tyssue.solvers package

Submodules

tyssue.solvers.base module

tyssue.solvers.base.set_pos(eptm, geom, pos)

Updates the vertex position of the Epithelium object.

Assumes that pos is passed as a 1D array to be reshaped as (eptm.Nv, eptm.dim)

tyssue.solvers.isotropic_solver module

tyssue.solvers.isotropic_solver.bruteforce_isotropic_relax(eptm, geom, model)

tyssue.solvers.quasistatic module

Quasistatic solver for vertex models

class tyssue.solvers.quasistatic.QSSolver(with_collisions=False, with_t1=False, with_t3=False)

Bases: object

Quasistatic solver performing a gradient descent on a tyssue.Epithelium object.

find_energy_min : energy minimization calling `scipy.optimize.minimize`

approx_grad : uses `optimize.approx_fprime` to compute an approximated

gradient.

check_grad : compares the approximated gradient with the one provided

by the model

Creates a quasistatic gradient descent solver with optional type1, type3 and collision detection and solving routines.

Parameters

• with_collisions (bool, default False) – wheter or not to solve collisions

• with_t1 (bool, default False) – whether or not to solve type 1 transitions at each iteration.

• with_t3 (bool, default False) – whether or not to solve type 3 transitions (i.e. elimnation of small triangular faces) at each iteration.

• corrections are applied in this order (Those) –

• 3 (type) –

• the collisions (then) –

approx_grad(eptm, geom, model)

check_grad(eptm, geom, model)

find_energy_min(eptm, geom, model, periodic=False, **minimize_kw)

Energy minimization function.

The epithelium’s total energy is minimized by displacing its vertices. This is a wrapper around scipy.optimize.minimize

Parameters

• eptm (a tyssue.Epithlium object) –

• geom (a geometry class) –

• must provide an update_all method that takes eptm (geom) – as sole argument and updates the relevant geometrical quantities

• model (a model class) – model must provide compute_energy and compute_gradient methods that take eptm as first and unique positional argument.

tyssue.solvers.sheet_vertex_solver module

Energy minimization solvers for the sheet vertex model

class tyssue.solvers.sheet_vertex_solver.Solver

Bases: object

classmethod approx_grad(sheet, geom, model)

classmethod check_grad(sheet, geom, model)

classmethod find_energy_min(sheet, geom, model, pos_idx=None, **settings_kw)

classmethod opt_energy(pos, pos_idx, sheet, geom, model)

static opt_grad(pos, pos_idx, sheet, geom, model)

static set_pos(pos, pos_idx, sheet)

tyssue.solvers.viscous module

Viscosity based ODE solver

class tyssue.solvers.viscous.EulerSolver(eptm, geom, model, history=None, auto_reconnect=False, manager=None, bounds=None, with_t1=False, with_t3=False)

Bases: object

Explicit Euler solver

creates an instance of EulerSolver

Parameters

• eptm (a tyssue.Epithelium instance) –

• geom (a Geometry class) –

• model (a Model class) –

• history (a tyssue.History or tyssue.Hdf5History instance) –

• auto_reconnect (bool) – if True, will automatically perform reconnections, default False

• manager (a tyssue.EventManager instance) –

• bounds (tuple of (min, max),) – bonds the displacement of the vertices at each time step

property current_pos

ode_func(t, pos)

Computes the models’ gradient.

dot_r : 1D np.ndarray of shape (self.eptm.Nv * self.eptm.dim, )

\[\]

rac{dr_i}{dt} = rac{ abla U_i}{eta_i}

record(t)

set_pos(pos)

Updates the eptm vertices position

solve(tf, dt, on_topo_change=None, topo_change_args=())

Solves the system of differential equations from the current time to tf with steps of dt with a forward Euler method.

Parameters

• tf (float, final time when we stop solving) –

• dt (float, time step) –

• on_topo_change (function, optional, default None) – function of self.eptm

• topo_change_args (tuple, arguments passed to on_topo_change) –

class tyssue.solvers.viscous.IVPSolver(*args, **kwargs)

Bases: object

tyssue.solvers.viscous.set_pos(eptm, geom, pos)

Updates the vertex position of the Epithelium object.

Assumes that pos is passed as a 1D array to be reshaped as (eptm.Nv, eptm.dim)

Module contents

solvers