Find a home for BigEndian and other needed core metadata

[crueden-x]

Bio-Formats needs certain core metadata in order to work with byte arrays. In particular, you have to know if a given byte buffer is big or little endian in order to decode it. You also need to know if it is interleaved, and how many components there are (e.g., for 8-bit RGB planes, the data is actually 24 total bits per pixel, patterned RGBRGBRGB...).

The OME schema unfortunately never had a place for this information. There was a BigEndian? field of BinData?, but we have now deprecated that (see #6858). So we need to create locations in the OME schema to store BigEndian? (boolean), and InterleavedChannelCount? (integer, default 1). My vote is Pixels (where BigEndian? used to live IIRC).

[crueden-x]

The motivation for this ticket was due to the fact that Bio-Formats uses an OME Metadata object (which is derived from OME-XML via xsd-fu code generation) when exporting. If you want to export e.g. 16-bit data, you have to know whether the byte[] planes being fed to IFormatWriter.saveBytes are big-endian or little-endian in nature.

However, with the SCIFIO refactoring, that coupling between OME-XML and the core architecture will be relaxed. The SCIFIO export layer is not yet written, but I expect that going forward, it will be based on the core ImageMetadata/DatasetMetadata? (formerly "CoreMetadata?") rather than the OME-XML-specific metadata objects.

So in short, I think this ticket will be made obsolete by the SCIFIO work, and it is not worth worrying about anymore.

[ajpatterson]

From email: Melissa gave a +1 to the following values:

/** Number of valid bits per pixel. */
 public int bitsPerPixel;
 /** Indicates whether or not each pixel's bytes are in little endian order. */
 public boolean littleEndian;
 /** True if channels are stored RGBRGBRGB...; false if channels are stored
     RRR...GGG...BBB... */
 public boolean interleaved;

[ajpatterson]

After discussion with Melissa, Curtis, Roger & Andrew: Adding Interleaved and BigEndian? to Pixels.

See: ​https://github.com/openmicroscopy/bioformats/pull/424

[Andrew J Patterson <workonly@…>]

(In [10ffb0a4d413d6baa3733b01d53f6f428f205393/ome.git] on branch develop) Adding Interleaved to Pixels, see #7309

[Andrew J Patterson <workonly@…>]

(In [d9e13eb2cb217fca4409fa4fad0c6ade1fcf09e3/ome.git] on branch develop) Adding BigEndian? to Pixels, see #7309