Leginon

This is a broader issue of how to define instruments for both leginon and appion...need to use a common table

The assumption we will make is that all images in the session have the same Cs value. Don't know if we might merge atomic resolution data from different TEM in the future. This will do for now since programs such as frealign only has one cs input for the whole dataset.

r15653 made the change in the appion. I have not done makestack2.py and makehelicalstack.py change since they can still get cs from ctf runs. Want to give it a bit of time after other codes are sure to work.
I put the call of getCsValueFromSession in checkConflicts function to be consistent although it is not really checking conflict but to set params. There are other set params in checkConflicts, so I've leave it that way, too.

r15654 made the change in myamiweb/processing. Cs values are no longer an input.

r15655 is the database schema update required to use existing database and microscopes.

See #1307 about problem that would cause if older appion upload is done or new microscope is added using current code after this revision.

I will need to test the Leginon side of cs value input on the scope and upgrade them at the scope all at the same day so that they are synced before other users start to get the new revision next day.

Testing:

Run each of the script I've changed. It should not crash and cs value in each ctf estimation/correction run and freealign job should come out right.

Amber, please code review these first and have someone test them. I will create a subtask for the Leginon new microscope part.

Anchi,
looks good.

One minor change I would make is in the schema update, rather than raising an exception if the user does not choose to continue with the script, I would display a message that the script is exiting and exit.

if not answer.lower().startswith('y'):
  raise RuntimeError

An unhandled exception might make it look like something terribly bad happened rather than the normal course of execution.

r15659 uses sys.exit() for rawinput of no.

Great.