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.
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 <walksl...@gmail.com>
> 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 <walksl...@gmail.com>
> > 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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