Module nlisim.modules.tgfb
Expand source code
from typing import Any, Dict
import attr
import numpy as np
from nlisim.coordinates import Voxel
from nlisim.diffusion import apply_diffusion
from nlisim.grid import RectangularGrid
from nlisim.module import ModuleModel, ModuleState
from nlisim.modules.molecules import MoleculesState
from nlisim.random import rg
from nlisim.state import State
from nlisim.util import activation_function, turnover_rate
def molecule_grid_factory(self: 'TGFBState') -> np.ndarray:
return np.zeros(shape=self.global_state.grid.shape, dtype=float)
@attr.s(kw_only=True, repr=False)
class TGFBState(ModuleState):
grid: np.ndarray = attr.ib(
default=attr.Factory(molecule_grid_factory, takes_self=True)
) # units: atto-mols
half_life: float # units: min
half_life_multiplier: float # units: proportion
macrophage_secretion_rate: float # units: atto-mol * cell^-1 * h^-1
macrophage_secretion_rate_unit_t: float # units: atto-mol * cell^-1 * step^-1
k_d: float # aM
class TGFB(ModuleModel):
"""TGFB"""
name = 'tgfb'
StateClass = TGFBState
def initialize(self, state: State) -> State:
tgfb: TGFBState = state.tgfb
# config file values
tgfb.half_life = self.config.getfloat('half_life') # units: min
tgfb.macrophage_secretion_rate = self.config.getfloat(
'macrophage_secretion_rate'
) # units: atto-mol * cell^-1 * h^-1
tgfb.k_d = self.config.getfloat('k_d') # units: aM
# computed values
tgfb.half_life_multiplier = 0.5 ** (
self.time_step / tgfb.half_life
) # units in exponent: (min/step) / min -> 1/step
# time unit conversions
tgfb.macrophage_secretion_rate_unit_t = tgfb.macrophage_secretion_rate * (
self.time_step / 60
) # units: atto-mol/(cell*h) * (min/step) / (min/hour)
return state
def advance(self, state: State, previous_time: float) -> State:
"""Advance the state by a single time step."""
from nlisim.modules.macrophage import MacrophageCellData, MacrophageState
from nlisim.modules.phagocyte import PhagocyteStatus
tgfb: TGFBState = state.tgfb
molecules: MoleculesState = state.molecules
macrophage: MacrophageState = state.macrophage
voxel_volume: float = state.voxel_volume
grid: RectangularGrid = state.grid
for macrophage_cell_index in macrophage.cells.alive():
macrophage_cell: MacrophageCellData = macrophage.cells[macrophage_cell_index]
macrophage_cell_voxel: Voxel = grid.get_voxel(macrophage_cell['point'])
if macrophage_cell['status'] == PhagocyteStatus.INACTIVE:
tgfb.grid[tuple(macrophage_cell_voxel)] += tgfb.macrophage_secretion_rate_unit_t
if (
activation_function(
x=tgfb.grid[tuple(macrophage_cell_voxel)],
k_d=tgfb.k_d,
h=self.time_step / 60, # units: (min/step) / (min/hour)
volume=voxel_volume,
b=1,
)
> rg.uniform()
):
macrophage_cell['status_iteration'] = 0
elif macrophage_cell['status'] not in {
PhagocyteStatus.APOPTOTIC,
PhagocyteStatus.NECROTIC,
PhagocyteStatus.DEAD,
}:
if (
activation_function(
x=tgfb.grid[tuple(macrophage_cell_voxel)],
k_d=tgfb.k_d,
h=self.time_step / 60, # units: (min/step) / (min/hour)
volume=voxel_volume,
b=1,
)
> rg.uniform()
):
macrophage_cell['status'] = PhagocyteStatus.INACTIVATING
macrophage_cell[
'status_iteration'
] = 0 # Previously, was no reset of the status iteration
# Degrade TGFB
tgfb.grid *= tgfb.half_life_multiplier
tgfb.grid *= turnover_rate(
x=np.array(1.0, dtype=np.float64),
x_system=0.0,
base_turnover_rate=molecules.turnover_rate,
rel_cyt_bind_unit_t=molecules.rel_cyt_bind_unit_t,
)
# Diffusion of TGFB
tgfb.grid[:] = apply_diffusion(
variable=tgfb.grid,
laplacian=molecules.laplacian,
diffusivity=molecules.diffusion_constant,
dt=self.time_step,
)
return state
