NEW: Add a collection of utilities and functions to alignment

[carterbox]

Purpose

Ports various feature additions from work on ADMM. Adds new features and parameters to the alignment module and one to laminography.

Pre-Merge Checklists

Submitter

• [x] Write a helpfully descriptive pull request title.
• [x] Organize changes into logically grouped commits with descriptive commit messages.
• [ ] Document all new functions.
• [ ] Write tests for new functions or explain why they are not needed.
• [ ] Build the documentation successfully
• [x] Use yapf to format python code.

Reviewer

• [ ] Actually read all of the code.
• [ ] Run the new code yourself.
• [ ] Write a summary of the changes as you understand them.
• [ ] Thank the submitter.