EMAN2 to Frealign script

[gclander]

I heavily edited the EMAN_to_FREALIGN.py script from the Frealign repository to work with all versions of IMAGIC and EMAN2 (no more EMAN1). It's also ~8X faster now, since the flipping, normalization, and reversal of particles is all done in a single step. This step could potentially be parallelized, but that will come at a later time.
The script additionally checks the parameter file to determine the number of models to account for.

I put this script in the EMAN2 repository namely due to its use of EMAN2, but also because I haven't checked out the Frealign repository :)
I will update the Nogaleslab wiki to point to this script.

It should be noted that THERE IS A BUG in the final EM2EM conversion, and this should be addressed in a later version of this script. During the conversion of the imagic stack to a 3D SPIDER stack, all the particles are shifted up by 1 pixel. This was present in the previous version of the script, and is not affected by the IMAGIC version.
It would be ideal to remove the EM2EM dependency altogether.

[mcianfrocco]

This is awesome Gabe! And it's really interesting that there is a single pixel error, something that only high resolution studies would find.

[gclander]

Frealign scripts should be updated to work with MRC files instead of SPI.