Description

This PR adds to unblur some options to process images with condensed beams as described here. Briefly, it first allows for measuring the image shifts in a subarea of the image, so that beam edges due not affect it. Then it implements a procedure to crop the image to the illuminated area and to replace unilluminated pixels with gaussian nose that matches the illuminated areas.

Fixes # (issue)

I have rebased my feature branch to be current with the master branch using to minimize conflicts and headaches

[ ] yes
[ ] no

Which compilers were tested

[ ] g++
[ ] icpc
[ ] clang
[ ] other (please specify)

These changes are isolated to the

[ ] gui
[ ] core library
[ ] gpu core library
[ ] program it modifies

How has the functionality been tested?

Please describe the tests that you ran to verify your changes. Please also note any relevant details for your test configuration.

[ ] Tested manually from GUI
[ ] Tested manually from CLI
[ ] Passed console tests
[ ] Passed samples functional testing
[ ] other (please specify)

Checklist:

[ ] I have not changed anything that did not need to be changed
[ ] I have performed a self-review of my own code
[ ] I have commented my code, (w.r.t. why), particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation {Ok to pass for now}
[ ] My changes generate no new warnings
[ ] Any dependent changes have been merged and published in downstream modules

timothygrant80 / cisTEM