TIFF: fix plane count calculation for pyramids with multiple planes

Fixes #12617.
Removing jpeg 2000 broken link
add RandomAccessOutputStream(byte[]) constructor

@imunro was missing this constructor
Fix URLHandleTest path for Windows
Metamorph: fix double value parsing for locales that use a comma separator

See
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-November/004864.html

Double.parseDouble does not account for locale, and assumes that the
decimal separator is '.'.
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1381 (Parse physical pixel sizes from CellSens .vsi datasets)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1385 (C++: Add TIFF reader)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1395 (C++: Various minor fixes)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1404 (Re-enable URLHandleTest)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1407 (TIFF: fix plane count calculation for pyramids with multiple planes)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1409 (Removing jpeg 2000 broken link (rebased onto develop))
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1410 (add RandomAccessOutputStream(byte[]) constructor)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1411 (Metamorph: fix double value parsing for locales that use a comma separator)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient' (label: breaking)
  # PR 1383 LeeKamentsky 'Fix im3 metadata' (user: LeeKamentsky)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1396 qidane 'Units introduction for remaining quantities' (label: breaking)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1366 ctrueden 'Miscellaneous cleanup' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements' (label: exclude)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
Already up-to-date.

Merged PRs:
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets'
  # PR 1385 rleigh-dundee 'C++: Add TIFF reader'
  # PR 1395 rleigh-dundee 'C++: Various minor fixes'
  # PR 1404 melissalinkert 'Re-enable URLHandleTest'
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes'
  # PR 1409 hflynn 'Removing jpeg 2000 broken link (rebased onto develop)'
  # PR 1410 mtbc 'add RandomAccessOutputStream(byte[]) constructor'
  # PR 1411 melissalinkert 'Metamorph: fix double value parsing for locales that use a comma separator'

Generated by OME-5.1-merge-push#561 (http://ci.openmicroscopy.org/job/OME-5.1-merge-push/561/)
Update auto-generated documentation

Repository: snoopycrimecop/bioformats

Generated by BIOFORMATS-5.1-merge-docs-autogen#95 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.1-merge-docs-autogen/95/)