ALEX alternation period definitions

[tritemio]

I found an inconsistency in the definition of the alternation period range in the ALEX histograms for donor and acceptor.

Currently (v0.3), these ranges are named:

alex_period_spectral_ch1 alex_period_spectral_ch2

By spectral_ch1/2 in the format we indicate the detection channels (resp. donor and acceptor). The previous naming is inconsistent (logically wrong!) because each of these periods refer to one excitation laser, not to one detection channel.

These names are present in both us-ALEX and ns-ALEX measurement types.

Let's discuss if we need to change them (probably yes) and which new names we should use.

[tritemio]

Proposal 1

alex_period alex_period_excitation1 alex_period_excitation2

Proposal 2

alex_period alex_period_range_excitation1 alex_period_range_excitation2

[tritemio]

FYI, the original documentation (0.3) is:

• http://photon-hdf5.readthedocs.org/en/version0.3/phdata.html#measurement-specs

and the new "tentative" docs using Proposal 1 can be found here:

• http://photon-hdf5.readthedocs.org/en/latest/phdata.html#measurement-specs

The changes in the document (the diff) can bee read here.

[tritemio]

Proposal 3

alex_period alex_excitation_range1 alex_excitation_range2

Proposal 4

alex_period alex_excitation1 alex_excitation2

[smXplorer]

I am glad to see that we agree that the only thing we can define for a photon is the excitation period it falls in (at least in ns ALEX; this is less of an issue for us ALEX and dyes with ns lifetime. But just think for a second of emitters with tens or hundreds of us lifetimes...) alex_excitation_period1, etc would seem to me a logical name.

Also note that the custom name for the inverse of a laser period is laser repetition rate, not laser pulse rate.

[tritemio]

Proposal 5

alex_period alex_excitation_period1 alex_excitation_period2

[tritemio]

@smXplorer, are you proposing to rename laser_pulse_rate to laser_repetition_rate? Both of them are unambiguous for me.

[smXplorer]

yes. it is just that usage favors laser repetition rate.

[tritemio]

I think the best options are Proposals 1 and 5.

In general I tend to prefer a name that goes from general to particular (like in programming languages) compared to "english language" order. It seems to me more logical.

So, I vote Proposal 1. @smXplorer votes proposal 5. @talaurence which one do you prefer?

[talaurence]

I vote Proposal 1 as well. It looks strange on first glance, but when you read the documentation it makes more sense than Proposal 5.... at least to me.

[tritemio]

@talaurence ok thanks, in case you wonder, right now phconvert 0.5 uses proposal 1, while phconvert 0.5.1 uses proposal 5.

@smXplorer, do you want to have a final word?

Regarding laser_pulse_rate vs laser_repetition_rate I'm absolutely ok with both, so since @smXplorer prefere the second I'll change it this way.

[talaurence]

It is actually OK either way - if @smXplorer likes it better, we don't have to go back to proposal 1

[smXplorer]

I am fine with option 1.

[tritemio]

Ok, it turns out to be equivalent so I stick to the latest implementation in phconvert 0.5.1 that is

alex_excitation_period1 alex_excitation_period2 laser_repetition_rate

I'll close the issue shortly, once I finish to update the docs.