2bm-tomo

tomo is commad-line-interface for running tomographic scans at beamline beamline 2bm of the Advanced Photon Source

Installation

$ git clone https://github.com/xray-imaging/2bm-tomo.git
$ cd 2bm-tomo
$ python setup.py install

in a prepared virtualenv or as root for system-wide installation.

Warning

If your python installation is in a location different from #!/usr/bin/env python please edit the first line of the bin/tomo file to match yours.

Usage

Running a scan

To run a tomographic scan:

$ tomo scan

from the command line. To get correct results, you may need to set specific options, for example to collect 10 tomographic dataset at 10 vertical positions separated by 1 mm:

$ tomo scan --scan-type vertical --vertical-scan-start 0 --vertical-scan-end 10 --vertical-scan-step-size 1

to list of all available options:

$ tomo scan -h

Configuration File

Scanning parameters are stored in tomo2bm.conf. You can create a template with:

$ tomo init

tomo2bm.conf is constantly updated to keep track of the last stored parameters, as initalized by init or modified by setting a new option value. For example to re-run the last scan with identical parameters just use:

$ tomo scan

A the end of each scan the current config file is copied in the raw data directory and renamed as sample_name.conf. To repeat the scan with the same condition just use:

$ tomo scan --config /data_folder/sample_name.conf