fixes to extract summary
Merge branch 'master' of github.com:losonczylab/sima
Merge branch 'master' of github.com:losonczylab/sima
Merge pull request #67 from nbdanielson/master

Extraction summary fixes for 3D
Improved robustness to case of constant intensity frame.
Masking of displacements with poor correlations in frame align.
Partial.
3D HMM calls frame_alignment with correlation criterion
Fix to correlation thresholding in frame alignment
Ignore masked frames in whole frame shifting
Fixes to 3D HMM and removal of itertool.chain(*
Bug fix.
Bug fix
Bug fix in frame alignment of 3D row-wise displacements
Changes to estimation of transition probabilities.
Cleanup and fixes to tests.
Stopped motion correction parameters from being changed during
estimation.