Command line
Install faser as a command line tool for scripting and automation.
In this guide, we will walk you through the process of installing faser as a CLI application.
Who is this guide for?
CLI usage is tailored to users that want to integrate faser into their own applications or workflows and are comfortable with the command line interface. To install the CLI version of faser, you need to have a basic understanding of Python and package management tools like pip.
Pre-requisites
In order to install faser as a CLI application, you will need the following:
- Python 3.9 or higher
- A package manager (pip, conda, poetry, uv)
Installation
Create a python environment
Using a tool like conda, poetry or uv (use uv, it's the best), create a virtual environment in the directory where you want to install faser.
python -m venv .venvActivate the environment
Activate the virtual environment using the following command on linux/mac
source .venv/bin/activateor on windows
.venv\Scripts\activateInstall faser
pip install "faser[cli]"The faser[cli] extra installs faser with the command line interface. The napari[pyqt5] package is not required for the CLI version of faser.
General usage
Once you have installed faser, you can use the command line interface to generate PSFs for your optical system. faser --help displays the available options; every field of the simulation config is exposed as a flag.
Example
To generate a PSF with a vertical tilt aberration of 0.1 and a numerical aperture of 1.4, you can run the following command:
faser --a1=0.1 --na=1.4This command will generate a PSF with a vertical tilt aberration of 0.1 and a numerical aperture of 1.4, and will output the PSF (and all of the parameters of the optical properties) to the current working directory.