#!/usr/bin/env python

import tables, numpy

# Our id type. Used often.
IdType = tables.IntCol

#
# Classes representing metadata
#

class Namespace(tables.IsDescription):
    """Map from short string (e.g. OME) to versioned namespace (e.g. http://...)"""
    ns         = tables.StringCol(255)
    namespace  = tables.StringCol(16000)

class Lsid(tables.IsDescription):
    """Map from integer to LSID string"""
    id     = IdType()
    value  = tables.StringCol(16000)

class Group(tables.IsDescription):
    id        = IdType()
    name      = tables.StringCol(255)
    # etc.

class Experimenter(tables.IsDescription):
    id        = IdType()
    omeName   = tables.StringCol(255)
    firstName = tables.StringCol(255)
    lastName  = tables.StringCol(255)
    # etc.

class Project(tables.IsDescription):
    """A description that has several nested columns"""
    id    = IdType()
    owner = IdType()
    group = IdType()
    name  = tables.StringCol(255)
    description = tables.StringCol(255)

class Dataset(tables.IsDescription):
    """A description that has several nested columns"""
    id    = IdType()
    owner = IdType()
    group = IdType()
    name  = tables.StringCol(255)
    description = tables.StringCol(255)

class Image(tables.IsDescription):
    """A description that has several nested columns"""
    id    = IdType()
    owner = IdType()
    group = IdType()
    name  = tables.StringCol(255)
    description = tables.StringCol(255)
    creationDate = tables.IntCol()

class Pixels(tables.IsDescription):
    """A sub-structure of Test"""
    id    = IdType()
    owner = IdType()
    group = IdType()
    sizex = tables.IntCol()
    sizey = tables.IntCol()
    sizez = tables.IntCol()
    sizet = tables.IntCol()
    sizec = tables.IntCol()
    order = tables.StringCol(16) # Should be enum

def insert(table, **kwargs):
    """Simple function to insert values into tables"""
    for k,v in kwargs.iteritems():
        table.row[k] = v
    table.row.append()

if __name__ == "__main__":

    filename = "example.h5"
    h5file = tables.openFile(filename, mode = "w", title = "Example OME-HDF File")
    try:
        root = h5file.root
        ns = h5file.createTable(root, "Namespace", Namespace)
        insert(ns, ns="OME",     namespace="http://www.openmicroscopy.org/Schemas/OME/2007-06")
        insert(ns, ns="Vendor1", namespace="http://www.example1.com")
        insert(ns, ns="Vendor2", namespace="http://www.example2.com")

        # Spaces for other vendors
        vr1 = h5file.createGroup(root, 'Vendor1', 'Data for Vendor1')
        vr2 = h5file.createGroup(root, 'Vendor2', 'Data for Vendor2')
        # ...

        # Main OME namespace
        ome = h5file.createGroup(root, 'OME', 'OME Group')

        lsid = h5file.createTable(ome,'Lsid', Lsid)
        grp  = h5file.createTable(ome,'Group', Group)
        exp  = h5file.createTable(ome,'Experimenter', Experimenter)
        dst  = h5file.createTable(ome,'Project', Project)
        prj  = h5file.createTable(ome,'Dataset', Dataset)
        img  = h5file.createTable(ome,'Image', Image)
        pix  = h5file.createTable(ome,'Pixel', Pixels)

        insert(lsid, id=0, value="urn:lsid:Pixels:0")
        insert(lsid, id=1, value="urn:lsid:Pixels:2")
        insert(pix, id=0, sizex=10, sizey=10, sizez=3, sizec=1, sizet=1, order="XYZCT")
        insert(pix, id=1, sizex=5, sizey=5, sizez=3, sizec=1, sizet=1, order="XYZCT")

        # Data
        data     = h5file.createGroup(ome, 'Data', 'Binary Data')
        pixels   = h5file.createGroup(data, 'Pixels', 'Pixels Binary Data')
        acquired = h5file.createCArray(pixels, 'id_0', tables.IntAtom(), [1,1,3,10,10], title="Original, acquired (example) data")
        subsample = h5file.createCArray(pixels, 'id_1', tables.IntAtom(), [1,1,3,5,5], title="Subsample")
        subsample.attrs.relatedTo = 0

        # Actually setting values. Done elsewhere.
        subsample[0][0][0][0][0] = 5

    finally:
        h5file.close()


    #
    # Working with the data
    #
    import exceptions

    h5file = tables.openFile(filename)
    Root = h5file.root
    try:
        Namespace = Root.Namespace
    except tables.exceptions.NoSuchNodeException:
        raise exceptions.Exception("No /Namespace group. Invalid OME-HDF file.")

    ns = None
    for row in Namespace:
        if row["namespace"] == "http://www.openmicroscopy.org/Schemas/OME/2007-06":
            ns = row["ns"]
    if ns == None:
        raise exceptions.Exception("No OME namespace found. Invalid OME-HDF file. Exiting")

    OME = Root.__getattr__(ns)
    pixId = OME.Pixel[0]["id"]                             # Default because first in array
    binary = OME.Data.Pixels.__getattr__("id_"+str(pixId)) # Could look nicer
    print binary[0][0][0]