Appion

Stop using EMAN boxer and instead write our own python code for particle selection and rotation in Appion.

From Neil, Issue #1056:
I think it is time to drop EMAN boxer and just do it in python. It would be so much cleaner...

For each image:
  image = mrc.read(...)
  rotated = scipy.ndimage.rotate(image, angle=##, reshape=False, order=1)
  partlist = []
  For each particle:
    part = rotate[x1':x2',y1':y2'] #note: rotated coordinate system, x2' = x1' + boxsize
    partlist.append(part)
  apImagicFile.writeImagic(partlist, image1stack)
apImagicFile.mergeStacks(image1stack, image2stack, ...)

and then (1) skip the whole proc2d/batchboxer non-sense, (2) do it in one pass, and (3) it would be much faster.