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