Atomic Column Integrator does not handle spectrum images correctly
The integrate_column_intensity
method does not correctly handle spectrum images through its data_to_integrate
argument.
The main function integrate
in tools.py
uses incorrect indexing of the resultant image (image.shape[0], image.shape[1] instead of image.shape[-2], image.shape[-1], i.e.).
I had a go at trying to fix it, but without proper knowledge of the remainder of the function, I ended up having some trouble. I'm happy to show the changes I've made so far.
It would be nice if there was a manner in which one could produce a hyperspy signal from a given atomap lattice object (one which uses the image data rather than generates a model). That would make it easy to handle the indexing problems mentioned above, by accessing s.axes_manager.signal_shape, and similar.