Usage

If Ptyrax was not installed via uv, replace all uv run ptyrax commands with python3 -m ptyrax. Ptyrax can be invoked using

uv run ptyrax [reconstruct, simulate, experiment] [ptychogram_path] [reconstruction_filename] {opts}

For example, you can reconstruct the example dataset in data/lenspaper.hdf5 using

uv run ptyrax reconstruct https://surfdrive.surf.nl/public.php/dav/files/sakpFtVESDmncRH data/lenspaper_reconstruction.hdf5 --log_dir logs/lenspaper --config configs/lenspaper.yaml

This will generate a reconstruction output lenspaper_reconstruction.hdf5 in the log_dir directory. The specific parameters used for the reconstruction are set using the gin-config file specified by config. The reconstruction process may be monitored by use of tensorboard using (in a new shell):

uvx --python 3.12 --from 'tensorboard' --with 'setuptools<82' tensorboard --logdir logs/lenspaper --samples_per_plugin images=200

After the reconstruction process has completed, the output will become available in the log_dir in hdf5 format (lenspaper_reconstruction.hdf5) and as a binary equinox file (lenspaper_reconstruction.eqx, for use when restarting from an intermediate solution). In addition to the output, everything that is written to stdout and stderr is logged to out.log. The tensorboard logs are converted to hdf5 tensorboard_logs.hdf5 for easy loading, and metadata.yaml specifies the exact version of the code that was used ptyrax, including possible diffs if under development.