IFormatReader: Remove deprecated getChannelDimLengths and getChannelDimTypes

The only reader overriding the default implementations was ICSReader.
This has been updated to use ModuloC, which copes with the case
where all channels are of the same length.

The users of these methods (plugins DisplayHandler, ImagePlusReader,
LociFunctions and BFVirtualStack) have been updated to make use of
ModuloC.

These methods have been dropped from all implementors of IFormatReader.
IFormatReader: Remove deprecated getCoreMetadata
Merge remote-tracking branch 'origin/develop' into reader-deprecated-rm
Bug Fix : saveROI checkbox
Bug fix : SaveROI checkbox
Merge pull request #1425 from jburel/tolerance

Convert tolerance to NonNegativeInt to NonNegativeFloat
Merge pull request #1439 from sbesson/bioformats_eclipse

Update Eclipse instructions for Bio-Formats with link to ome-devel thread
Merge pull request #1434 from rleigh-dundee/cmake-boostchecks

cpp: cmake: RegexChecks: Improve include usage for portability
OME-XML: prevent IndexOutOfBoundsException if BinData is empty
Merge branch 'ome-xml-fix' of github.com:melissalinkert/bioformats into ome-xml-fix
Merge pull request #1436 from rleigh-dundee/cpp-module2

cpp: compat: Add path type lookups to module
Merge pull request #1418 from rleigh-dundee/reader-deprecated-rm

IFormatReader: Remove deprecated methods
Merge pull request #1440 from melissalinkert/12624

DICOM: fix byte skipping for >8 bit data
Merge pull request #1428 from rleigh-dundee/cpp-metadata

C++: Incremental metadata processing work
merge develop -Dorg -Ssuccess-only: PR 1407 (TIFF: fix plane count calculation for pyramids with multiple planes)
merge develop -Dorg -Ssuccess-only: PR 1420 (Updating samples and adding units samples)
merge develop -Dorg -Ssuccess-only: PR 1431 (Specification: Add XML catalogues for released schemas)
merge develop -Dorg -Ssuccess-only: PR 1441 (Fix OME-XML BinData decoding)
merge develop -Dorg -Ssuccess-only: PR 1442 (Update roi handler)
merge develop -Dorg -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1447 sbesson 'Add python-bioformats to the documentation' (status: pending)
  # PR 1437 stelfrich 'Changed handling of empty series names in ND2 files' (user: stelfrich)
  # PR 1444 snoopycrimecop 'Update auto-generated documentation' (status: pending)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets' (label: exclude)
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1443 joshmoore 'Genshi ZIP' (label: exclude)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1448 melissalinkert 'Metamorph: allow both sanitized and unsanitized delimiters' (status: pending)
  # PR 1383 LeeKamentsky 'Fix im3 metadata' (user: LeeKamentsky)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1435 joshmoore 'Ordered MapPairs implementation' (label: breaking)
  # PR 1366 ctrueden 'Miscellaneous cleanup' (label: exclude)
  # PR 1426 qidane 'Initial Rendering Definitions schema' (exclude comment)
Updating c2525bf..b9213df
Previously merged:
  # PR 1428 rleigh-dundee 'C++: Incremental metadata processing work'
  # PR 1440 melissalinkert 'DICOM: fix byte skipping for >8 bit data'
  # PR 1418 rleigh-dundee 'IFormatReader: Remove deprecated methods'
  # PR 1436 rleigh-dundee 'cpp: compat: Add path type lookups to module'
  # PR 1434 rleigh-dundee 'cpp: cmake: RegexChecks: Improve include usage for portability'
  # PR 1439 sbesson 'Update Eclipse instructions for Bio-Formats with link to ome-devel thread'
  # PR 1425 jburel 'Convert tolerance to NonNegativeInt to NonNegativeFloat'

Merged PRs:
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes'
  # PR 1420 qidane 'Updating samples and adding units samples'
  # PR 1431 rleigh-dundee 'Specification: Add XML catalogues for released schemas'
  # PR 1441 melissalinkert 'Fix OME-XML BinData decoding'
  # PR 1442 bramalingam 'Update roi handler'

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