cytocalc.csmsimulation module¶

class cytocalc.csmsimulation.CSMSimulation[source]¶

Bases: object

Contains a set of CSMFrames that form a simulation. Also contains the simulation parameters.

add_frame(csmframe)[source]¶: Adds a CSMFrame to the simulation at the correct time (frame1.time < frame2.time)

bound_couple_vs_time(start_frame: int = 0, end_frame: int = -1)[source]¶: Deprecated. Use sim.misc.bound_couple_vs_time() instead. Ref: cytocalc.sim_analysis.SimAnalyzerMisc.bound_couple_vs_time()

compute_msd(start_frame: int = 0, end_frame: int = -1, box_size: List[float] = [])[source]¶: Deprecated. Use sim.msd.msd() instead. Ref: cytocalc.sim_analysis.SimAnalyzerMSD.msd()

compute_time_avg_msd(start_frame: int = 0, end_frame: int = -1, box_size: List[float] = [])[source]¶: Deprecated. Use sim.msd.msd() instead. Ref: cytocalc.sim_analysis.SimAnalyzerMSD.msd()

contraction_rate(start_frame=None, end_frame=None, r_sq=0.9)[source]¶: Deprecated. Use sim.network.contraction_rate() instead. Ref: cytocalc.sim_analysis.SimAnalyzerNetwork.contraction_rate()

get_np_object(start_frame='0', end_frame=None)[source]¶: Constructs a numpy object from csm frame data of shape (n_frames,n_particles,3)