Create hdf5 file

gistfile1.txt

import h5py
import numpy as np

eeg1 = np.arange(500000)
raw1 = np.arange(500000)
eeg2 = np.arange(500000)
raw2 = np.arange(500000)
hypnogram = np.random.randint(0, 5, size=500)
ecg = np.arange(15368)
cool_tensor = np.arange(24).reshape((2, 3, 4))


# Create h5 file
with h5py.File("h5_test.h5", "w") as f:
    # Root
    f["/"].attrs["start_time"] = "8h35"
    f["/"].attrs["type"] = 2
    f["/"].attrs["hey"] = "yo"
    f["/"].attrs["device"] = "dreem"

    # EEG
    group_eeg = f.create_group("eeg")
    group_eeg.attrs["fs"] = 250

    group_channel1 = group_eeg.create_group("/eeg/channel1")
    group_channel1.attrs["location"] = "Fp1"
    group_channel1.create_dataset("raw", data=raw1, compression="gzip")
    dataset = group_channel1.create_dataset("filtered", data=eeg1, compression="gzip")
    dataset.attrs['filter_HP'] = 20

    group_channel2 = group_eeg.create_group("/eeg/channel2")
    group_channel2.attrs["location"] = "Fp2"
    group_channel2.create_dataset("raw", data=raw2, compression="gzip")
    dataset = group_channel2.create_dataset("filtered", data=eeg2, compression="gzip")
    dataset.attrs['filter_HP'] = 20

    # ECG
    group_ecg = f.create_group("ecg")
    group_ecg.attrs["subsampling"] = 3
    group_ecg.create_dataset("ecg", data=ecg, compression="gzip")

    # hypnogram
    dataset = f.create_dataset("hypnogram", data=hypnogram)
    dataset.attrs["start_time"] = "8h85"
    dataset.attrs["scorer"] = "Philip J. fry"

    # cool_matrix
    f.create_dataset("tensor", data=cool_tensor)


# Read h5 file
f = h5py.File("h5_test.h5", "r")

f["/eeg/channel1/filtered"][:16]

f["/hypnogram"][-10:]

f["/tensor"][-1:, 2, 1]


""" Note on chunked storage

>>> dset = f.create_dataset("chunked", (1000, 1000), chunks=(100, 50))

the data in dset[0:100,0:50] will be stored together in the file,
as will the data points in range dset[400:500, 100:150].
"""

""" Note on Modification

Once some data is written int a h5file it should not be modified.

New data can be added to a h5 file (e.g. new group, new dataset etc.)

New data can be APPENDED to a dataset on any axis ONLY IF
max_shape has been set to None on that axis.
One should do a reshape before appending any data on any axis.
http://docs.h5py.org/en/latest/high/dataset.html#resizable-datasets

>>> dset = f.create_dataset("unlimited", (10, 10), maxshape=(None, 10))
dset[0:10, 0:10] = np.ones((10, 10))
dset.resize((40, 10))
dset[10:40, 0:10] = np.ones((30, 10))

"""

HDFView to browse through a h5file