Add Mask storage to OmeroTables

[jamoore]

Rather than store the masks in the database, support should be added to the preview for storing them in OmeroTables. Note: this is the 3rd potential storage location for masks (Mask.pixels and Mask.bytes are the other two).

[jmoore]

r5591 has the initial MaskColumn type. Next step is to add support for an VLArray which contains the bytes. Whether or not they are always loaded or must be manually loaded remains to be seen.

[jmoore]

r5593 includes storage of the byte masks as tables.UInt8Atom arrays in a separate VLArray ("%s_masks" % name). For some reason, Ice is printing "unexpected value" warnings for the byte arrays, but they convert correctly:

In [1]: import omero
In [2]: c = omero.client("localhost")
In [3]: s = c.createSession("root","xxx")
In [4]: r = s.sharedResources()
In [5]: h = r.newTable(1,"/tmp")
...
In [8]: m = omero.grid.MaskColumn("name", "desc", [1], [1], [1], [1.0], [1.0], [1.0], [1.0], [[1,2,3,4,5]])

In [9]: m
Out[9]: 
object #0 (::omero::grid::MaskColumn)
{
    name = name
    description = desc
    imageId = 
    {
        [0] = 1
    }
    theZ = 
    {
        [0] = 1
    }
    theT = 
    {
        [0] = 1
    }
    x = 
    {
        [0] = 1.0
    }
    y = 
    {
        [0] = 1.0
    }
    w = 
    {
        [0] = 1.0
    }
    h = 
    {
        [0] = 1.0
    }
    bytes = 
    {
        [0] = 
        {
            [0] = 1
            [1] = 2
            [2] = 3
            [3] = 4
            [4] = 5
        }
    }
}

In [10]: h.initialize([m])

In [11]: h.addData([m])

In [12]: h.slice(None,None)
Out[12]: 
object #0 (::omero::grid::Data)
{
    lastModification = 1256571786936
    rowNumbers = 
    {
    }
    columns = 
    {
        [0] = object #1 (::omero::grid::MaskColumn)
        {
            name = name
            description = 
            imageId = 
            {
                [0] = 1
            }
            theZ = 
            {
                [0] = 1
            }
            theT = 
            {
                [0] = 1
            }
            x = 
            {
                [0] = 1.0
            }
            y = 
            {
                [0] = 1.0
            }
            w = 
            {
                [0] = 1.0
            }
            h = 
            {
                [0] = 1.0
            }
            bytes = 
            {
                [0] = 
                {
                    [0] = <invalid value - expected byte>
                    [1] = <invalid value - expected byte>
                    [2] = <invalid value - expected byte>
                    [3] = <invalid value - expected byte>
                    [4] = <invalid value - expected byte>
                }
            }
        }
    }
}

In [13]: import numpy

In [14]: rv = h.slice(None,None)

In [17]: import tables


In [19]: rv.columns[0].bytes[0]
Out[19]: '\x01\x02\x03\x04\x05'

In [21]: numpy.fromstring(rv.columns[0].bytes[0], count=len(rv.columns[0].bytes[0]), dtype=tables.UInt8Atom())
)
Out[22]: array([1, 2, 3, 4, 5], dtype=uint8)

[cxallan]

Initial support within the importer for masks in r5620.

[jmoore]

Closing with a note to review in #1638