Gatan: fix physical dimension parsing when the Z size is missing

Fixes #12478.
Deltavision: conditionally ignore stage positions values of 0

If only two unique positions are present in X and Y, and one of them is
0 in both cases, then we ignore the 0 positions (with the result being
that there is only one tile).  See gh-1320.
Use in-place caching by default in Memoizer

This commit sets the in-place caching attribute to true by default. The
immediate consequence is that all constructors now become usable (with only
the constructors using a directory input overriding this behavior). The
constructor using a boolean value now becomes obsolete and is removed. Unit
tests are added for each supported constructor using getMemoFile().
ND2: prevent NumberFormatExceptions when parsing text data
Preserve current behavior if null directory is passed

With this commit doInplaceCaching is false by default and set to true if a
constructor with no directory is passed independently of the nullability of
directory.
Merge pull request #1317 from melissalinkert/ticket-12478

Gatan: fix physical dimension parsing when the Z size is missing
Merge pull request #1324 from melissalinkert/dv-stages

Deltavision: conditionally ignore stage position values of 0
Merge pull request #1335 from melissalinkert/rebased/develop/ticket-12536

ND2: prevent NumberFormatExceptions when parsing text data (rebased onto develop)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 1054 (Additional annotation points throughout the model)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 1328 (Use in-place caching by default in Memoizer)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1339 melissalinkert 'Amaris FlowSight' (user: melissalinkert)
  # PR 1340 joshmoore 'kryo: update to 2.24.0 with shading changes (see #10852)' (user: joshmoore)
  # PR 1265 qidane 'New units' (label: exclude)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories' (user: melissalinkert)
  # PR 1302 sbesson 'Add branch-specific link for downloading the JAR file if unfound (rebased onto develop)' (user: sbesson)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1249 PremyslFiala 'ND2 - Bug fixes' (user: PremyslFiala)
  # PR 1342 joshmoore 'Catch all exceptions on loadMemo' (user: joshmoore)
  # PR 1331 rleigh-dundee 'C++: Add FormatWriter interface' (user: rleigh-dundee)
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter' (user: melissalinkert)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1315 LeeKamentsky 'IM3Reader for Perkin-Elmer Nuance' (user: LeeKamentsky)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (user: melissalinkert)
  # PR 1323 melissalinkert 'Add bit-level operations to RandomAccess{Input, Output}Stream' (user: melissalinkert)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1336 melissalinkert 'Minor memoizing fixes' (user: melissalinkert)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
Updating 0819d22..5c5731a
Previously merged:
  # PR 1335 melissalinkert 'ND2: prevent NumberFormatExceptions when parsing text data (rebased onto develop)'
  # PR 1324 melissalinkert 'Deltavision: conditionally ignore stage position values of 0'
  # PR 1317 melissalinkert 'Gatan: fix physical dimension parsing when the Z size is missing'

Merged PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model'
  # PR 1328 sbesson 'Use in-place caching by default in Memoizer'

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