Minor fix to sequence.py

Missing type cast caused motion correction to fail on Windows
Sped up some slow tests by clipping the dataset
bug fixes in slicing _motion_corrected_sequence
bug fix for memory issue related to *it.chain
bug fixes in slicing _Motion_Corrected_Sequence
fixes for 3D extraction summary pdf

NOTE: Pools currently hang
Fix for large datasets hanging extraction pools. Added chunksize limit.
Now pass frame index in to the workers so they can be read-out unordered.
adapted imaging parameters to Prairie v5.2
support for old prairieview xml
Merge pull request #57 from jzaremba/mc_bug_fixes

Mc bug fixes & changes to extraction
Reducing redundancy between 2D & 3D motion correction
Update reference during 3D volume alignment
Partial HMM refactoring