Module nlisim.oldmodules.plot

Expand source code 
import attr
import matplotlib.pyplot as plt
import numpy as np

from nlisim.module import ModuleModel, ModuleState
from nlisim.state import State

MAX_ARRAY_LENGTH = 1000


@attr.s(kw_only=True)
class PlotState(ModuleState):
    step_num: int = attr.ib(default=0)
    fungal_burdens: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=int))
    macrophage_counts: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=int))
    neutrophil_counts: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=int))
    time_steps: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=float))


class Plot(ModuleModel):
    name = 'plot'
    StateClass = PlotState

    def advance(self, state: State, previous_time: float):
        step_num = state.plot.step_num

        state.plot.time_steps[step_num] = state.time
        state.plot.fungal_burdens[step_num] = len(state.fungus.cells.alive())
        state.plot.macrophage_counts[step_num] = len(state.macrophage.cells.alive())
        state.plot.neutrophil_counts[step_num] = len(state.neutrophil.cells.alive())
        # define additional values to be plotted here

        state.plot.step_num += 1

        return state

    def finalize(self, state: State):
        num_steps = state.plot.step_num
        time_steps = state.plot.time_steps[:num_steps]
        fungal_burdens = state.plot.fungal_burdens[:num_steps]
        macrophage_counts = state.plot.macrophage_counts[:num_steps]
        neutrophil_counts = state.plot.neutrophil_counts[:num_steps]
        # define additional y_val here

        plt.figure()
        plt.xlabel('Time')
        plt.grid(True)

        for y_val, y_label, title, filename in [
            (fungal_burdens, 'Fungal Burden', 'Fungal Burden vs Time', 'fungal_burden_vs_time'),
            (
                macrophage_counts,
                'Macrophage Count',
                'Macrophage Count vs Time',
                'macrophage_count_vs_time',
            ),
            (
                neutrophil_counts,
                'Neutrophil Count',
                'Neutrophil Count vs Time',
                'neutrophil_count_vs_time',
            ),
            # define additional plots here at 4-tuples
        ]:
            plt.clf()
            plt.plot(time_steps, y_val)
            plt.ylabel(y_label)
            plt.title(title)
            plt.savefig(f'{filename}.png')

        return state

Classes

class Plot (config: SimulationConfig)
Expand source code 
class Plot(ModuleModel):
    name = 'plot'
    StateClass = PlotState

    def advance(self, state: State, previous_time: float):
        step_num = state.plot.step_num

        state.plot.time_steps[step_num] = state.time
        state.plot.fungal_burdens[step_num] = len(state.fungus.cells.alive())
        state.plot.macrophage_counts[step_num] = len(state.macrophage.cells.alive())
        state.plot.neutrophil_counts[step_num] = len(state.neutrophil.cells.alive())
        # define additional values to be plotted here

        state.plot.step_num += 1

        return state

    def finalize(self, state: State):
        num_steps = state.plot.step_num
        time_steps = state.plot.time_steps[:num_steps]
        fungal_burdens = state.plot.fungal_burdens[:num_steps]
        macrophage_counts = state.plot.macrophage_counts[:num_steps]
        neutrophil_counts = state.plot.neutrophil_counts[:num_steps]
        # define additional y_val here

        plt.figure()
        plt.xlabel('Time')
        plt.grid(True)

        for y_val, y_label, title, filename in [
            (fungal_burdens, 'Fungal Burden', 'Fungal Burden vs Time', 'fungal_burden_vs_time'),
            (
                macrophage_counts,
                'Macrophage Count',
                'Macrophage Count vs Time',
                'macrophage_count_vs_time',
            ),
            (
                neutrophil_counts,
                'Neutrophil Count',
                'Neutrophil Count vs Time',
                'neutrophil_count_vs_time',
            ),
            # define additional plots here at 4-tuples
        ]:
            plt.clf()
            plt.plot(time_steps, y_val)
            plt.ylabel(y_label)
            plt.title(title)
            plt.savefig(f'{filename}.png')

        return state

Ancestors

Inherited members

class PlotState (*, global_state: State, step_num: int = 0, fungal_burdens: numpy.ndarray = NOTHING, macrophage_counts: numpy.ndarray = NOTHING, neutrophil_counts: numpy.ndarray = NOTHING, time_steps: numpy.ndarray = NOTHING)

Base type intended to store the state for simulation modules.

This class contains serialization support for basic types (float, int, str, bool) and numpy arrays of those types. Modules containing more complicated state must override the serialization mechanism with custom behavior.

Method generated by attrs for class PlotState.

Expand source code 
class PlotState(ModuleState):
    step_num: int = attr.ib(default=0)
    fungal_burdens: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=int))
    macrophage_counts: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=int))
    neutrophil_counts: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=int))
    time_steps: np.ndarray = attr.ib(factory=lambda: np.zeros(MAX_ARRAY_LENGTH, dtype=float))

Ancestors

Class variables

var fungal_burdens : numpy.ndarray
var macrophage_counts : numpy.ndarray
var neutrophil_counts : numpy.ndarray
var step_num : int
var time_steps : numpy.ndarray

Inherited members