def summary_stats(self, state: State) -> Dict[str, Any]:
tgfb: TGFBState = state.tgfb
voxel_volume = state.voxel_volume
return {
'concentration (nM)': float(np.mean(tgfb.grid) / voxel_volume / 1e9),
}
def visualization_data(self, state: State):
tgfb: TGFBState = state.tgfb
return 'molecule', tgfb.grid
Functions
def molecule_grid_factory(self: TGFBState) ‑> numpy.ndarray
-
Expand source code
def molecule_grid_factory(self: 'TGFBState') -> np.ndarray: return np.zeros(shape=self.global_state.grid.shape, dtype=float)
Classes
class TGFB (config: SimulationConfig)
-
TGFB
Expand source code
class TGFB(ModuleModel): """TGFB""" name = 'tgfb' StateClass = TGFBState def initialize(self, state: State) -> State: tgfb: TGFBState = state.tgfb # config file values tgfb.half_life = self.config.getfloat('half_life') # units: min tgfb.macrophage_secretion_rate = self.config.getfloat( 'macrophage_secretion_rate' ) # units: atto-mol * cell^-1 * h^-1 tgfb.k_d = self.config.getfloat('k_d') # units: aM # computed values tgfb.half_life_multiplier = 0.5 ** ( self.time_step / tgfb.half_life ) # units in exponent: (min/step) / min -> 1/step # time unit conversions tgfb.macrophage_secretion_rate_unit_t = tgfb.macrophage_secretion_rate * ( self.time_step / 60 ) # units: atto-mol/(cell*h) * (min/step) / (min/hour) return state def advance(self, state: State, previous_time: float) -> State: """Advance the state by a single time step.""" from nlisim.modules.macrophage import MacrophageCellData, MacrophageState from nlisim.modules.phagocyte import PhagocyteStatus tgfb: TGFBState = state.tgfb molecules: MoleculesState = state.molecules macrophage: MacrophageState = state.macrophage voxel_volume: float = state.voxel_volume grid: RectangularGrid = state.grid for macrophage_cell_index in macrophage.cells.alive(): macrophage_cell: MacrophageCellData = macrophage.cells[macrophage_cell_index] macrophage_cell_voxel: Voxel = grid.get_voxel(macrophage_cell['point']) if macrophage_cell['status'] == PhagocyteStatus.INACTIVE: tgfb.grid[tuple(macrophage_cell_voxel)] += tgfb.macrophage_secretion_rate_unit_t if ( activation_function( x=tgfb.grid[tuple(macrophage_cell_voxel)], k_d=tgfb.k_d, h=self.time_step / 60, # units: (min/step) / (min/hour) volume=voxel_volume, b=1, ) > rg.uniform() ): macrophage_cell['status_iteration'] = 0 elif macrophage_cell['status'] not in { PhagocyteStatus.APOPTOTIC, PhagocyteStatus.NECROTIC, PhagocyteStatus.DEAD, }: if ( activation_function( x=tgfb.grid[tuple(macrophage_cell_voxel)], k_d=tgfb.k_d, h=self.time_step / 60, # units: (min/step) / (min/hour) volume=voxel_volume, b=1, ) > rg.uniform() ): macrophage_cell['status'] = PhagocyteStatus.INACTIVATING macrophage_cell[ 'status_iteration' ] = 0 # Previously, was no reset of the status iteration # Degrade TGFB tgfb.grid *= tgfb.half_life_multiplier tgfb.grid *= turnover_rate( x=np.array(1.0, dtype=np.float64), x_system=0.0, base_turnover_rate=molecules.turnover_rate, rel_cyt_bind_unit_t=molecules.rel_cyt_bind_unit_t, ) # Diffusion of TGFB tgfb.grid[:] = apply_diffusion( variable=tgfb.grid, laplacian=molecules.laplacian, diffusivity=molecules.diffusion_constant, dt=self.time_step, ) return state def summary_stats(self, state: State) -> Dict[str, Any]: tgfb: TGFBState = state.tgfb voxel_volume = state.voxel_volume return { 'concentration (nM)': float(np.mean(tgfb.grid) / voxel_volume / 1e9), } def visualization_data(self, state: State): tgfb: TGFBState = state.tgfb return 'molecule', tgfb.grid
Ancestors
Methods
def advance(self, state: State, previous_time: float) ‑> State
-
Advance the state by a single time step.
