"""
Small event module
=======================
"""
import logging
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from ...utils.decorators import face_lookup
from .actions import (
decrease,
detach_vertices,
exchange,
increase,
increase_linear_tension,
merge_vertices,
remove,
)
logger = logging.getLogger(__name__)
[docs]def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5
or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
[docs]@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
[docs]@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
[docs]@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
[docs]@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
[docs]def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
[docs]@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
