Source code for tyssue.behaviors.monolayer.apoptosis_events

import logging

from ...topology.bulk_topology import HI_transition, IH_transition
from .actions import contract, shrink

logger = logging.getLogger(__name__)


default_apoptosis_spec = {
    "cell_id": -1,
    "contract_rate": 2.0,
    "critical_area": 1e-2,
    "shrink_rate": 0.4,
    "critical_volume": 0.1,
}


def apoptosis(monolayer, manager, **kwargs):
    """Apoptotic behavior

    Parameters
    ----------
    monolayer : a :cass:`Monolayer` object
    manager : a :class:`EventManager` object

    Optional Parameters
    -------------------
    cell_id : int
       id of the apoptotic cell
    contract_rate : float, default 2.
    critical_area : float, default 1e-2,
    shrink_rate : float, default 0.4,
    critical_volume : float, default 0.1,
    """
    apoptosis_spec = default_apoptosis_spec
    apoptosis_spec.update(**kwargs)

    cell = apoptosis_spec["cell_id"]
    if cell == -1:
        return
    done = False

    cell_to_face = monolayer.get_orbits("cell", "face")
    try:
        apical_face = monolayer.face_df[
            (monolayer.face_df.index.isin(cell_to_face[cell]))
            & (monolayer.face_df.segment == "apical")
        ].index[0]
    except Exception:  # TODO fix that
        apical_face = None
    # Apical face has already been removed.
    # It needs to eliminate lateral face until obtain a cell with 4 faces.
    if apical_face is None:
        faces_in_cell = monolayer.face_df.loc[cell_to_face[cell].unique()]
        if len(faces_in_cell) > 4:
            # Remove lateral face with 3 sides
            face_to_eliminate = faces_in_cell[
                (faces_in_cell.segment == "lateral") & (faces_in_cell.num_sides == 3)
            ].index[0]

            prev_nums = {
                "edge": monolayer.Ne,
                "face": monolayer.Nf,
                "vert": monolayer.Nv,
            }
            HI_transition(monolayer, face_to_eliminate)
            monolayer.face_df.loc[prev_nums["face"] :, "contractility"] = 0
            done = False
        elif len(faces_in_cell) == 4:
            # Volume reduction
            if monolayer.cell_df.loc[cell, "vol"] > apoptosis_spec["critical_volume"]:
                shrink(monolayer, cell, apoptosis_spec["shrink_rate"])
                done = False
            else:
                done = True
    else:
        # Contract apical surface until reached a critical area
        if monolayer.face_df.loc[apical_face, "area"] > apoptosis_spec["critical_area"]:
            contract(monolayer, apical_face, apoptosis_spec["contract_rate"], True)
            done = False

        elif (
            monolayer.face_df.loc[apical_face, "area"]
            <= apoptosis_spec["critical_area"]
        ):
            # Reduce neighbours for the apical face (until 3)
            if monolayer.face_df.loc[apical_face, "num_sides"] > 3:
                e_min = monolayer.edge_df[monolayer.edge_df["face"] == apical_face][
                    "length"
                ].idxmin()
                prev_nums = {
                    "edge": monolayer.Ne,
                    "face": monolayer.Nf,
                    "vert": monolayer.Nv,
                }

                monolayer.settings["threshold_length"] = 1e-3
                IH_transition(monolayer, e_min)
                monolayer.face_df.loc[prev_nums["face"] :, "contractility"] = 0

                done = False

            elif monolayer.face_df.loc[apical_face, "num_sides"] == 3:
                prev_nums = {
                    "edge": monolayer.Ne,
                    "face": monolayer.Nf,
                    "vert": monolayer.Nv,
                }
                HI_transition(monolayer, apical_face)
                done = False

    if not done:
        manager.append(apoptosis, **apoptosis_spec)