Data and OMERO Tables

[icaoberg]

i downloaded one of the generated tables with feature values but they are empty. i think i might be doing something wrong.

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    resources = session.sharedResources()
    repositories = resources.repositories()
    fileLink = omero.model.ImageAnnotationLinkI()
   
    #features
    featuresTable = resources.newTable( iid, str(iid) + '_features.h5' )
    featuresFileAnnotation = omero.model.FileAnnotationI()
    featuresFileAnnotation.file = featuresTable.getOriginalFile()
    fileLink.link( omero.model.ImageI(iid, False), featuresFileAnnotation)
    session.getUpdateService().saveObject(fileLink)
   
    features_column = omero.grid.DoubleColumn("feature_value", """Feature value""", [] )
    featuresTable.initialize([features_column])
    for i in range(len(features)):
        features_column.values.append( features[i] )
    featurestable.addData([features_column])

[jmoore]

With a few modifications like capitalizations and parsing to double:

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def test(session, features, iid):
    resources = session.sharedResources()
    repositories = resources.repositories()
    fileLink = omero.model.ImageAnnotationLinkI()

    #features
    featuresTable = resources.newTable( iid, str(iid) + '_features.h5' )
    featuresFileAnnotation = omero.model.FileAnnotationI()
    featuresFileAnnotation.file = featuresTable.getOriginalFile()
    fileLink.link( omero.model.ImageI(iid, False), featuresFileAnnotation)
    session.getUpdateService().saveObject(fileLink)

    features_column = omero.grid.DoubleColumn("feature_value", """Feature value""", [] )
    featuresTable.initialize([features_column])
    for i in range(len(features)):
        features_column.values.append( float(features[i]) )
    featuresTable.addData([features_column])

    print featuresTable.read([0], 0, 10)


I get this result:

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In [30]: test(client.sf, range(10), i.id.val)
object #0 (::omero::grid::Data)
{
    lastModification = 1288712208046
    rowNumbers =
    {
        [0] = 0
        [1] = 1
        [2] = 2
        [3] = 3
        [4] = 4
        [5] = 5
        [6] = 6
        [7] = 7
        [8] = 8
        [9] = 9
    }
    columns =
    {
        [0] = object #1 (::omero::grid::DoubleColumn)
        {
            name = feature_value
            description =
            values =
            {
                [0] = 0.0
                [1] = 1.0
                [2] = 2.0
                [3] = 3.0
                [4] = 4.0
                [5] = 5.0
                [6] = 6.0
                [7] = 7.0
                [8] = 8.0
                [9] = 9.0
            }
        }
    }
}


Hope that helps.
~Josh

[jmoore]

Ah, something else that occurs to me: try closing the table instance (which I should have done as well). Only when it's closed does the server update the length, and that's how much you download. See http://trac.openmicroscopy.org.uk/omero/ticket/2908 for more information.

~J.

[icaoberg]

shouldnt i be able to open the created h5 file using

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table = resources.openTable( "iid4401_features.h5" )

but i get the error

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In [35]: table = resources.openTable( 'iid4401_features.h5')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/afs/cs.cmu.edu/user/bhcho/<ipython console> in <module>()

/usr0/local/omero.server/OMERO.server-Beta-4.2.0/lib/python/omero_SharedResources_ice.pyc in openTable(self, file, _ctx)
    105
    106         def openTable(self, file, _ctx=None):
--> 107             return _M_omero.grid.SharedResources._op_openTable.invoke(self, ((file, ), _ctx))
    108
    109         def checkedCast(proxy, facetOrCtx=None, _ctx=None):

ValueError: invalid value for argument 1 in operation `openTable'


[jmoore]

Hi Ivan,

SharedResoures.openTable doesn't take a string but an omero.model.OriginalFile object. If you only have the id of the file, then you can use:

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resources.openTable(omero.model.OriginalFileI(FILE_ID, False))


Cheers,
~Josh

[icaoberg]

is there a way to retrieve the table using the file name? or an image id? or is there a way to keep track of the table?

the thing is for every image with image id <iid> we create an h5 table named <iid>-features.h5

i want a way to retrieve all the tables by this <iid> but im navigating through the api and cant seem to find a way.

[jmoore]

Ivan,

have you had any luck with the solution we discussed?

Cheers,
~Josh

[icaoberg]

Yes I get a list of all the attachments. But I have a question: can I make a query and search for filename and get the file ID for that filename? I mean, can I query say table.h5 and get the file ID? if so what would be the query? sorry i really have no clue on how to do this.

[jmoore]

I'm not sure exactly what you're asking but perhaps something like this:

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iQuery.projection("select f.id from OriginalFile f where f.path = '/dir/' and f.name = 'table.h5'");


If you'd like to also use the annotation metadata you'll need a query like this:

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select f.id from FileAnnotation fa join fa.file f where fa.ns = 'CMU:abc' and f.name = 'table.h5'


Hope that helps.
~Josh.

[icaoberg]

say i save a table and i name it features.h5 and omero returns a file id 1 -which i dont know-. on disk the file features.h5 doesn't exist, a file with name 1 exist in the repository. since i know the name of the file -not the file id-, is there a way to make a query where given the filename i get the file id? i know i cant do this through the api, since i can only load a table using the file id not the file name.

ivan

ps your previous solution works but it returns every file link and i would like to know if there is a more efficient way.