["python","hdf5"]
How to read HDF5 files in Python

I am trying to read data from hdf5 file in Python. I can read the hdf5 file using h5py, but I cannot figure out how to access data within the file. My code import h5py import numpy as np f1 = h5py.File(file_name,'r+') This works and the file is read. But how can I access data inside the file object f1?
Read HDF5 import h5py filename = "file.hdf5" with h5py.File(filename, "r") as f: # Print all root level object names (aka keys) # these can be group or dataset names print("Keys: %s" % f.keys()) # get first object name/key; may or may NOT be a group a_group_key = list(f.keys())[0] # get the object type for a_group_key: usually group or dataset print(type(f[a_group_key])) # If a_group_key is a group name, # this gets the object names in the group and returns as a list data = list(f[a_group_key]) # If a_group_key is a dataset name, # this gets the dataset values and returns as a list data = list(f[a_group_key]) # preferred methods to get dataset values: ds_obj = f[a_group_key] # returns as a h5py dataset object ds_arr = f[a_group_key][()] # returns as a numpy array Write HDF5 import h5py # Create random data import numpy as np data_matrix = np.random.uniform(-1, 1, size=(10, 3)) # Write data to HDF5 with h5py.File("file.hdf5", "w") as data_file: data_file.create_dataset("dataset_name", data=data_matrix) See h5py docs for more information. Alternatives JSON: Nice for writing human-readable data; VERY commonly used (read & write) CSV: Super simple format (read & write) pickle: A Python serialization format (read & write) MessagePack (Python package): More compact representation (read & write) HDF5 (Python package): Nice for matrices (read & write) XML: exists too *sigh* (read & write) For your application, the following might be important: Support by other programming languages Reading / writing performance Compactness (file size) See also: Comparison of data serialization formats In case you are rather looking for a way to make configuration files, you might want to read my short article Configuration files in Python