"""
This module will collect tools for reading, writing and testing structured
HDF5_ files.
HDF5 Format Specification
-------------------------
Here is a sample of the HDF5 file format.
::
/
attributes: {'date': '2014-07-22',
'time': '13:00:00',
'hdf5_version': 'v0.1', # Version of the format specification
'source': 'PSB-B19-AFM',
'help': 'What is this data?'
'extra_dimensions': 'x2'
'comment': 'This is an example HDF5 file with multiple dimensions, and several averages for each data point.'}
x
attributes: {'name': 'Frequency',
'unit': 'Hz',
'label': 'f [Hz]'
'label_latex': r'$f \\: [\\mathrm{Hz}]$',
'initial': 0.0,
'step': 0.5,
'help': 'Frequency array for PSD.'}
[0, 0.5, 1.0, 1.5]
x2
attributes: {'name': 'Laser Power',
'unit': 'mW',
'label': 'P [mW]',
'label_latex': r'$P \\: [\\mathrm{mW}]$',
'help': 'Interferometer Output Laser Power'
}
[2.0]
y/
attributes: {'name': 'Power Spectral Density of position fluctuations',
'unit': 'nm^2/Hz',
'label': 'PSD [nm^2 / Hz]',
'label_latex': r'$P_{\\delta x} \: [\\mathrm{nm}^2 / \\mathrm{Hz}]',
'n_avg': 4, # If n_avg is not equal to one, there should be a dataset y_std containing standard deviations
'help': 'Power spectral density of position fluctuations.'}
[1, 2.1, 2.9, 4]
y_std/
[0.2, 0.3, 0.4, 0.5]
workup/
FFT
[1, 2, 3]
FTTunit
'nm'
Note: If ``x`` is an empty array, we can determine the array from
the initial and step attributes.
Note: If ``y['n_avg'] == 1``, then ``y`` is a dataset rather than a group,
with ``y`` data stored directly, as shown below.
::
y
attributes: {'name': 'PSD_{\delta x}'
'n_avg': 1,
'unit': 'nm^2/Hz',
'help': 'Power spectral density of position fluctuations.'}
[1, 2.1, 2.9, 4]
After the data has been processed, you can output any fitting or workup
parameters to a group called ``workup``.
.. _HDF5: http://www.hdfgroup.org/HDF5/
"""
[docs]def update_attrs(h5_attrs, attrs):
"""Update the attributes in ``h5_attrs``, an ``h5py`` group or dataset,
by adding attributes in the dictionary attrs.
This will overwrite existing attributes.
"""
for key, val in attrs.items():
h5_attrs[key] = val