Allow OME Zarr group

[melissalinkert]

See glencoesoftware/bioformats2raw#157

This updates the series finding logic to ignore the OME Zarr group, if it exists. Without this change, attempting to convert data generated by glencoesoftware/bioformats2raw#157 resulted in something like:

Exception in thread "main" picocli.CommandLine$ExecutionException: Error while calling command (com.glencoesoftware.pyramid.PyramidFromDirectoryWriter@635eaaf1): java.lang.RuntimeException: java.io.IOException: Path '/home/melissa/test-series/10' is not a valid path or not a directory.
	at picocli.CommandLine.executeUserObject(CommandLine.java:1792)
	at picocli.CommandLine.access$900(CommandLine.java:145)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2150)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2144)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2108)
	at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1968)
	at picocli.CommandLine.parseWithHandlers(CommandLine.java:2349)
	at picocli.CommandLine.parseWithHandler(CommandLine.java:2284)
	at picocli.CommandLine.call(CommandLine.java:2560)
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.main(PyramidFromDirectoryWriter.java:210)
Caused by: java.lang.RuntimeException: java.io.IOException: Path '/home/melissa/test-series/10' is not a valid path or not a directory.
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.call(PyramidFromDirectoryWriter.java:242)
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.call(PyramidFromDirectoryWriter.java:97)
	at picocli.CommandLine.executeUserObject(CommandLine.java:1783)
	... 9 more
Caused by: java.io.IOException: Path '/home/melissa/test-series/10' is not a valid path or not a directory.
	at com.bc.zarr.ZarrUtils.ensureDirectory(ZarrUtils.java:159)
	at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:94)
	at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:87)
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.getZarrGroup(PyramidFromDirectoryWriter.java:498)
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.findNumberOfResolutions(PyramidFromDirectoryWriter.java:552)
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.initialize(PyramidFromDirectoryWriter.java:649)
	at com.glencoesoftware.pyramid.PyramidFromDirectoryWriter.call(PyramidFromDirectoryWriter.java:228)
	... 11 more

Since raw2ometiff converts all series anyway, I haven't changed this to read the series list from the OME group attributes.

This should continue to work with Zarr data that doesn't have an OME group at all.

[sbesson]

Thanks @melissalinkert. This matches the proposed introduction of a special OME Zarr group in the output of bioformats2raw. This metadata-only group should not be accounted for when computing the series during the OME-TIFF conversion.

Tested with glencoesoftware/bioformats2raw#157 with both HCS and non-HCS data:

(java11) sbesson@Sebastiens-MacBook-Pro-2 bioformats2raw % ./bioformats2raw-0.5.0-SNAPSHOT/bin/bioformats2raw test.fake /tmp/test.ome.zarr
(java11) sbesson@Sebastiens-MacBook-Pro-2 bioformats2raw % ./bioformats2raw-0.5.0-SNAPSHOT/bin/bioformats2raw "plate&plateRows=1&plateCols=1.fake" /tmp/plate.ome.zar

Without this PR, raw2ometiff would fail on the non-HCS NGFF with the cryptic error mentioned in the description but would succeed with the HCS NGFF as the plate handling is different than enumerating the number of top-level groups.

With this PR included, both NGFF samples convert successfully into valid OME-TIFF.

(java11) sbesson@Sebastiens-MacBook-Pro-2 raw2ometiff % ./raw2ometiff-0.3.1-SNAPSHOT/bin/raw2ometiff /tmp/test.ome.zarr  /tmp/test.ome.tiff
(java11) sbesson@Sebastiens-MacBook-Pro-2 raw2ometiff % ./raw2ometiff-0.3.1-SNAPSHOT/bin/raw2ometiff /tmp/plate.ome.zarr /tmp/plate.ome.tiff

I also tried to test various source layout using the --no-root-group and --no-ome-meta-export but the second step of the conversions failed with different errors, which are all in-line with the help of these options

      --no-ome-meta-export   Turn off OME metadata exporting [Will break
                               compatibility with raw2ometiff]
      --no-root-group        Turn off creation of root group and corresponding
                               metadata [Will break compatibility with
                               raw2ometiff]

@melissalinkert is it worth testing compatibility with a NGFF layout generated by bioformats2raw 0.4.0 or have we diverged enough that this should only be compatible with bioformats2raw 0.5.0?

[melissalinkert]

I'd expect this to still work with bioformats2raw 0.4.0 data.

[sbesson]

Regenerated a sample OME-NGFF using the recently released NGFF-converter which is still using bioformats2raw 0.4.0.
An execution of raw2ometiff with this PR included generated an OME-TIFF without issues