Source code for sbmlsim.examples.experiments.covid.experiments.carcione2020

from pathlib import Path
from typing import Dict

from sbmlsim.experiment import SimulationExperiment
from sbmlsim.model import AbstractModel
from sbmlsim.plot import Axis, Figure
from sbmlsim.simulation import Timecourse, TimecourseSim
from sbmlsim.task import Task


class Carcione2020(SimulationExperiment):
    def models(self) -> Dict[str, AbstractModel]:
        Q_ = self.Q_
        models = {
            "model": AbstractModel(
                source=Path(__file__).parent
                / ".."
                / "models"
                / "Carcione2020"
                / "Carcione2020.xml",
                language_type=AbstractModel.LanguageType.SBML,
                changes={},
            )
        }
        return models

    def tasks(self) -> Dict[str, Task]:
        tasks = {}
        if self.simulations():
            tasks = {
                f"task_{key}": Task(model="model", simulation=key)
                for key in self.simulations()
            }
        return tasks

    def simulations(self) -> Dict[str, TimecourseSim]:
        Q_ = self.Q_

        tcsims = {}
        tcsims["sim1"] = TimecourseSim(
            [
                Timecourse(
                    start=0,
                    end=80,
                    steps=8001,
                    changes={},
                )
            ]
        )
        return tcsims

    def figures(self) -> Dict[str, Figure]:
        return {**self.figure_plot_1()}

    def figure_plot_1(self):
        unit_time = "time"
        unit_y = "substance"

        selections = ["Susceptible", "Exposed", "Infected", "Recovered"]
        self.add_selections_data(["time"] + selections)

        fig_1 = Figure(self, sid="plot_1", name=f"{self.sid} (plot_1)", num_rows=1)
        plots = fig_1.create_plots(Axis("time", unit=unit_time), legend=True)
        plots[0].set_yaxis("y", unit_y)

        # simulation
        colors = ["black", "blue", "red", "green"]
        for k, skey in enumerate(selections):
            plots[0].add_data(
                task="task_sim1",
                xid="time",
                yid=skey,
                label=skey,
                color=colors[k],
                linewidth=2,
            )
        # plots[1].add_data(
        #     task="task_sim1",
        #     xid="time",
        #     yid="Deceased",
        #     label="Deceased",
        #     color="black",
        #     linewidth=2,
        # )

        return {"plot_1": fig_1}