Photon selections

In this module we define the class Ph_sel used to specify a “selection” of a sub-set of photons/timestamps (i.e. all-photons, Donor-excitation-period photons, etc...).

A photon selection is one of the base photon streams or a combination of them. Base photon streams are photon from the donor (or acceptor) emission channel detected during the donor (or acceptor) excitation period. For non-ALEX data there is only the donor excitation period.

The following table shows base photon streams for smFRET data (non-ALEX):

Photon selection Syntax
D-emission Ph_sel(Dex='Dem')
A-emission Ph_sel(Dex='Aem')

and for ALEX data:

Photon selection Syntax
D-emission during D-excitation Ph_sel(Dex='Dem')
A-emission during D-excitation Ph_sel(Dex='Aem')
D-emission during A-excitation Ph_sel(Aex='Dem')
A-emission during A-excitation Ph_sel(Aex='Aem')

Additionally, all the photons can be selected with Ph_sel('all') (that is a shortcut for Ph_sel(Dex='DAem', Aex='DAem').


  • Ph_sel(Dex='DAem', Aex='DAem') or Ph_sel('all') select all photons.
  • Ph_sel(Dex='DAem') selects only donor and acceptor photons emitted during donor excitation. These are all the photons for non-ALEX data.
  • Ph_sel(Dex='Aem', Aex='Aem') selects all the photons detected from the acceptor-emission channel.

The documentation for the Ph_sel class follows.

class fretbursts.ph_sel.Ph_sel

Class that describes a selection of photons.

This class takes two arguments Dex and Aex. Valid values for the arguments are the strings ‘DAem’, ‘Dem’, ‘Aem’ or None. These values select, respectively, donor+acceptor, donor-only, acceptor-only or no photons during an excitation period (Dex or Aex).

The class must be called with at least one keyword argument or using the string ‘all’ as the only argument. Calling Ph_sel('all') is equivalent to Ph_sel(Dex='DAem', Aex='DAem'). Not specifying a keyword argument is equivalent to setting it to None.