Source code for cytocalc.csmframe

#! /usr/bin/env python3

import numpy as np
import pandas as pd



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




    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) """
        if self._npobj is None or len(self._npobj) == 0:
            raise ValueError("Cannot compute center of mass: no position data available")
        return np.mean(self._npobj, axis=0)




    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)"""
        if self._npobj is None or len(self._npobj) == 0:
            raise ValueError("Cannot compute radius: no position data available")
        # get position vectors of all points
        radial_vectors = self._npobj - self.compute_com()
        radial_dist = np.linalg.norm(radial_vectors, axis=1)
        radius = np.sqrt(2*np.mean(radial_dist**2))
        return radius