Sample HDF5 experiments

creating.py

import h5py
import numpy as np

# Hack for interactive use with iPython notebook:
try: 
    f.close()
except (NameError, ValueError):
    pass

# Create archive
f = h5py.File('test.hdf5', 'w')

n_times = 20000
n_wavelengths = 2000

# Create a "dataset" which is like a numpy.ndarray
spectra = f.create_dataset('spectra', dtype=np.float64, 
                           shape=(n_times, n_wavelengths)) #, compression="lzf")

# Fill it with data like you would do for a numpy.ndarray
for i in range(n_times):
    spectra[i, :] = np.random.randn(n_wavelengths)
    
# Save associated metadata: 
wavelengths = np.linspace(100, 1000, n_wavelengths)
spectra.attrs['wavelengths'] = wavelengths
    
f.close()

reading.py

import h5py
import numpy as np
import matplotlib.pyplot as plt

# Open the file stream
f = h5py.File('test.hdf5', 'r')

# Get the dataset that you care about
spectra = f['spectra']

# Collect its metadata
wavelengths = spectra.attrs['wavelengths']

# access one spectrum
plt.plot(wavelengths, spectra[4, :])
plt.show()