Re: [Pytables-users] recursive walk question

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

On Sat, Jun 16, 2012 at 8:50 PM, Andre' Walker-Loud <wal...@gm...>wrote:

> Hi Anthony,
>
> I forgot to say Thanks!
>
> I tried using the _v_depth attr but that didn't give me an answer I
> understood.  for example, the _v_depth of f.root was 0, and the _v_depth of
> my final data path was 2.  But I have something that works now.
>
> also - help like this
>
> > 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)
>
> is very helpful to me.  I have not been properly trained in any
> programming, I have just hacked as needed for work/research, so things like
> this are not yet common for me to realize.
>

No worries, that is what we are here for ;)


>
>
> Cheers,
>
> Andre
>
>
>
>
>
> On Jun 14, 2012, at 3:28 PM, Anthony Scopatz wrote:
>
> > 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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