direct ptycho to-dos from Steph/Georgios notebooks

[bobleesj]

Direct Ptycho #115 is merged.

@smribet shared a notebook and contained 5 to-do items:

1. Use consistent angle/rad

direct_ptycho = em.diffractive_imaging.direct_ptychography.DirectPtychography.from_dataset4d(
    dc,
    energy=ENERGY,
    semiangle_cutoff=PROBE_SEMIANGLE,
    aberration_coefs={'C10':10}, # start close to focus
    device="gpu",
    rotation_angle=np.deg2rad(-169), # known rotation
    max_batch_size=32
)

direct ptycho uses angles in rad and iterative uses it in angles. @smribet prefers to have everything in angles.

2. Add plotting function after direct pycho

todo add plotting funciton (something like this): 
initial_parallax = direct_ptycho.reconstruct(
    upsampling_factor=1,
    deconvolution_kernel='quadratic',
).visualize(
   show_fft = True

add .visualize

3. Plot after fitting - show whole grid of outcomes and print error/parameters

# todo plotting. it should show the whole grid of outcomes and print error/parameters. 

direct_ptycho.grid_search_hyperparameters(
    aberration_coefs={
        "C10":-348,
        "C12":OptimizationParameter(0, 40, n_points=5),
        "phi12":OptimizationParameter(-np.pi/2, np.pi/2, n_points=5)
    },
    rotation_angle=np.deg2rad(-169),
    deconvolution_kernel='quadratic',
   
)

Pending after 1, 2, 3

4. Optimization may need a bit more user-friendlyness

from quantem.diffractive_imaging.direct_ptychography import OptimizationParameter
direct_ptycho.optimize_hyperparameters(
    aberration_coefs={
        "C10":OptimizationParameter(-400,400),
        "C12":OptimizationParameter(0, 100),
        "phi12":OptimizationParameter(-np.pi/2, np.pi/2)
    },
    rotation_angle=OptimizationParameter(np.deg2rad(-180), np.deg2rad(-160)),
    deconvolution_kernel='quadratic',
)

5 Resolve ambiguity?

direct_ptycho.fit_hyperparameters(
    # bin_factors=(5,5,5,5,5,4,4,4,3,3,3,2,2,2,1,1,1,),
    # deconvolution_kernel='quadratic', # use parallax for post-fit reconstruction,
    # pair_connectivity = 8,
    # alignment_method = "reference",

)

some way to force rotation to deal with 180 degree ambiguity?

I will first go through 1-3 and bring up a discussion on 4-5.

[bobleesj]

Once #122 is merged, I will make another PR for .visualize( show_fft = True) for DirectPtycho