phaserEM 0.1

Weapon of choice for electron ptychographic reconstructions

phaser: The weapon of choice for ptychographic reconstructions

phaser is a fully-featured package for multislice electron ptychography.

Features

• ePIE, LSQ-MLs, and gradient descent algorithms
• numpy, cupy, and jax backends.
• Single and multislice ptychography
• Multiple incoherent probe modes
• Probe position correction
• Upsampled (sPIE) and segmented ptychography (work in progress)
• Adaptive propagator correction (work in progress)

Installation

To install, first clone the repository from github:

$ git clone https://github.com/hexane360/phaser
# enter phaser directory
$ cd phaser

If you're using cupy or jax with a GPU, follow the installation instructions for those packages.

Then, install with pip:

$ python -m pip install -e .

For the jax or cupy backend, or for the optional webserver, install with the corresponding options:

$ python -m pip install -e '.[cupy,web]' # or '.[jax,web]'

Running

After installation, the phaser command should be available. Phaser can be run from the command line, or through a job server.

To run a single reconstruction on the command line, call phaser run <file>, where file is the path to a reconstruction plan file.

To run the webserver, call phaser serve. By default, the server serves on https://localhost:5050/, so navigate there in a web browser. The server interface can be used to start workers and schedule reconstruction jobs.

To run a worker, call phaser worker <url>, where url is the URL of a running job server.

Alternatives

Other notable ptychography packages:

• fold_slice branch of PtychoShelves
• py4DSTEM
• PtyLab.m/py/jl
• PtyPy