how to export HDF5 file to NumPy using H5PY?

python numpy hdf5 h5py
l.z.lz picture l.z.lz · Apr 23, 2012 · Viewed 20.4k times · Source

I have an existing hdf5 file with three arrays, i want to extract one of the arrays using h5py.

Answer

Danica picture Danica · Apr 23, 2012

h5py already reads files in as numpy arrays, so just:

with h5py.File('the_filename', 'r') as f:
    my_array = f['array_name'][()]

The [()] means to read the entire array in; if you don't do that, it doesn't read the whole data but instead gives you lazy access to sub-parts (very useful when the array is huge but you only need a small part of it).

Related questions

Read HDF5 file into numpy array

I have the following code to read a hdf5 file as a numpy array: hf = h5py.File('path/to/file', 'r') n1 = hf.get('dataset_name') n2 = np.array(n1) and when I print n2 I get this: Out[15]: …

Read More
HDF5 file created with h5py can't be opened by h5py

I created an HDF5 file apparently without any problems, under Ubuntu 12.04 (32bit version), using Anaconda as Python distribution and writing in ipython notebooks. The underlying data are all numpy arrays. For example, import numpy as np import h5py f = …

Read More
How to append data to one specific dataset in a hdf5 file with h5py

I am looking for a possibility to append data to an existing dataset inside a .h5 file using Python (h5py). A short intro to my project: I try to train a CNN using medical image data. Because of the …

Read More