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Source code for 4D model-based iterative reconstruction of tomographic data
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README.rst

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

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.
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