XLuminA v1.0.0

Release notes: ✨ XLuminA v1.0.0 ✨

🐍 System requirements update

• Python Version: The project requires Python>=3.10. We suggest to use Python 3.11.
• JAX Version: An updated version of JAX is required. Please refer to the installation instructions for the specific version.

❗️ Major new features:

🦾🤖 Noise-aware optimization strategy

• Implemented a new robust, noise-aware optimization scheme for simulating real-world experimental conditions.
• The strategy includes imperfections, misalignment, and noise sources in all optical components: including SLMs, wave plates, misalignment, and beam splitters.
• Optimization ncan be run on multiple parallel optical tables using vmap, each with randomly sampled noise.
• Detailed explanation of the strategy is available in the project's README.md.

📖 New step-by-step guides

• Added noisy_optimization.ipynb: A guide on setting up optimization using the new noise-aware scheme.
• Added noisy_4f_system.ipynb: A guide on adding noise to optical elements.

✨ New functions in optical_elements.py

Optical elements

• sSLM_with_amplitude: Implements a super-Spatial Light Modulator (sSLM) with phase and amplitude modulation.
• jones_sSLM_with_amplitude: Defines the Jones matrix of super-SLM that modulates both phase and amplitude sSLM_with_amplitude.
• BS_symmetric: Implements a classical lossy two-mode beam splitter.
• BS_symmetric_SI: Implements a classical lossy single-input beam splitter.
• cylindrical_lens: Defines a transparent plano-convex cylindrical lens.
• axicon_lens: Implements an axicon lens function that produces a Bessel beam.

Optical setups

• bb_amplitude_and_phase_mod: Implements a basic building block for general setup construction, containing an sSLM with amplitude and phase modulation and a WP liked by propagation distance z.
• robust_discovery: Implements a single-wavelength 3x3 setup for hybrid (topology + optical settings) discovery. Includes noise settings.

Noise simulation

• shake_setup: Creates noise for different optical elements on an optical table.
• shake_setup_jit: JIT-compilable version of shake_setup for use in optimization.

✨ New functions in toolbox.py

Image processing

• image_to_binary_mask: Converts an image to a binary mask given a threshold.

Mathematical functions

• gaussian: Returns a 1D Gaussian distribution.
• gaussian_2d: Returns a 2D Gaussian distribution.
• lorentzian: Returns a 1D Lorentzian function.
• lorentzian_2d: Returns a 2D Lorentzian function.

Data analysis

• fwhm_1d_fit: Computes the Full Width at Half Maximum (FWHM) of a 1D array using a fit function (Gaussian or Lorentzian).
• fwhm_2d_fit: Computes the FWHM of a 2D array using a fit function (Gaussian or Lorentzian).
• compute_fwhm: Calculates the FWHM in 1D or 2D for various field components.

Data Processing

• MultiHDF5DataLoader: A class for loading data from multiple HDF5 files, designed for use with JAX. This module is used in four_f_optimizer.py.

Minor modifications in wave_optics.py and vectorized_optics.py:

• Improved readability: print statemets now display time to 4 decimal places.

🚩 Removals and deprecations

Removed functions in optical_elements.py:

• Several functions related to optical setups from previous versions of the paper have been removed: general_setup, vSTED, sharp_focus and xl_setup.

Removed functions in loss_functions.py:

• small_area: Fraction of intensity comprised inside the area of a mask.
• small_area_STED: Fraction of intensity comprised inside the area of a mask - STED version.

Removed files from experiments:

• Several files related to optical setups from previous versions of the paper have been removed: sharp_focus_optical_table.py, sharp_focus_optimizer.py, vsted_optical_table.py, vsted_optimizer.py, xl_optical_table.py and xl_optimizer.py.