Source code for cytocalc.csmframe

#! /usr/bin/env python3

import warnings
from cytocalc.frame_analysis.network import FrameAnalyzerNetwork




class CSMFrame:
    """
    Class representing a single frame of a simulation.
    The data extracted from a frame file is stored in
    frame.data as a pandas object.
    """

    def __init__(self, pandas_obj, **kwargs):
        self.data = pandas_obj
        self._npobj = self._get_pos_nparray()
        self.time = None  # time after simulation started
        self.network = FrameAnalyzerNetwork(self)



    def _get_pos_nparray(self):
        """
        obtains 3D position frome parsed
        data. If simulation is 2D or 1D
        other dimensions are set to 0
        """
        obj = self.data
        if "posX" not in obj.columns:
            return None
        if "posY" not in obj.columns:
            obj["posY"] = 0
        if "posZ" not in obj.columns:
            obj["posZ"] = 0
        return obj[["posX", "posY", "posZ"]].to_numpy(dtype=float)




    def compute_com(self):
        """returns centre of mass of all filaments together (uniform mass)"""
        warnings.warn("Deprecated. Use FrameAnalyzerNetwork(frame).center_of_mass() instead", DeprecationWarning)
        return self.network.center_of_mass()




    def compute_radius(self):
        """returns a measure of "network radius" of filaments (see appendix of Belmonte et al. Mol Syst Biol. 2017 Sep 27;13(9):941. doi: 10.15252/msb.20177796 in https://pmc.ncbi.nlm.nih.gov/articles/instance/5615920/bin/MSB-13-941-s001.pdf)"""
        warnings.warn("Deprecated. Use FrameAnalyzerNetwork(frame).radius() instead", DeprecationWarning)
        return self.network.radius()