APS 2-BM & 32-IDΒΆ

This section contains a script to read the APS 2-BM and 32-ID tomography dataset and reconstruct it with tomoPy.

Download file: rec_aps_32id_full.py

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#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
TomoPy example script to reconstruct TXM data set.
"""

from __future__ import print_function
import tomopy
import dxchange

if __name__ == '__main__':

    # Set path to the micro-CT data to reconstruct.
    fname = 'data_dir/sample.h5'

    # Select sinogram range to reconstruct.
    start = 0
    end = 16

    # Read APS 32-ID raw data.
    proj, flat, dark, theta = dxchange.read_aps_32id(fname, sino=(start, end))

    # If data collection angles is not defined in the hdf file then set it as equally spaced between 0-180 degrees.
    if (theta is None):
        theta = tomopy.angles(proj.shape[0])
    else:
        pass

    # Flat-field correction of raw data.
    proj = tomopy.normalize(proj, flat, dark)

    # Find rotation center.
    rot_center = tomopy.find_center(proj, theta, ind=0, init=1024, tol=0.5)
    print("Center of rotation: ", rot_center)

    proj = tomopy.minus_log(proj)

    # Reconstruct object using Gridrec algorithm.
    rec = tomopy.recon(proj, theta, center=rot_center, algorithm='gridrec')

    # Mask each reconstructed slice with a circle.
    rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)

    # Write data as stack of TIFs.
    dxchange.write_tiff_stack(rec, fname='recon_dir/recon')