r0.0.2 Candidate

[ichristen]

Staging pull request for dev -> main for r0.0.2. This message should be treated as an editable draft of the release notes.

r0.0.2

New Features (checkbox is ready for release)

• Simulation of hardware with SimulatedSLM and SimulatedCamera, modeling experimental effects.
• New toolbox.phase functions
  • sinusoid() grating.
  • binary() grating.
  • 2D general polynomial().
• Fitting the SLM's source amplitude data to recenter grids and derive scales.
  • For instance, functions like lens() which use the SLM grid are now centered on the source amplitude and will focus coaxially.
  • This also is now used in choosing a radius for structured light conversions and Zernike data (see next).
• Revamped Zernike functionality.
  • New convert_zernike_index() function to convert between common indexing standards.
  • Auto-choosing a good Zernike aperture from fitted source amplitude data.
  • Zernike derivatives (computed via the chain rule, so fast).
• 3D support for convert_vector() (previously known as convert_blaze_vector()) and new units, including:
  • "zernike", which expresses 3D points as the result of coordinates (in radians) directly multiplied with normalized tilt and focus Zernike polynomials.
  • metric units in camera-space, making use of knowledge of the camera pixel size and magnification between the camera and experiment.
• 3D spot arrays CompressedSpotHologram. 3D Spots #41
• Spot arrays with unique Zernike aberration compensation for every spot (generalization of the above). Every spot goes to the desired point in 'aberration space'.
• Conjugate gradient optimization of holograms using pytorch working alongside cupy.
• Quadratic initial phase guess (instead of random) to promote a smoother hologram.
• Wavefront calibration wavefront_calibrate() that simultaneously measures at multiple calibration points.
  • When combined with the above, implemented Wavefront calibration over a field of view #60 in spot arrays.
  • This also includes other updates to wavefront calibration Wavefront calibration fit & correct the center of the spots array #42
  • New calibration algorithm based on removal of Zernike terms.
• More robust fourier_calibrate() fitting.
• pixel_calibrate() measuring phase swing and crosstalk.
• settle_calibrate() measuring the $1/e$ SLM settle time.
• Revamped calibration internal storage and saving.
• format_2vectors() generalized to format_vectors() with N-dimensional support.
• Allow moments to accept arbitrary grids, among other small changes.
• Divide and conquer algorithm for smallest_distance() (now can handle millions of points in $O(N\log N)$ time).
• Artificial bitdepth enhancement for cameras:
  • Multi-exposure High Dynamic Range imaging,
  • Software averaging.
• Added untested Instrumental #17
• Added skeleton for Holoeye #26

Breaking Changes

• Changed toolbox.phase functions:
  • zernike() and zernike_sum() are completely changed.
  • blaze() had the offset= parameter removed as it was redundant with +=.
• Renamed variables in cameras and SLMs to reduce clutter:
  • dx_um, dy_um -> pitch_um
  • dx, dy -> pitch
  • x_grid, y_grid -> grid
  • phase_correction, measured_amplitude, -> source
  • Constructors are also modified in some cases.
  • Default parameters are changed in most cases.
  • High-level SLMs (Santec, Meadowlark, ...) should largely be fine, but direct calls to the SLM constructor might break.
• Renamed variables in Holograms:
  • method was moved to flags.
• Renaming in FourierSLM:
  • Different calibrations are now stored in a single dict calibrations.
  • wavefront_calibrate() has renamed and reorganized variables.
• TODO

Bugfixes

• Warning for slmsuite.holography.toolbox.smallest_distance unexpected behavior #49
• TODO: take does not work properly for stacks of images. #53
• Unusual behavior with take using even pixel number. #62
• Some AlliedVision cameras don't have binning attributes. #63
• Support for numpy 2.0.0.
• Many small things.

Under the Hood

• Major reorganization of internal files.
  • algorithms is split into many smaller files.
  • fitfunctions and files are moved from misc to analysis and toolbox.
• Introduced a number of custom CUDA kernels (in cuda.cu).
• Docs have moved from the readthedocs theme to the very nice pydata theme (used by numpy, etc).