coupled recontruction

[mlz-EM]

Implementation of coupled reconstruction. I/O are hard coded. Tested on exmaple data and patterns with given ID have zero gradient on the probes with different ID. The raw and output files are availbale at supercloud ~/lebeau_shared/tcPty.

Workflow will

1. Individual reconstruction.
2. Post reconstruction registration across datasets, which yields an affine matrix for each scan to align with the first (maybe) and updated
3. Combined reconstruction by loading the tilt and scan from individual states

What's needed is utils for step2 (I have some preliminary code if needed) and clean up I/O for step 3