Params Overview

Params Overview#

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 (required)

  2. hypertune_params (only needed in hypertune mode)

  3. model_params (optional)

  4. loss_params (optional)

  5. constraint_params (optional)

  6. recon_params (optional)

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 ~ 15-30 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/'

Where to go next?#

You don’t need to write these parameters from scratch!

PtyRAD bundles plenty examples, walkthrough, and templates YAML files with your installation.

You can instantly generate a starter workspace containing all these files in your current directory by running the following commands:

  • If you want a full starter kit working directory containing params/, scripts/, notebooks/ (recommended if you haven’t done so in Quickstart):

    ptyrad init

  • If you just want the params/ folder with examples, walkthrough, and templates YAML files:

    ptyrad get-params

We also organize those params files into the following sections for easier reference:

Examples: Ready-to-run parameter files for included demo datasets (e.g., tBL_WSe2, PSO). Perfect for verifying your installation and seeing PtyRAD in action.

Walkthrough: Tutorial-driven parameter files designed to guide you through specific features (e.g., multislice, advanced constraints, and hyperparameter tuning)

Templates: Templates ranging from minimal setups to full API reference. Copy and paste these to start your own custom reconstruction tasks.

Params API Reference: The complete list of all available PtyRAD params and their individual options with detailed descriptions.

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