hdf5 file to pandas dataframe

Question

I downloaded a dataset which is stored in .h5 files. I need to keep only certain columns and to be able to manipulate the data in it.

To do this, I tried to load it in a pandas dataframe. I've tried to use:

pd.read_hdf(path)

But I get: No dataset in HDF5 file.

I've found answers on SO ( read HDF5 file to pandas DataFrame with conditions ) but I don't need conditions, and the answer adds conditions about how the file was written but I'm not the creator of the file so I can't do anything about that.

I've also tried using h5py:

df = h5py.File(path)

But this is not easily manipulable and I can't seem to get the columns out of it (only the names of the columns using df.keys() ) Any idea on how to do this ?

Answer 1

Easiest way to read them into Pandas is to convert into h5py , then np.array , and then into DataFrame . It would look something like:

df = pd.DataFrame(np.array(h5py.File(path)['variable_1']))

Answer 2

Pandas HDF support needs the HDF file to be formated very specifically. You can see https://stackoverflow.com/a/33644128/4128030 for more info.