As discussed with @PinkShnack, it would be better to have a model fitting procedure for initial assignment of atom configurations, rather than the current "hard intensity limit" method. This would help measure error in atom assignments.
It should calculate the intensity of each atom site in a sublattice, plot a histogram of the intensities, and then fit one gaussian to the histogram for each type of atom configuration. Gaussian overlaps are ambiguous - could take some user input to decide how to interpret them.
Might not work for particularly noisy images, as individual histogram peaks might be difficult to detect.
What needs to be done:
[ ] Create a function to plot histogram of sublattice intensities, fit gaussians based on element lists, and assign elements to each site.
[ ] Add function to Model Creation module.
[ ] Wrap function as a method into the Model Refiner class.
As discussed with @PinkShnack, it would be better to have a model fitting procedure for initial assignment of atom configurations, rather than the current "hard intensity limit" method. This would help measure error in atom assignments.
It should calculate the intensity of each atom site in a sublattice, plot a histogram of the intensities, and then fit one gaussian to the histogram for each type of atom configuration. Gaussian overlaps are ambiguous - could take some user input to decide how to interpret them.
Might not work for particularly noisy images, as individual histogram peaks might be difficult to detect.
What needs to be done: