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 with
pip install H2MMburstsH2MMbursts 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.
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.
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.