Function tttr_toolbox::tttr_tools::g2::g2[−][src]

pub fn g2(f: &File, params: &G2Params, mode: G2Mode) -> Result<G2Result, Error>
Expand description

Computes the second order autocorrelation (g2) between two channels on a TCSPC module.

Parameters

The parameters to the algorithm are passed via a G2Params struct that contains the following:

  • channel_1: The number of the first input channel into the TCSPC,
  • channel_2: The number of the second input channel into the TCSPC,
  • correlation_window: Length of the correlation window of interest in seconds,
  • resolution: Resolution of the g2 histogram in seconds,

Algorithm description

The streaming g2 algorithm measures the time difference between a photon arriving at a channel and all the photons that came before it and arrived at the other channel. A histogram of time differences is then built and is the output we are after.

Computational constraints force us to define beforehand the maximum and minimum time differences, the correlation window, that can fit into the histogram. Having a finite value for the time difference we can store implies that we don’t need to measure every single photon arriving at channel A against every previous photon on channel B. Instead, only a finite number of clicks into the past need to be considered.

Past clicks on each channel are pushed into circular buffers that keep the last N photons that arrived at each of them. A circular buffer allows to always have time ordered arrival times if we look from the head position of the buffer backwards. second order click orderings

Mode

The mode determines what version of the g2 algorithm will be used. The symmetric version computes relative delays between channels 1 and 2 and between channels 2 and 1. This makes it possible to access both negative and positive time delays on the g2 historgram. The asymmetric mode only provides positive delays in exchange for a slight performance boost. If you are unsure of what to use go for G2Mode::Symmetric.

Finite buffer artifacts

Not being capable to look back to all photons that came before can be a potential source of artifacts on the calculated g2 histograms. At it’s most extreme if N=1 we only look into the immediately previous photon. This introduces an exponential decay artifact on the g2.

The maximum size of the correlation window that is artifact free is dependent on the click rate. A quick estimate can be obtained by multiplying the inverse of the click rate times the size of the buffer. E.g. for a buffer of 4096 photons and a click rate of 10e6 Hz we get an artifcat free window of 0.4 milliseconds. Taking into consideration typical emitter lifetimes and collection optics efficiency this should be more than enough to capture any relevant dynamics. If this is not the case for you will need to modify the hard coded maximum buffer size defined on src/tttr_tools/g2.rs.