Params files

PtyRAD uses a single parameters file to fully configure the reconstruction task.

These files are called “params files” and contains 6 nested dictionaries with a total of more than 100 fields, making PtyRAD extremely customizable and flexible for each reconstruciton task.

For example, a complete PtyRAD params file includes:

1. init_params

2. hypertune_params (optional)

3. model_params

4. loss_params

5. constraint_params

6. recon_params

These nested dictionaries can be provided by a range of common file formats, including the native .py, .json, .toml, or .yaml.

The recommended file format for PtyRAD is .yaml (YAML) for its excellent readability and compatibility.

Although PtyRAD contains many customizable options, usually for each reconstruction task a user only needs to specify ~ 15 fields.

For example, a minimal params.yaml might look like this:

init_params
    probe_kv            : 80
    probe_conv_angle    : 24.9
    probe_defocus       : 0
    meas_Npix           : 128
    pos_N_scan_slow     : 128
    pos_N_scan_fast     : 128
    pos_scan_step_size  : 0.4290
    probe_pmode_max     : 6
    obj_Nlayer          : 6
    obj_slice_thickness : 2
    meas_params         : {'path': 'data/tBL_WSe2/Panel_g-h_Themis/scan_x128_y128.raw'}
recon_params
    NITER               : 200
    SAVE_ITERS          : 10
    output_dir          : 'output/tBL_WSe2/'