Re: [Pytables-users] Row.append()

[Jim K. <jim...@sp...>]

Speed is the problem.  I am looking for the fastest possible way to do this.  I was thinking of using Pandas and was able to achieve fair performance using that lib.   It just seemed like I was using panada as a middle man it introduces some issues with the data types.  Could it be faster to pull it into a numpy array in chunks and write it out?

From: Anthony Scopatz [mailto:sc...@gm...]
Sent: Friday, May 03, 2013 2:14 PM
To: Discussion list for PyTables
Subject: Re: [Pytables-users] Row.append()

On Fri, May 3, 2013 at 1:15 PM, Jim Knoll <jim...@sp...<mailto:jim...@sp...>> wrote:
I am trying to make this better / faster...
Data comes faster than I can store it on one box.  So My though was to have many boxes each storing their own part in their own table.
Later I would concatenate the tables together with something like this:

dest_h5f = pt.openFile(path + 'big_mater.h5','a')
for source_path in source_h5_path_list:
    h5f = pt.openFile(source_path,'r')
    for node in h5f.root:
        dest_table = dest_h5f.getNode('/', name = node.name<http://node.name>)
        print node.nrows
        if node.nrows > 0 and node.nrows < 1000000:   # found I needed to limit the max size or I would crash
            dest_table.append(node.read())
            dest_table.flush()
    h5f.close()
dest_h5f.close()

I could add the logic to iter in chunks over the source data to overcome the crash and  but I suspect there could be a better way.

Hi Jim,

You can just iterate over each row in the table (ie "for row in node").  This is slow, but would solve the problem.

 Take a table in one h5 file and append it to a table in another h5 file.   Looked like Table.copy() would do the trick but don't see how I get it to append to an existing table.

You could append directly by using the where_append() method with the condition "'True'" to append the whole table.  This will automatically do the chunking for you.

Be Well
Anthony


My h5 files have 4 rec arrays all stored in root.

Any suggestions?

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