weights : np.array
normalization : {{'no', 'front', 'ever'}}
extreme_points_as_reference_points : bool
Returns
-------
rnsga2 : :class:`~pymoo.model.algorithm.Algorithm`
Returns an RNSGA2 algorithm object.
"""
rnsga2 = nsga2(**kwargs)
rnsga2.epsilon = epsilon
rnsga2.weights = weights
rnsga2.normalization = normalization
rnsga2.selection = RandomSelection()
rnsga2.survival = RankAndModifiedCrowdingSurvival(
ref_points, epsilon, weights, normalization,
extreme_points_as_reference_points)
return rnsga2
parse_doc_string(rnsga2)
One strategy to introduce adaptive weights (F) during one run. The option allows
the same dither to be used in one iteration ('scalar') or a different one for
each individual ('vector).
jitter : bool
Another strategy for adaptive weights (F). Here, only a very small value is added or
substracted to the weight used for the crossover for each individual.
Returns
-------
de : :class:`~pymoo.model.algorithm.Algorithm`
Returns an DifferentialEvolution algorithm object.
"""
_, _selection, _n, _mutation, = variant.split("/")
return DifferentialEvolution(
variant,
CR,
F,
dither,
jitter,
pop_size=pop_size,
sampling=sampling,
**kwargs)
parse_doc_string(de)
self.arrow_style = kwargs["arrow_style"]
def _do(self):
# initial a figure with a single plot
self.init_figure()
# equal axis length and no ticks
equal_axis(self.ax)
no_ticks(self.ax)
# determine the overall scale of points
_F = np.row_stack([e[0] for e in self.to_plot])
_min, _max = _F.min(axis=0), _F.max(axis=0)
V = get_uniform_points_around_circle(self.n_dim)
plot_axes_arrow(self.ax, V, extend_factor=self.axis_extension, **{**self.axis_style, **self.arrow_style})
plot_axis_labels(self.ax, V, self.get_labels(), **self.axis_label_style)
# normalize in range for this plot - here no implicit normalization as in radviz
bounds = parse_bounds(self.bounds, self.n_dim)
to_plot_norm = normalize(self.to_plot, bounds)
for k, (F, kwargs) in enumerate(to_plot_norm):
N = (F[..., None] * V).sum(axis=1)
self.ax.scatter(N[:, 0], N[:, 1], **kwargs)
parse_doc_string(StarCoordinate.__init__)
denom = nadir_point - utopian_point
denom[denom == 0] = 1e-12
# normalize by ideal point and intercepts
N = (F - utopian_point) / denom
dist_matrix = load_function("calc_perpendicular_distance")(N, niches)
niche_of_individuals = np.argmin(dist_matrix, axis=1)
dist_to_niche = dist_matrix[np.arange(F.shape[0]), niche_of_individuals]
return niche_of_individuals, dist_to_niche, dist_matrix
def calc_niche_count(n_niches, niche_of_individuals):
niche_count = np.zeros(n_niches, dtype=np.int)
index, count = np.unique(niche_of_individuals, return_counts=True)
niche_count[index] = count
return niche_count
# =========================================================================================================
# Interface
# =========================================================================================================
def nsga3(*args, **kwargs):
return NSGA3(*args, **kwargs)
parse_doc_string(NSGA3.__init__)
# make a step and create the offsprings
self.off = self._step()
# evaluate the offsprings
self.evaluator.eval(self.problem, self.off, algorithm=self)
survivors = []
for k in range(self.pop_size):
parent, off = self.pop[k], self.off[k]
rel = get_relation(parent, off)
if rel == 0:
survivors.extend([parent, off])
elif rel == -1:
survivors.append(off)
else:
survivors.append(parent)
survivors = Population.create(*survivors)
if len(survivors) > self.pop_size:
survivors = RankAndCrowdingSurvival().do(self.problem, survivors,
self.pop_size)
self.pop = survivors
parse_doc_string(GDE3.__init__)
for i in range(len(sections) - 1):
t = np.linspace(sections[i], sections[i + 1], 100)
v = np.column_stack([np.cos(t), np.sin(t)])
P = np.row_stack([center, F[i] * v])
plot_polygon(ax, P, color=self.colors[i])
# draw the outer circle
plot_circle(ax, **self.axis_style)
plot_axes_lines(ax, V, **self.axis_style)
def _do(self):
n_rows = len(self.to_plot)
n_cols = max([len(e[0]) for e in self.to_plot])
self.init_figure(n_rows=n_rows,
n_cols=n_cols,
force_axes_as_matrix=True)
# normalize the input
bounds = parse_bounds(self.bounds, self.n_dim)
to_plot_norm = normalize(self.to_plot, bounds, reverse=self.reverse)
for k, (F, kwargs) in enumerate(to_plot_norm):
for j, _F in enumerate(F):
self._plot(self.ax[k, j], _F)
parse_doc_string(Petal.__init__)
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
selection : {selection}
crossover : {crossover}
mutation : {mutation}
eliminate_duplicates : {eliminate_duplicates}
n_offsprings : {n_offsprings}
Returns
-------
ga : :class:`~pymoo.model.algorithm.Algorithm`
Returns an SingleObjectiveGeneticAlgorithm algorithm object.
"""
return SingleObjectiveGeneticAlgorithm(pop_size=pop_size,
sampling=sampling,
selection=selection,
crossover=crossover,
mutation=mutation,
survival=FitnessSurvival(),
eliminate_duplicates=eliminate_duplicates,
n_offsprings=n_offsprings,
**kwargs)
parse_doc_string(ga)
self.off = self.crossover.do(self.problem, pop, P, algorithm=self)
# then do the mutation (which is actually )
_pop = self.off.new().merge(self.pop).merge(self.off)
_P = np.column_stack(
[np.arange(len(pop)),
np.arange(len(pop)) + len(pop)])
self.off = self.mutation.do(self.problem, _pop, _P,
algorithm=self)[:len(self.pop)]
# bounds back if something is out of bounds
self.off = BoundsBackRepair().do(self.problem, self.off)
# evaluate the results
self.evaluator.eval(self.problem, self.off, algorithm=self)
_F, _CV, _feasible = self.off.get("F", "CV", "feasible")
_F = parameter_less(_F, _CV)
# find the individuals which are indeed better
is_better = np.where((_F <= F)[:, 0])[0]
# replace the individuals in the population
pop[is_better] = self.off[is_better]
# store the population in the algorithm object
self.pop = pop
parse_doc_string(DE.__init__)
# set the crowding to all individuals
pop[front].set("crowding", crowding)
# extend the survivors by all or selected individuals
survivors.extend(front[I])
# inverse of crowding because nsga2 does maximize it (then tournament selection can stay the same)
pop.set("crowding", -pop.get("crowding"))
return pop[survivors]
def calc_norm_pref_distance(A, B, weights, ideal, nadir):
D = np.repeat(A, B.shape[0], axis=0) - np.tile(B, (A.shape[0], 1))
N = ((D / (nadir - ideal))**2) * weights
N = np.sqrt(np.sum(N, axis=1) * len(weights))
return np.reshape(N, (A.shape[0], B.shape[0]))
# =========================================================================================================
# Interface
# =========================================================================================================
def rnsga2(*args, **kwargs):
return RNSGA2(*args, **kwargs)
parse_doc_string(RNSGA2.__init__)
#Levy Flight
#pick the best one from random optimum nests (leas infeasibles or PF members)
best = self.opt[np.random.randint(len(self.opt), size=len(X))]
G_X = np.array([best_nest.get("X") for best_nest in best])
step_size = self._get_global_step_size(X)
_X = X + np.random.rand(*X.shape) * step_size * (G_X - X)
_X = set_to_bounds_if_outside_by_problem(self.problem, _X)
#Evaluate
off = Population(len(_X)).set("X", _X)
self.evaluator.eval(self.problem, off, algorithm=self)
#Local Random Walk
_X = off.get("X")
dir_vec = self._get_local_directional_vector(X)
_X = _X + dir_vec
_X = set_to_bounds_if_outside_by_problem(self.problem, _X)
off = Population(len(_X)).set("X", _X)
self.evaluator.eval(self.problem, off, algorithm=self)
#append offspring to population and then sort for elitism (survival)
self.pop = Population.merge(pop, off)
self.pop = self.survival.do(self.problem,
self.pop,
self.pop_size,
algorithm=self)
parse_doc_string(MOCS.__init__)
# the angle of niche to nearest neighboring niche
gamma = self.gamma[k]
# the angle from the individuals of this niches to the niche itself
theta = acute_angle[assigned_to_niche, k]
# the penalty which is applied for the metric
penalty = problem.n_obj * (
(n_gen / n_max_gen)**self.alpha) * (theta / gamma)
# calculate the angle-penalized penalized (APD)
apd = dist_to_ideal[assigned_to_niche] * (1 + penalty)
# the individual which survives
survivor = assigned_to_niche[apd.argmin()]
# set attributes to the individual
pop[assigned_to_niche].set(theta=theta,
apd=apd,
niche=k,
best=False)
pop[survivor].set("best", True)
# select the one with smallest APD value
survivors.append(survivor)
return pop[survivors]
parse_doc_string(RVEA.__init__)
for e in ant.path:
if e.pheromone is None:
raise Exception(
"The ant has to set the pheromone of each entry in the path."
)
else:
self.pheromones.update(e.key, e.pheromone * pheromones.rho)
self.pop, self.off = colony, colony
self.opt = opt
def _set_optimum(self, **kwargs):
pass
parse_doc_string(ACO.__init__)
# =========================================================================================================
# TSP Example
# =========================================================================================================
class GraphAnt(Ant):
def __init__(self, **kwargs) -> None:
super().__init__(**kwargs)
self.not_visited = None
self.costs = 0.0
def initialize(self, *args, **kwargs):
super().initialize(*args, **kwargs)
self.not_visited = np.full(self.problem.n_var, True)
----------
ref_dirs : {ref_dirs}
decomposition : {{ 'auto', 'tchebi', 'pbi' }}
The decomposition approach that should be used. If set to `auto` for two objectives `tchebi` and for more than
two `pbi` will be used.
n_neighbors : int
Number of neighboring reference lines to be used for selection.
prob_neighbor_mating : float
Probability of selecting the parents in the neighborhood.
