Re: [Pytables-users] recursive walk question

[Anthony S. <sc...@gm...>]

On Thu, Jun 14, 2012 at 4:30 PM, Andre' Walker-Loud <wal...@gm...>wrote:

> Hi Anthony,
>
> On Jun 14, 2012, at 11:30 AM, Anthony Scopatz wrote:
>
> > On Wed, Jun 13, 2012 at 8:23 PM, Andre' Walker-Loud <wal...@gm...>
> wrote:
> > Hi All,
> >
> > Still trying to sort out a recursive walk through an hdf5 file using
> pytables.
> >
> > I have an hdf5 file with an unknown depth of groups/nodes.
> >
> > I am trying to write a little function to walk down the tree (with user
> input help) until a data file is found.
> >
> > I am hoping there is some function one can use to query whether you have
> found simply a group/node or an actual numpy array of data.  So I can do
> something like
> >
> > if f.getNode('/',some_path) == "data_array":
> >    return f.getNode('/',some_path), True
> > else:
> >    return f.getNode('/',some_path), False
> >
> > where I have some function that if the second returned variable is True,
> will recognize the file as data, where as if it is False, it will query the
> user for a further path down the tree.
> >
> >
> > I suppose I could set this up with a try: except: but was hoping there
> is some built in functionality to handle this.
> >
> > Yup, I think that you are looking for the File.walkNodes() method.
> http://pytables.github.com/usersguide/libref.html#tables.File.walkNodes
>
> I wasn't sure how to use walkNodes in an interactive search.  Here is what
> I came up with so far (it works on test cases I have given it).  Comments
> are welcome.
>
> One feature I would like to add to the while loop in the second function
> is an iterator counting the depth of the search.  I want to compare this to
> the maximum tree/node/group depth in the file, so if the search goes over
> (maybe my collaborators used createTable instead of createArray) the while
> loop won't run forever.
>
> Is there a function to ask the deepest recursion into the hdf5 file?
>

Hello Andre,

Every Node object has a _v_depth attr that you can access (
http://pytables.github.com/usersguide/libref.html#tables.Node._v_depth).
 In your walk function, therefore, you could test to see if you are over or
under the maximal value that you set.


>
> Cheers,
>
> Andre
>
>
> def is_array(file,path):
>    data = file.getNode(path)
>    if str(type(data)) == "<class 'tables.array.Array'>":
>        found_array = True
>

Just one quick comment.   You probably shouldn't test the string of the
type of the data.
Use the builtin isinstance() instead:

found_array = isinstance(data, tables.Array)

Be Well
Anthony


>    else:
>        found_array = False
>        for g in file.getNode(path):
>            print g
>    return data, found_array
>
> def pytable_walk(file):
>    found_data = False
>    path = ''
>    while found_data == False:
>        for g in file.getNode('/',path):
>            print g
>        path_new = raw_input('which node would you like?\n     ')
>        path = path+'/'+path_new
>        data,found_data = is_array(file,path)
>    return path,data
>
>
>
>
>
>
>
>
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