Add some cautionary statements about adjusting tile sizes

[melissalinkert]

First try at expanding the tile size documentation, as discussed earlier today. This will also warn if --tile_width or --tile_height is changed from the default at all.

[sbesson]

(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % ./bioformats2raw-0.7.0-SNAPSHOT/bin/bioformats2raw test.fake test.zarr -h 256 -w 512
2023-01-23 09:31:42,862 [main] WARN  c.g.bioformats2raw.Converter - Non-default tile size: 512 x 256. This may cause performance issues in some applications.
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % cat test.zarr/.zattrs 
{
  "bioformats2raw.layout" : 3
}%                         
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % cat test.zarr/0/0/.zarray 
{
  "chunks" : [ 1, 1, 1, 256, 512 ],
  "compressor" : {
    "clevel" : 5,
    "blocksize" : 0,
    "shuffle" : 1,
    "cname" : "lz4",
    "id" : "blosc"
  },
  "dtype" : "|u1",
  "fill_value" : 0,
  "filters" : null,
  "order" : "C",
  "shape" : [ 1, 1, 1, 512, 512 ],
  "dimension_separator" : "/",
  "zarr_format" : 2
}%      

Testing various combinations of input arguments

(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % rm -r test.zarr 
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % ./bioformats2raw-0.7.0-SNAPSHOT/bin/bioformats2raw test.fake test.zarr -h 256       
2023-01-23 09:33:48,554 [main] WARN  c.g.bioformats2raw.Converter - Non-default tile size: 1024 x 256. This may cause performance issues in some applications.
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % rm -r test.zarr                                                               
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % ./bioformats2raw-0.7.0-SNAPSHOT/bin/bioformats2raw test.fake test.zarr -w 256 
2023-01-23 09:33:56,066 [main] WARN  c.g.bioformats2raw.Converter - Non-default tile size: 256 x 1024. This may cause performance issues in some applications.
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % rm -r test.zarr                                                               
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % ./bioformats2raw-0.7.0-SNAPSHOT/bin/bioformats2raw test.fake test.zarr -w 1024
(java8) sbesson@Sebastiens-MacBook-Pro-2 Downloads % rm -r test.zarr 

Code-wise all looks good to me

[erindiel]

The added descriptions for --tile_width and --tile_height options in --help output are very clear and improve the understanding of related chunk size and read size:

  -h, --tile_height=<tileHeight>
                             Maximum tile height (default: 1024). This is both
                               the chunk size (in Y) when writing Zarr and the
                               tile size used for reading from the original
                               data. Changing the tile size may have
                               performance implications.

  -w, --tile_width=<tileWidth>
                             Maximum tile width (default: 1024). This is both
                               the chunk size (in X) when writing Zarr and the
                               tile size used for reading from the original
                               data. Changing the tile size may have
                               performance implications.

README advice is also clear.