H2MMbursts

Project Description

Extension of smfBursts for working with H²MM. H2MMbursts provides the StatePath and Dwell tables which represent the results of Viterbi processing burst data, finding the most likely state of each photon for a given H²MM model.

Install

Install with

pip install H2MMbursts

Features

Viterbi based classes

H2MMbursts adds a new Table classes for using H²MM with smfBursts The two primary table types are StatePath and Dwells.

StatePath records (per burst) the state of each photon (it is a ChildPhotonTable). Use the StatePath.optimize_models() classmethod to perform H²MM optimizations on a given set of data, this will create a set of StatePath based on the optimized models of increasing numbers of states.

While Dwells is a BasePhotonTable that separates bursts into dwells of consecutive photons of the same state, allowing the user to treat these dwells like bursts.

Error analysis

The function bhm.error.statepath_ll_error() is used to assess the error of each parameter for a given H²MM model based on the data.

Simulations

The bhm.sim.H2MMSim table also allows a Monte-Carlo recoloring of photons in data, which can be used to compare the predicted results of a model vs the actual.