CLI
In this guide, we will walk you through the process of installing faser as as cli application.
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
The installation process for faser is straightforward. Follow the steps below to get started.
-
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.Terminal window python -m venv .venv -
Activate the environment
Activate the virtual environment using the following command on linux/mac
Terminal window source .venv/bin/activateor on windows
Terminal window .venv\Scripts\activate -
Install faser and napari
install Faser using
Terminal window pip install "faser[cli]" -
Run faser
Run the following command (inside your activated virtual environemnt) to start the standalone application
Terminal window faser
General Usage
Once you have installed faser, you can use the command line interface to generate PSFs for your optical system.
faser --helpThis will display the available commands and options for faser. You can use these commands to generate PSFs with different parameters and save them to disk for further analysis.
➜ ~ faser --help
Usage: faser [OPTIONS]
╭─ Options ────────────────────────────────────────────────────────────────────╮│ --config FILENAME Path to a JSON file ││ --detector_gaussian_noise FLOAT Detector Gaussian noise ││ --gaussian_beam_noise FLOAT Gaussian_beam noise ││ --add_noise NOISE ││ --loaded_phase_mask OPTIONAL Loaded Phasemak ││ --p FLOAT Ratio between Donut (p) and ││ Bottle (1-p) intensity ││ --mask_offset_y FLOAT Y offset of the phase mask in ││ regard to pupil center ││ --mask_offset_x FLOAT X offset of the phase mask in ││ regard to pupil center ││ --ring_radius FLOAT Radius of the ring phase mask ││ (on unit pupil) ││ --rc FLOAT Ring charge (should be odd to ││ produce bottle) ││ --vc FLOAT Vortex charge (should be ││ integer to produce donut) ││ --epsilon FLOAT Ellipticity of the ││ polarization (in °) ││ --psi FLOAT Direction of the polarization ││ (in °) ││ --ampl_offset_y FLOAT Y offset of the amplitude ││ profile in regard to pupil ││ center ││ --ampl_offset_x FLOAT X offset of the amplitude ││ profile in regard to pupil ││ center ││ --waist FLOAT Diameter of the input beam on ││ the objective pupil (in µm) ││ --wavelength FLOAT Wavelength of light (in µm) ││ --polarization POLARIZATION ││ --mode MODE ││ --aberration_offset_y FLOAT Y offset of the aberration ││ function in regard to pupil ││ center ││ --aberration_offset_x FLOAT X offset of the aberration ││ function in regard to pupil ││ center ││ --a24 ABERRATIONFLOAT Secondary spherical ││ --a12 ABERRATIONFLOAT Primary spherical ││ --a9 ABERRATIONFLOAT Oblique Trefoil ││ --a8 ABERRATIONFLOAT Horizontal Coma ││ --a7 ABERRATIONFLOAT Vertical Coma ││ --a6 ABERRATIONFLOAT Vertical Trefoil ││ --a5 ABERRATIONFLOAT Vertical Astigmatism ││ --a4 ABERRATIONFLOAT Defocus ││ --a3 ABERRATIONFLOAT Oblique Astigmatism ││ --a2 ABERRATIONFLOAT Horizontal Tilt ││ --a1 ABERRATIONFLOAT Vertical Tilt ││ --a0 ABERRATIONFLOAT Piston ││ --wind_offset_y FLOAT Y offset of the cranial window ││ in regard to pupil center ││ --wind_offset_x FLOAT X offset of the cranial window ││ in regard to pupil center ││ --wind_depth FLOAT Depth of the cranial window ││ (in mm) ││ --wind_radius FLOAT Diameter of the cranial window ││ (in mm) ││ --window WINDOW ││ --tilt FLOAT Tilt angle of the coverslip ││ (in °) ││ --depth FLOAT Imaging depth in the sample ││ (in µm) ││ --collar FLOAT Correction collar setting to ││ compensate coverslip thickness ││ --thickness FLOAT Thickness of the coverslip (in ││ µm) ││ --n3 FLOAT Refractive index of the sample ││ --n2 FLOAT Refractive index of the ││ coverslip ││ --n1 FLOAT Refractive index of the ││ immersion medium ││ --wd FLOAT Working Distance of the ││ objective lens (in µm) ││ --na FLOAT Numerical Aperture of ││ Objective Lens ││ --normalize NORMALIZE ││ --nphi INTEGER Integration sted of the ││ aximutal angle on the pupil ││ --ntheta INTEGER Integration sted of the ││ focalization angle ││ --nz INTEGER Discretization of Z axis - ││ better be odd number for ││ perfect 0 ││ --nxy INTEGER Discretization of image plane ││ - better be odd number for ││ perfect 0 ││ --l_obs_z FLOAT Observation scale in Z (in µm) ││ --l_obs_xy FLOAT Observation scale in XY (in ││ µm) ││ --help Show this message and exit. │╰──────────────────────────────────────────────────────────────────────────────╯This will display the available commands and options for faser. You can use these commands to generate PSFs with different parameters and save them to disk for further analysis.
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 vetrical 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.
Directoryfolder_where_you_ran_the_cli
- psf_config.JSON
- psf.tiff