Hi Mike, you'll need to add your new classes to the __all__ list in tables/__init__.py to have them appear via "from tables import *". They are available via "import tables" since tables/__init__.py imports everything from tables/atom.py with the line "from tables.atom import *".
However, there will be other changes that you will need to make. What do you think about forking https://github.com/PyTables/PyTables and applying your changes so we can take a look? One next place will be AtomToHDF5Type which does not handle your "link" kind: def AtomToHDF5Type(atom, char *byteorder): cdef hid_t tid cdef hsize_t *dims # Create the base HDF5 type if atom.type in PTTypeToHDF5: tid = H5Tcopy(PTTypeToHDF5[atom.type]) # Fix the byteorder if atom.kind != 'time': set_order(tid, byteorder) elif atom.kind in PTSpecialKinds: # Special cases (the byteorder doesn't need to be fixed afterwards) if atom.type == 'complex64': tid = create_ieee_complex64(byteorder) elif atom.type == 'complex128': tid = create_ieee_complex128(byteorder) elif atom.kind == 'string': tid = H5Tcopy(H5T_C_S1); H5Tset_size(tid, atom.itemsize) elif atom.kind == 'bool': tid = H5Tcopy(H5T_STD_B8); elif atom.kind == 'enum': tid = enumToHDF5(atom, byteorder) else: raise TypeError("Invalid type for atom %s" % (atom,)) Cheers, ~Josh. On Jun 23, 2011, at 1:41 AM, Tallhamer, Mike wrote: > Here is some additional information on the issue... > > I see that if I type the following in ipython... > > [1] import tables > > I do get access to tables.LinkAtom and tables.LinkCol > > If I type... > > [2] from tables import * > > Neither LinkAtom or LinkCol are available. Furthermore, if I use > tables.LinkCol in an IsDescription class and try to assign a string to > it I get a TypeError like the one below. > > In [3]: class Test(IsDescription): > ...: name = StringCol(100) > ...: link_col = tables.LinkCol(100) > ...: > ...: > > In [4]: h5file = openFile('mytables.h5','w') > > In [5]: h5file.createTable('/', 'Test', Test, title='Test Table') > > ------------------------------------------------------------------------ > --- > TypeError Traceback (most recent call > last) > > C:\tmp\<ipython console> in <module>() > > C:\Python27\lib\site-packages\tables\file.pyc in createTable(self, > where, name, > description, title, filters, expectedrows, chunkshape, byteorder, > createparents) > 772 description=description, title=title, > 773 filters=filters, expectedrows=expectedrows, > --> 774 chunkshape=chunkshape, byteorder=byteorder) > 775 > 776 > > C:\Python27\lib\site-packages\tables\table.pyc in __init__(self, > parentNode, name, description, title, filters, expectedrows, chunkshape, > byteorder, _log) > 590 > 591 super(Table, self).__init__(parentNode, name, new, > filters, > --> 592 byteorder, _log) > 593 > 594 > > C:\Python27\lib\site-packages\tables\leaf.pyc in __init__(self, > parentNode, name, new, filters, byteorder, _log) > 289 # is a lazy property that automatically handles their > loading. > > 290 > --> 291 super(Leaf, self).__init__(parentNode, name, _log) > 292 > 293 > > C:\Python27\lib\site-packages\tables\node.pyc in __init__(self, > parentNode, name, _log) > 294 # Create or open the node and get its object ID. > > 295 if new: > --> 296 self._v_objectID = self._g_create() > 297 else: > 298 self._v_objectID = self._g_open() > > C:\Python27\lib\site-packages\tables\table.pyc in _g_create(self) > 745 # set because it is needed for setting attributes > afterwards. > > 746 self._v_objectID = self._createTable( > --> 747 self._v_new_title, self.filters.complib or '', > obversion ) > 748 self._v_recarray = None # not useful anymore > 749 self._rabyteorder = None # not useful anymore > > C:\Python27\lib\site-packages\tables\tableExtension.pyd in > tables.tableExtension.Table._createTable > (tables\tableExtension.c:1822)() > > C:\Python27\lib\site-packages\tables\utilsExtension.pyd in > tables.utilsExtension.createNestedType (tables\utilsExtension.c:7912)() > > C:\Python27\lib\site-packages\tables\utilsExtension.pyd in > tables.utilsExtension.AtomToHDF5Type (tables\utilsExtension.c:5703)() > > TypeError: Invalid type for atom LinkCol(itemsize=100, shape=(), > dflt='', pos=0) > > > > Any thoughts or ideas? > > -Mike > > > > -----Original Message----- > > I would like to create my own atom class but appear to be doing > something wrong. I basically just need a StringAtom but want to define a > new class with a new PyTables 'kind' of 'link' instead of 'string.' > > I have added the following code to the atom.py file... > > class LinkAtom(Atom): > """ > Defines an atom of type ``link``. > > The item size is the *maximum* length in characters of strings. > """ > kind = 'link' > itemsize = property( > lambda self: self.dtype.base.itemsize, > None, None, "Size in bytes of a sigle item in the atom." ) > type = 'string' > _defvalue = '' > > def __init__(self, itemsize, shape=(), dflt=_defvalue): > if not hasattr(itemsize, '__int__') or int(itemsize) < 0: > raise ValueError( "invalid item size for kind ``%s``: %r; " > "it must be a positive integer" > % ('string', itemsize) ) > Atom.__init__(self, 'S%d' % itemsize, shape, dflt) > > > However, when I run ipython and import tables a LinkAtom and by > extension a LinkCol is not created. Can someone tell me what I'm doing > wrong? This method of generating class in PyTables doesn't seen to be > very intuitive and/or pythonic. > > -Mike ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense.. http://p.sf.net/sfu/splunk-d2d-c1 _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
