mbir-demos

Demo scripts and sample data

This package contains demo shell scripts and sample data to accompany the sv-mbirct project found here:
       https://github.com/HPImaging/sv-mbirct

Please refer to that site for the source code, compiling instructions, command line usage and data format descriptions.

Sample Data

This package contains two sample data sets,

1. shepp is a single slice of a generated Shepp-Logan phantom
2. xradia is a 4-slice sequence out of a volume scan taken from a Zeiss Xradia microCT scanner.

Scripts

The run folder contains a script runDemo.sh that sets the command line arguments and executes the reconstruction. This script assigns variables for file names and locations of the various input arguments, including the location of the MBIR executable, so these can be be modified to suit your directory organization.

In the current context, if the projects sv-mbirct and mbir-demos, are located in the same base directory, the run scripts will find the proper locations of the executable and input files.

To run the script from a terminal, cd into the run folder and type one of the following:

./runDemo.sh ../shepp
./runDemo.sh ../xradia

The script will first read the image and sinogram parameter files and determine if the system matrix file has already been computed and saved to a file. If not, the matrix is computed and placed in the relative folder sysmatrix. Then the reconstruction is called. After the process completes, the output images are written in the recon folder in the associated data folder.

There's a basic Matlab script included that will display the output reconstructions. If Matlab is not available, the OpenMBIR-ParBeam project includes a Python utility for displaying these images as well.