Expand source code
def advance(self, state: State, previous_time: float) -> State: """Advance the state by a single time step.""" from nlisim.modules.macrophage import MacrophageCellData, MacrophageState from nlisim.modules.phagocyte import PhagocyteStatus tgfb: TGFBState = state.tgfb molecules: MoleculesState = state.molecules macrophage: MacrophageState = state.macrophage voxel_volume: float = state.voxel_volume grid: RectangularGrid = state.grid for macrophage_cell_index in macrophage.cells.alive(): macrophage_cell: MacrophageCellData = macrophage.cells[macrophage_cell_index] macrophage_cell_voxel: Voxel = grid.get_voxel(macrophage_cell['point']) if macrophage_cell['status'] == PhagocyteStatus.INACTIVE: tgfb.grid[tuple(macrophage_cell_voxel)] += tgfb.macrophage_secretion_rate_unit_t if ( activation_function( x=tgfb.grid[tuple(macrophage_cell_voxel)], k_d=tgfb.k_d, h=self.time_step / 60, # units: (min/step) / (min/hour) volume=voxel_volume, b=1, ) > rg.uniform() ): macrophage_cell['status_iteration'] = 0 elif macrophage_cell['status'] not in { PhagocyteStatus.APOPTOTIC, PhagocyteStatus.NECROTIC, PhagocyteStatus.DEAD, }: if ( activation_function( x=tgfb.grid[tuple(macrophage_cell_voxel)], k_d=tgfb.k_d, h=self.time_step / 60, # units: (min/step) / (min/hour) volume=voxel_volume, b=1, ) > rg.uniform() ): macrophage_cell['status'] = PhagocyteStatus.INACTIVATING macrophage_cell[ 'status_iteration' ] = 0 # Previously, was no reset of the status iteration # Degrade TGFB tgfb.grid *= tgfb.half_life_multiplier tgfb.grid *= turnover_rate( x=np.array(1.0, dtype=np.float64), x_system=0.0, base_turnover_rate=molecules.turnover_rate, rel_cyt_bind_unit_t=molecules.rel_cyt_bind_unit_t, ) # Diffusion of TGFB tgfb.grid[:] = apply_diffusion( variable=tgfb.grid, laplacian=molecules.laplacian, diffusivity=molecules.diffusion_constant, dt=self.time_step, ) return state
Inherited members
class TGFBState (*, global_state: State, grid: 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 TGFBState.
Expand source code
class TGFBState(ModuleState): grid: np.ndarray = attr.ib( default=attr.Factory(molecule_grid_factory, takes_self=True) ) # units: atto-mols half_life: float # units: min half_life_multiplier: float # units: proportion macrophage_secretion_rate: float # units: atto-mol * cell^-1 * h^-1 macrophage_secretion_rate_unit_t: float # units: atto-mol * cell^-1 * step^-1 k_d: float # aM
Ancestors
Class variables
var grid : numpy.ndarray
var half_life : float
var half_life_multiplier : float
var k_d : float
var macrophage_secretion_rate : float
var macrophage_secretion_rate_unit_t : float
Inherited members