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
Merge branch 'master' into nathan_3D_extract_fix
Merge branch 'master' into nathan_3D_extract_fix
support for old prairieview xml
Merge branch 'master' into nathan_3D_extract_fix
Merge pull request #56 from nbdanielson/3D_fixes

3D fixes
Merge branch 'master' into no_pool_frame_align