Dynamic sparse X-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst: Raw data and reconstruction software

Dynamic sparse X-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst: Raw data and reconstruction software

Dataset structure:

    - Dynamic_PEFC_data.h5  # Raw projection data for dynamic tomography imaging of PEFC catalyst hydration.
        - /sinogram         # Sinogram of all projections, 3-dimensional array with axes (Nangle,X axis,Y axis).
        - /tomo_angle       # Tomography rotation angle for each projection, 1D array with axis (Nangle).
        - /humidity_readout # Relative humidity value at the time each projection is measured, 1D array with axis (Nangle).
        - /Deform_X         # X/Y/Z components for the deformation vector field which characterize nonrigid deformation of the sample.
        - /Deform_Y
        - /Deform_Z

    - liquid_simulation.h5  # Numerical simulation of dynamic liquid filling process.
        - /sinogram         # Sinogram of all projections, 3-dimensional array with axes (Nangle,X axis,Y axis).
        - /tomo_angle       # Tomography rotation angle for each projection, 1D array with axis (Nangle).
        - /groundtruth_tomograms    # Ground truth of the simulated tomograms, 4-dimensional array with axes (Timeframe,Y axis, Z axis, X axis).

    - phasetran_simulation.h5   # Numerical simulation of gradual linear density change process.
        - /sinogram         # Sinogram of all projections, 3-dimensional array with axes (Nangle,X axis,Y axis).
        - /tomo_angle       # Tomography rotation angle for each projection, 1D array with axis (Nangle).
        - /groundtruth_tomograms    # Ground truth of the simulated tomograms, 4-dimensional array with axes (Timeframe,Y axis, Z axis, X axis).

Reconstruction codes:

    - astra_nonrigid.zip    # Compressed python package of modified version of astra-toolbox with nonrigid computed tomography implementation.
        - /astra            # Python package folder, need to be added to Python import search path (sys.path).
    # If the pre-compiled version doesn't work, source code of the pacakge can be downloaded:
    # https://github.com/zr-gao/astra-toolbox-nonrigid
    # Follow the instructions and requirements on the website to compile and install the package.

    - reconstruction_PEFC.py    # Python script for sparse dynamic tomography of the PEFC dataset.
                                # Need to be in the same folder with Dynamic_PEFC_data.h5 to load data.
                                # Follow the instructions in the code to set reconstruction parameters and export results.
                                # Requirements: cupy, numpy, astra(with nonrigid)*, h5py
    # * !!! Nonrigid computed tomography is used for the reconstruction, therefore the astra package with nonrigid implementation (in astra_nonrigid.zip) is required.

    - reconstruction_simulation.py  # Python script for sparse dynamic tomography of numerical simulations.
                                    # Need to be in the same folder with liquid_simulation.h5 or phasetran_simulation.h5, loaded filename is selected in the code.
                                    # Follow the instructions in the code to set reconstruction parameters and export results.
                                    # Requirements: cupy, numpy, astra**, h5py
    # ** Reconstruction of numerical simulations does not use nonrigid computed tomography, therefore both the astra_nonrigid.zip and the official astra-toolbox package will work.
    # To download and install the official astra-toolbox refer to the repository:
    # https://github.com/astra-toolbox/astra-toolbox