Writing Photon-HDF5 files in python

This notebook shows how to create a Photon-HDF5 file from scratch using dummy data and phconvert.

For more info see Writing Photon-HDF5 files.

In [ ]:
import phconvert as phc

1. Create some dummy data

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import numpy as np
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timestamps = np.random.randint(low=0, high=2e8, size=10000).astype('int64')
timestamps_unit = 10e-9  # 10 ns, units are always S.I.
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detectors = np.random.randint(low=0, high=1, size=10000).astype('uint8')

2. Create some metadata

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description = 'This is a fake dataset which mimics smFRET data.'

author = 'Author Name'
author_affiliation = 'Name of Research Institution'

sample_name = 'describe the sample here'
buffer_name = 'describe the buffer here'
dye_names = 'Cy3B, ATTO647N'   # Comma separates names of fluorophores

3. Create Photon-HDF5 data structure

In this section we create all the mandatory and non mandatory groups. Not all of the are required to save a valid Photon-HDF5 file (see example in section 4).

3.1 photon_data group

Contains arrays of photon-data: timestamps, detectors, nanotimes, etc...

See photon_data group reference

In [ ]:
photon_data = dict(
    timestamps_specs={'timestamps_unit': timestamps_unit})

3.2 setup group

The /setup group contains information about the measurement setup.

See setup group reference.

In [ ]:
setup = dict(
    ## Mandatory fields
    num_pixels = 2,                   # using 2 detectors
    num_spots = 1,                    # a single confoca excitation
    num_spectral_ch = 2,              # donor and acceptor detection 
    num_polarization_ch = 1,          # no polarization selection 
    num_split_ch = 1,                 # no beam splitter
    modulated_excitation = False,     # CW excitation, no modulation 
    excitation_alternated = [False],  # CW excitation, no modulation 
    lifetime = False,                 # no TCSPC in detection
    ## Optional fields
    excitation_wavelengths = [532e-9],         # List of excitation wavelenghts
    excitation_cw = [True],                    # List of booleans, True if wavelength is CW
    detection_wavelengths = [580e-9, 640e-9],  # Nominal center wavelength 
                                               # each for detection ch

3.3 provenance group

Non-mandatory group containing info about the original file prior to Photon-HDF5 conversion. If some information is not available the relative field may be omitted.

See provenance group documentation.

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provenance = dict(
    software='Acquisition Software Name')

3.4 identity group

Non-mandatory group containing info about information this specific Photon-HDF5 file.

See identity group documentation.

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identity = dict(

3.5 measurement_specs group

The optional /photon_data/measurement_specs group contains additional information allowing unambiguous interpretation of the data for each specific type of measurement.

See measurement_specs group documentation.

In [ ]:
measurement_specs = dict(
    measurement_type = 'smFRET',
    detectors_specs = {'spectral_ch1': [0],  # list of donor's detector IDs
                       'spectral_ch2': [1]}  # list of acceptor's detector IDs

4. Save Photon-HDF5 files

To save a file we need to join together the root fields and group in a single dictionary. Here we provide a few examples.

4.1 Minimal file

Create a bare-bone Photon-HDF5 file with only mandatory fields.

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data = dict(
    photon_data = photon_data,
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phc.hdf5.save_photon_hdf5(data, h5_fname='dummy_dataset_barebone.h5', overwrite=True)

NOTE: a user of this file can read the data but does not know what kind of measurement it is (e.g. smFRET with single laser excitation and 2-colors detection).

4.2 Expanded Photon-HDF5

Create a Photon-HDF5 with non-mandatory fields (including measurement_specs):

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photon_data['measurement_specs'] = measurement_specs

data = dict(
    photon_data = photon_data,
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phc.hdf5.save_photon_hdf5(data, h5_fname='dummy_dataset_complete.h5', overwrite=True)

NOTE: a user of this file can correctly interpret the data reading that the measurement type is 'smFRET' (meaning smFRET with single laser excitation and 2-colors detection) and the IDs of donor and acceptor detectors (from detectors_specs/spectral_ch1 and spectral_ch2 respectively).