Australian SynchrotronΒΆ
This section contains a script to read the Australian Synchrotron Facility tomography dataset and reconstruct it with tomoPy.
Download file: rec_australian.py
1#!/usr/bin/env python
2# -*- coding: utf-8 -*-
3
4"""
5TomoPy example script to reconstruct the Australian Synchrotron Facility
6data as original tiff.
7"""
8
9from __future__ import print_function
10import tomopy
11import dxchange
12
13if __name__ == '__main__':
14
15 # Set path to the micro-CT data to reconstruct.
16 fname = 'data_dir/'
17
18 proj_start = 0
19 proj_end = 1801
20 flat_start = 0
21 flat_end = 10
22 dark_start = 0
23 dark_end = 10
24
25 ind_tomo = range(proj_start, proj_end)
26 ind_flat = range(flat_start, flat_end)
27 ind_dark = range(dark_start, dark_end)
28
29 # Select the sinogram range to reconstruct.
30 start = 290
31 end = 294
32
33 # Read the Australian Synchrotron Facility data
34 proj, flat, dark = dxchange.read_aus_microct(fname, ind_tomo, ind_flat, ind_dark, sino=(start, end))
35
36 # Set data collection angles as equally spaced between 0-180 degrees.
37 theta = tomopy.angles(proj.shape[0])
38
39 # Flat-field correction of raw data.
40 proj = tomopy.normalize(proj, flat, dark)
41
42 # Find rotation center.
43 rot_center = tomopy.find_center(proj, theta, init=1024, ind=0, tol=0.5)
44 print("Center of rotation: ", rot_center)
45
46 proj = tomopy.minus_log(proj)
47
48 # Reconstruct object using Gridrec algorithm.
49 rec = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec')
50
51 # Mask each reconstructed slice with a circle.
52 rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
53
54 # Write data as stack of TIFs.
55 dxchange.write_tiff_stack(rec, fname='recon_dir/aus_')