import display
#%% Initialize a geometry record:
# Initialization:
geo = geometry.circular(src2obj=100,
det2obj=50,
det_pixel=0.1,
img_pixel=0.05,
ang_range=(0, 180),
unit='mm')
# Print geometry parameters:
print('\n', geo)
# Additional parameters:
geo['axs_pitch'] = 30
# Plot the source orbit:
orbit = geo.get_source_orbit(50)
display.plot3d(orbit[:, 0],
orbit[:, 1],
orbit[:, 2],
connected=True,
from flexdata import display
from flextomo import phantom # Simulate
from flextomo import model
from flextomo import projector # Reconstruct
from flexcalc import analyze
from flexcalc import process
import numpy
#%% Short version of the spectral modeling:
# Geomtery:
geom = geometry.circular(src2obj=100,
det2obj=100,
det_pixel=0.2,
ang_range=[0, 360])
# This is our phantom:
vol = phantom.cuboid([1, 128, 128], geom, 8, 8, 8)
display.slice(vol, title='Phantom')
# Spectrum of the scanner:
kv = 90
filtr = {'material': 'Cu', 'density': 8, 'thickness': 0.1}
detector = {'material': 'Si', 'density': 5, 'thickness': 1}
E, S = model.effective_spectrum(kv=kv, filtr=filtr, detector=detector)
# Display:
display.plot(E, S, title='Effective spectrum')
import numpy
#%% Create volume and forward project:
# Initialize images:
h = 512 # volume size
vol = numpy.zeros([32, h, h], dtype='float32')
proj = numpy.zeros([32, 361, h], dtype='float32')
# Define a simple projection geometry:
src2obj = 100 # mm
det2obj = 100 # mm
det_pixel = 0.001 # mm (1 micron)
geom = geometry.circular(src2obj, det2obj, det_pixel, ang_range=[0, 360])
# Create phantom (150 micron wide, 15 micron wall thickness):
vol = phantom.sphere(vol.shape, geom, 0.08)
vol -= phantom.sphere(vol.shape, geom, 0.07)
# Project:
projector.forwardproject(proj, vol, geom)
# Show:
display.slice(vol, title='Phantom')
display.slice(proj, dim=0, title='Sinogram')
#%% Get the material refraction index of calcium carbonate:
c = model.find_nist_name('Calcium Carbonate')
