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Condensate movement

Module: condensate_movement.py#

Overview#

The condensate_movement module contains classes and functions for simulating and managing the movement and properties of condensates. Condensates are defined as spherical entities characterized by their center coordinates (x, y, z), radius (r), and time (t). This module provides functionalities to create, manipulate, and analyze condensates within a simulation environment.

Classes#

Condensate#

Description#

The Condensate class is used to store and manage data related to condensates. Each condensate is defined by its initial position, time, diffusion coefficient, Hurst exponent, and other relevant parameters.

Parameters#

  • initial_position: np.ndarray
    The initial position of the condensate. Default is np.array([0, 0, 0]).

  • initial_time: float
    The initial time of the condensate. Default is 0.

  • diffusion_coefficient: float
    The diffusion coefficient of the condensate. Default is 0.

  • hurst_exponent: float
    The Hurst exponent of the condensate. Default is 0.

  • units_time: str
    The units of time. Default is 's'. The time units work as follows:

  • For 'ms', 1 unit represents 1 millisecond.
  • For 's', 1 unit represents 1 second.

  • For '20ms', 1 unit represents 20 milliseconds.

  • units_position: str
    The units of position. Default is 'um'.

  • condensate_id: int
    The ID of the condensate. Default is 0.

  • initial_scale: float
    The initial scale of the condensate. Default is 0.

Usage#
condensate = Condensate(**{
    "initial_position": np.array([0, 0, 0]),
    "initial_time": 0,
    "diffusion_coefficient": 0,
    "hurst_exponent": 0,
    "units_time": 'ms',
    "units_position": 'um',
    "condensate_id": 0,
    "initial_scale": 0,
})

Functions#

create_condensate_dict#

Description#

Creates a dictionary of condensates for simulation. Each condensate is initialized with specific parameters such as initial centers, scales, diffusion coefficients, and Hurst exponents.

Parameters#

  • initial_centers: np.ndarray
    An array of shape (num_condensates, 2) representing the initial centers of the condensates.

  • initial_scale: np.ndarray
    An array of shape (num_condensates, 2) representing the initial scales of the condensates.

  • diffusion_coefficient: np.ndarray
    An array of shape (num_condensates, 2) representing the diffusion coefficients of the condensates.

  • hurst_exponent: np.ndarray
    An array of shape (num_condensates, 2) representing the Hurst exponents of the condensates.

  • cell: RectangularCell
    The rectangular cell that contains the condensates.

  • kwargs: dict
    Additional arguments passed to the Condensate class.

Returns#
  • dict: A dictionary of Condensate objects with keys as condensate IDs.
Usage#
condensates = create_condensate_dict(
    initial_centers=np.array([[0, 0], [1, 1]]),
    initial_scale=np.array([1, 2]),
    diffusion_coefficient=np.array([0.1, 0.2]),
    hurst_exponent=np.array([0.5, 0.6]),
    cell=RectangularCell(),
)

_generate_transition_tracks#

Description#

Generates tracks with state transitions for condensates. This function is used to simulate the movement of condensates under varying conditions defined by transition matrices and state probabilities.

Parameters#

  • track_generator: Track_generator
    An instance of the track generator.

  • track_lengths: list | np.ndarray | int
    The lengths of the tracks to be generated.

  • initial_positions: np.ndarray
    The initial positions of the condensates.

  • starting_frames: int
    The starting frames for the tracks.

  • diffusion_parameters: np.ndarray
    The diffusion parameters for the condensates.

  • hurst_parameters: np.ndarray
    The Hurst parameters for the condensates.

  • diffusion_transition_matrix: np.ndarray
    The transition matrix for diffusion states.

  • hurst_transition_matrix: np.ndarray
    The transition matrix for Hurst states.

  • diffusion_state_probability: np.ndarray
    The state probability for diffusion.

  • hurst_state_probability: np.ndarray
    The state probability for Hurst.

Returns#
  • tuple[dict, dict]: A tuple containing the tracks dictionary and points per time dictionary.

_convert_tracks_to_trajectory#

Description#

Converts the generated tracks into a trajectory format.

Parameters#
  • tracks: dict
    The dictionary of tracks to be converted.
Returns#
  • dict: The converted trajectory data.

Dependencies#

  • matplotlib.pyplot
  • numpy
  • RectangularCell from ..cells.rectangular_cell
  • cache from ..utils.decorators
  • Track_generator from track_gen

Usage Example#

import numpy as np
from ..cells.rectangular_cell import RectangularCell
from .condensate_movement import create_condensate_dict, Condensate

# Initialize a rectangular cell
cell = RectangularCell()

# Create condensates
condensates = create_condensate_dict(
    initial_centers=np.array([[0, 0], [1, 1]]),
    initial_scale=np.array([1, 2]),
    diffusion_coefficient=np.array([0.1, 0.2]),
    hurst_exponent=np.array([0.5, 0.6]),
    cell=cell,
)

# Access a condensate
condensate = condensates['0']

# Get position and scale at a given time
result = condensate(times=10, time_unit='ms')
print(result)

This documentation provides a comprehensive overview of the condensate_movement module, detailing its classes, functions, and dependencies. The provided example demonstrates how to initialize and use the Condensate class and related functions for simulating condensate movements.