TIMBIR

TIMBIR is a method for 4D time-space reconstruction of data acquired using synchrotron X-ray computed tomography. This software can be used to reconstruct any tomographic data in 3D or 4D.

Documentation:

http://timbir.readthedocs.org

Dependencies

• MPI compiler
• Open MP
• Make utility
• HDF library (optional)

Demo/Examples

• Unix/Linux/Mac OS

  • 3D Reconstruction: Change directory to demo/recon_3d/shepp-logan-3D/ and run the script run_unix.sh
  • 4D Reconstruction: Change directory to demo/recon_4d/cahn-hilliard-4D/ and run the script run_unix.sh

• Supercomputing cluster (Rice cluster at Purdue)

  • 3D Reconstruction: Change directory to demo/recon_3d/shepp-logan-3D/ and run the script run_cluster.sh
  • 4D Reconstruction: Change directory to demo/recon_4d/cahn-hilliard-4D/ and run the script run_cluster.sh

Compiling TIMBIR

• To compile the MBIR algorithm code, run the following commands in a terminal:

  • git clone https://github.com/adityamnk/timbir.git timbir
  • cd timbir/src/MBIR_4D
  • make clean
  • make

This generates library files in timbir/src/lib. For more information, read the README in timbir/src/MBIR_4D.

Running the reconstruction algorithm

• If the input data format is a standard binary, compile and run the code in timbir/src/reconstruct/bin_data.

  • cd timbir/src/reconstruct/bin_data
  • make clean
  • make
  • # This generates executables in the same folder.
  • # For more information on binary data format and running the code, read the README in timbir/src/reconstruct/bin_data:

• If the input data is in HDF format used at APS, compile and run the code in timbir/src/reconstruct/aps_data.

  • cd timbir/src/reconstruct/aps_data
  • make clean
  • make
  • # This generates executables in the same folder.
  • # For more information on APS data format and running the code, read the README in timbir/src/reconstruct/aps_data:

• If the input data is in standard HDF format, compile and run the code in timbir/src/reconstruct/std_data.

  • cd timbir/src/reconstruct/std_data
  • make clean
  • make
  • # Generates executables in the same folder
  • # For more informantion on standard HDF data format and running the code, read the README in timbir/src/reconstruct/std_data:

Help/Support:

Email K. Aditya Mohan at the address adityakadri[at]gmail[dot]com

Citation

• K. A. Mohan, S. V. Venkatakrishnan, J. W. Gibbs, E. B. Gulsoy, X. Xiao, M. De Graef, P. W. Voorhees, and C. A. Bouman, "TIMBIR: A method for time-space reconstruction from interlaced views," IEEE Transactions on Computational Imaging, vol. 1, no. 2, pp. 96.111, June 2015.