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