Switch from jzarr to zarr-java for v2/NGFF 0.4

[melissalinkert]

This fully removes the dependency on jzarr, and uses zarr-java for all versions.

There are a few test failures here, which are specific to v2 plate data. See note in Converter line 2816. Since there have been a few relevant fixes in zarr-java since 0.0.9 (especially zarr-developers/zarr-java#36), I expect to keep this as a draft until a new zarr-java version is released.

There are also a few commented to-do items around compression properties (likely needs documentation in addition to code changes), and testing of group key counts.

[dominikl]

zarr-java 0.0.10 has been released now. Are you holding of with a new release for this PR? Would be nice do have a release with the --ngff-version argument for generating v3 zarrs.

[melissalinkert]

Mentioned separately, but note that 0.12.0-rc1 includes the --ngff-version option and can be used to write v3. We're still reviewing this PR; c37e250 updated to zarr-java 0.0.10 as soon as it was available.

[sbesson]

Converted the same set of source samples as used in #290 (review) using bioformats2raw 0.11.0 (i.e. with jzarr) as well as this library.

Conversion times for a range of compression options is given below

Version	Options	Leica-1.scn	NIRHTa+001	LuCa-7color_Scan1.qptiff
0.11.0	--compression null	0m51.015s	0m43.750s	0m44.531s
0.11.0	--compression zlib	1m24.959s	1m20.042s	0m59.944s
0.11.0	--compression blosc	0m55.334s	0m46.729s	0m40.767s
0.11.0	--compact	0m55.951s	0m49.904s	0m39.888s
0.12.0-SNAPSHOT	--compression null	1m24.377s	0m50.734s	0m50.381s
0.12.0-SNAPSHOT	--compression zlib	1m57.604s	2m10.099s	1m38.594s
0.12.0-SNAPSHOT	--compression blosc	1m41.235s	2m12.802s	1m30.536s
0.12.0-SNAPSHOT	--compact	1m40.051s	2m9.259s	1m30.725s

and dataset sizes

Version	Options	Leica-1.scn	NIRHTa+001	LuCa-7color_Scan1.qptiff
0.11.0	--compression null	5.5G	4.3G	5.8G
0.11.0	--compression zlib	3.4G	2.4G	2.1G
0.11.0	--compression blosc	4.3G	4.0G	3.2G
0.11.0	--compact	4.3G	4.0G	3.2G
0.12.0-SNAPSHOT	--compression null	5.5G	4.3G	5.8G
0.12.0-SNAPSHOT	--compression zlib	3.2G	2.4G	2.0G
0.12.0-SNAPSHOT	--compression blosc	3.2G	2.3G	1.9G
0.12.0-SNAPSHOT	--compact	3.2G	2.3G	1.9G

The compression internal are not strictly identical between jzarr and zarr-java

• --compression blosc with jzarr

    "compressor" : {
    "clevel" : 5,
    "blocksize" : 0,
    "shuffle" : 1,
    "cname" : "lz4",
    "id" : "blosc"
  },

• --compression blosc with zarr-java

  "compressor" : {
    "id" : "blosc",
    "cname" : "zstd",
    "shuffle" : 0,
    "clevel" : 5,
    "typesize" : 1,
    "blocksize" : 0
  },
  

• --compression zlib with jzarr

  "compressor" : {
   "level" : 1,
   "id" : "zlib"
  },

• --compression zlib with zarr-java

  "compressor" : {
    "id" : "zlib",
    "level" : 5
  },

Independently of the above, the results above suggest a performance degradation when using zarr-java especially when compression is enabled. This is consistent with the results observed in the review of #290

[melissalinkert]

ca328fe switches to the default compression settings that jzarr used (https://jzarr.readthedocs.io/en/latest/tutorial.html#compressors), and should now respect compression properties options again. That substantially speeds up the conversion time for LuCa-7color_Scan1.qptiff with zarr-java when testing locally.

[sbesson]

Thanks @melissalinkert, with the latest commit, the size and conversion times are now very consistent when using 0.11.0 with jzarr and this PR with zarr-java

Version	Options	Leica-1.scn	NIRHTa+001	LuCa-7color_Scan1.qptiff
0.11.0	--compression null	5.5G	4.3G	5.8G
0.11.0	--compression zlib	3.4G	2.4G	2.1G
0.11.0	--compression blosc	4.3G	4.0G	3.2G
0.11.0	--compact	4.3G	4.0G	3.2G
0.12.0-SNAPSHOT	--compression null	5.5G	4.3G	5.8G
0.12.0-SNAPSHOT	--compression zlib	3.4G	2.4G	2.1G
0.12.0-SNAPSHOT	--compression blosc	4.3G	2.5G	3.2G
0.12.0-SNAPSHOT	--compact	4.3G	2.5G	3.2G

Version	Options	Leica-1.scn	NIRHTa+001	LuCa-7color_Scan1.qptiff
0.11.0	--compression null	1m2.504s	0m45.412s	0m45.840s
0.11.0	--compression zlib	1m25.445s	1m24.885s	0m59.913s
0.11.0	--compression blosc	1m1.152s	0m48.590s	0m45.504s
0.11.0	--compact	1m0.541s	0m47.545s	0m44.798s
0.12.0-SNAPSHOT	--compression null	1m4.281s	0m51.738s	0m50.975s
0.12.0-SNAPSHOT	--compression zlib	1m33.890s	1m32.787s	1m11.114s
0.12.0-SNAPSHOT	--compression blosc	1m2.873s	0m54.470s	0m45.983s
0.12.0-SNAPSHOT	--compact	1m2.827s	0m49.999s	0m46.317s