Set Objective.NominalMagnification in the SVS reader
TiffSaver: pad truncated strips with zeros
JPEG-2000: allow boxing to be stripped

Also, fix how quality settings are propagated.
TiffWriter: update internal API scope to ease subclassing
TiffWriter: make checkParams protected so that subclasses can use it
JPEG2000Codec: make sure the last input stream is closed
Fix JPEG-2000 options to unbreak tests
Merge pull request #979 from melissalinkert/tiff-export-fixes

SVS import and TIFF export fixes
Update auto-generated documentation

Repository: openmicroscopy/bioformats
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Generated by BIOFORMATS-5.0-latest-docs-autogen#185 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest-docs-autogen/185/)