Kirkland-parametrized ptychography example
Now that examples/lightning.py
can reconstruct a reasonable potential from Mark's data, we should try constraining to atomic potentials using the Kirkland parametrization.
Plan
To do this, we should add a flag like --kirkland
which when enabled, adds two coarse-scale image parameters: species
and position
which is relative to the coarse voxel center.
We will need to be able to specify the grid spacing for the parametrization independently of the potential (finer) grid, and we need to be able to specify the atomic species as a list of element symbols. In the training_step
we will convert these to a full scale potential then call our existing Multislice object.
Note that for thicker potential slices, it may make more sense to implement 3D FDES using projected potentials. This can be done but should be user-selected, with a warning when using above around .1 A dz.