This winter solstice, we celebrate the wonders of the parallax effect

[gvarnavi]

Various updates and new functionality to parallax.
Notably:

• Realspace mask during preprocess

parallax.preprocess(
    realspace_mask = mask,
    apply_realspace_mask_to_stack=True, # default
)

• Explicit bin setting during reconstruct

parallax.reconstruct(
    alignment_bin_values = [32,16,8,8,4,4,2,2,2,2]
)

• Improvements to aberration fitting:

  • force_rotation_deg
  • explicitly setting aberrations to include in fit

  parallax.aberration_fit(
      fit_BF_shifts=True,
      fit_aberrations_mn = [[1,0,0],[2,1,0],[2,1,1]], # defocus and coma only
  )

  • convert fitted aberrations to polar dictionary for use in ptycho

  ptycho = py4DSTEM.process.phase.SingleslicePtychographicReconstruction(
      polar_parameters = parallax.aberration_dict_polar
  )

• Improvements to upsampling interpolation methods

  • Correct DF and BF warning limits
  • Bilinear interpolation (default)
  • Lanczos interpolation

  parallax.subpixel_alignment(
      lanczos_interpolation_order = 2
  )

  • Nearest-neighbor rolling

  parallax.subpixel_alignment(
      integer_pixel_rolling_alignment = True
  )

• Probe position refinement

Fixed-step gradient descent or "checker-boarding" algorithm with initial_step_size, decreasing geometrically by step_size_factor up to a minimum step of min_step_size.

parallax.subpixel_alignment(
    position_correction_num_iter = 2,
    position_correction_checkerboard_steps = False, # default
    position_correction_initial_step_size=0.125,
    position_correction_min_step_size=0.1,
    position_correction_step_size_factor=0.75,
    position_correction_butterworth_q_lowpass = (0.05,0.05),
    position_correction_butterworth_q_highpass = (0.005,0.005),
    position_correction_butterworth_order = (4,4),
)

Probe-position refinement results can be inspected using

parallax.show_probe_position_shifts(
     # vmin=-0.5,
     # vmax=0.5,
)

[sezelt]

All looks good, mostly just highlighted a few missing/incomplete docstring things