Roll pxCov and indexMovie into motion correction, so that original tiffs are only loaded once

[Selmaan]

It is essentially wasteful to load the raw data and write the motion corrected files to disk, and then separately read the motion corrected files back from disk 2 independent times while used in the pxCov and indexMovie calculations. We could save substantial time by loading the raw data once, motion corrected, and performing all pxCov + indexing functions on this data while still in memory before writing to disk.