API

saspt is an object-oriented Python 3 library. The classes perform discrete roles:

• TrajectoryGroup represents a set of trajectories to be analyzed by state arrays

• Likelihood represents a likelihood function, or physical model for the type of motion. Some examples of likelihood functions include Brownian motion with localization error (RBME), various approximations of RBME, and fractional Brownian motion (FBM). The Likelihood class also defines the grid of state parameters on which the state array is constructed.

• StateArrayParameters is a struct with the settings for state array inference, including the pixel size, frame rate, and other imaging parameters.

• StateArray implements the actual state array inference routines.

• StateArrayDataset parallelizes state arrays across multiple target files, and provides some tools and visualizations for comparing between experimental conditions.

• Note on input format
• TrajectoryGroup
  • TrajectoryGroup
• Likelihood
  • Likelihood
  • RBMELikelihood
  • RBMEMarginalLikelihood
  • GammaLikelihood
  • FBMELikelihood
• StateArrayParameters
  • StateArrayParameters
• StateArray
  • StateArray
• StateArrayDataset
  • StateArrayDataset
• File reading
  • saspt.io.is_detections()
  • saspt.io.load_detections_from_file()
  • saspt.load_detections()
  • saspt.io.empty_detections()
  • saspt.io.sample_detections()
  • saspt.io.concat_detections()
• Utilities
  • saspt.utils.track_length()
  • saspt.utils.assign_index_in_track()
  • saspt.utils.cartesian_product()