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