Source code for cytocalc.csmsimulation

#! /usr/bin/env python3
# A CSMSimulation is a collection of CSMFrames and the
# simulation parameters (read from configurations.cym)

import warnings
from bisect import insort
from typing import List

import numpy as np

from cytocalc.sim_analysis.msd import SimAnalyzerMSD
from cytocalc.sim_analysis.misc import SimAnalyzerMisc
from cytocalc.sim_analysis.network import SimAnalyzerNetwork



[docs]
class CSMSimulation:
    """
    Contains a set of CSMFrames that form a simulation.
    Also contains the simulation parameters.
    """

    def __init__(self):
        self.frames = []  # list containing cytosim frames
        self.params = {}  # dict containing simulation
        self.msd = SimAnalyzerMSD(self)
        self.network = SimAnalyzerNetwork(self)
        self.misc = SimAnalyzerMisc(self)


[docs]
    def add_frame(self, csmframe):
        """Adds a CSMFrame to the simulation
        at the correct time (frame1.time < frame2.time)"""
        insort(self.frames, csmframe, key=lambda x: x.time)



[docs]
    def get_np_object(self, start_frame="0", end_frame=None):
        """Constructs a numpy object from csm frame data
        of shape (n_frames,n_particles,3)"""
        np_frames = [frame._npobj for frame in self.frames[start_frame:end_frame]]
        return np.stack(np_frames)



[docs]
    def contraction_rate(self, start_frame=None, end_frame=None, r_sq=0.9):
        """
        Deprecated. Use sim.network.contraction_rate() instead. Ref: :func:`cytocalc.sim_analysis.SimAnalyzerNetwork.contraction_rate`
        """
        warnings.warn("Deprecated. Use sim.network.contraction_rate() instead", DeprecationWarning)
        return self.network.contraction_rate(start_frame, end_frame, r_sq)



[docs]
    def compute_msd(self, start_frame: int = 0, end_frame: int = -1, box_size: List[float] = []):
        """
        Deprecated. Use sim.msd.msd() instead. Ref: :func:`cytocalc.sim_analysis.SimAnalyzerMSD.msd`
        """
        warnings.warn("Deprecated. Use sim.msd.msd() instead", DeprecationWarning)
        return self.msd.msd(start_frame = start_frame,
                                        end_frame   = end_frame,
                                        box_size    = box_size,
                                        mode        = 'direct')



[docs]
    def compute_time_avg_msd(
        self, start_frame: int = 0, end_frame: int = -1, box_size: List[float] = []
    ):
        """
        Deprecated. Use sim.msd.msd() instead. Ref: :func:`cytocalc.sim_analysis.SimAnalyzerMSD.msd`
        """
        warnings.warn("Deprecated. Use sim.msd.msd() instead", DeprecationWarning)
        return self.msd.msd(start_frame = start_frame,
                                        end_frame   = end_frame,
                                        box_size    = box_size,
                                        mode        = 'window')



[docs]
    def bound_couple_vs_time(self, start_frame: int = 0, end_frame: int = -1):
        """
        Deprecated. Use sim.misc.bound_couple_vs_time() instead. Ref: :func:`cytocalc.sim_analysis.SimAnalyzerMisc.bound_couple_vs_time`
        """
        warnings.warn("Deprecated. Use sim.misc.bound_couple_vs_time() instead", DeprecationWarning)
        return self.misc.bound_couple_vs_time(start_frame, end_frame)