Returns
-------
moead : :class:`~pymoo.model.algorithm.MOEAD`
Returns an MOEAD algorithm object.
"""
return MOEAD(ref_dirs,
n_neighbors=n_neighbors,
decomposition=decomposition,
prob_neighbor_mating=prob_neighbor_mating,
**kwargs)
parse_doc_string(moead)
eliminate_duplicates=True,
**kwargs)
self.n_elites = n_elites
self.n_mutants = n_mutants
self.bias = bias
self.default_termination = SingleObjectiveDefaultTermination()
def _next(self):
pop = self.pop
elites = np.where(pop.get("type") == "elite")[0]
# actually do the mating given the elite selection and biased crossover
off = self.mating.do(self.problem, pop, n_offsprings=self.n_offsprings, algorithm=self)
# create the mutants randomly to fill the population with
mutants = FloatRandomSampling().do(self.problem, self.n_mutants, algorithm=self)
# evaluate all the new solutions
to_evaluate = Population.merge(off, mutants)
self.evaluator.eval(self.problem, to_evaluate, algorithm=self)
# finally merge everything together and sort by fitness
pop = Population.merge(pop[elites], to_evaluate)
# the do survival selection - set the elites for the next round
self.pop = self.survival.do(self.problem, pop, len(pop), algorithm=self)
parse_doc_string(BRKGA.__init__)
return mutant
for k in range(self.problem.n_var):
# create the the individual and evaluate it
mutant = step(center.X, self.explr_delta, k)
self.evaluator.eval(self.problem, mutant, algorithm=self)
self.pop = Population.merge(self.pop, mutant)
if is_better(mutant, opt):
center, opt = mutant, mutant
else:
# inverse the sign of the delta
self.explr_delta[k] = -self.explr_delta[k]
# now try the other sign if there was no improvement
mutant = step(center.X, self.explr_delta, k)
self.evaluator.eval(self.problem, mutant, algorithm=self)
self.pop = Population.merge(self.pop, mutant)
if is_better(mutant, opt):
center, opt = mutant, mutant
return opt
parse_doc_string(PatternSearch.__init__)
N.append(pop[k])
n_cand_neighbors = pop[k].get("neighbors")
rnd = np.random.permutation(
len(n_cand_neighbors))[:self.crossover.n_parents - 1]
[N.append(e) for e in n_cand_neighbors[rnd]]
parents = np.reshape(np.arange(len(N)), (-1, self.crossover.n_parents))
N = Population.create(*N)
bias = super()._do(problem, N, n_neighbors, parents, **kwargs)
return Population.merge(bias, other)
parse_doc_string(MMGA.__init__)
if __name__ == '__main__':
problem = MultiModalSimple2()
algorithm = MMGA(pop_size=20, eliminate_duplicates=True)
ret = minimize(problem,
algorithm,
termination=('n_gen', 100),
seed=1,
save_history=True,
verbose=False)
def plot(algorithm):
pop = algorithm.pop
F, G = pop.get("F", "G")
f = F[:, 0]
if problem.n_constr == 0:
I = f.argsort()
else:
phi = (np.maximum(0, G) ** 2).sum(axis=1)
J = np.arange(len(phi))
I = load_function("stochastic_ranking")(f, phi, self.PR, J)
return pop[I][:n_survive]
class SRES(ES):
def __init__(self, PF=0.45, **kwargs):
"""
Stochastic Ranking Evolutionary Strategy (SRES)
Parameters
----------
PF: float
The stochastic ranking weight for choosing a random decision while doing the modified bubble sort.
"""
super().__init__(survival=StochasticRankingSurvival(PF), **kwargs)
self.PF = PF
parse_doc_string(SRES.__init__)
("s", 70), ("alpha", 0.3))
def _do(self):
# initial a figure with a single plot
self.init_figure()
# equal axis length and no ticks
equal_axis(self.ax)
no_ticks(self.ax)
V = get_uniform_points_around_circle(self.n_dim)
plot_axis_labels(self.ax, V, self.get_labels(),
**self.axis_label_style)
# draw the outer circle and radar lines
plot_circle(self.ax, **self.axis_style)
plot_radar_line(self.ax, V, **self.axis_style)
# draw the endpoints of each objective
if self.endpoint_style:
self.ax.scatter(V[:, 0], V[:, 1], **self.endpoint_style)
# plot all the points
for k, (F, kwargs) in enumerate(self.to_plot):
N = (F[..., None] * V).sum(axis=1) / F.sum(axis=1)[:, None]
self.ax.scatter(N[:, 0], N[:, 1], **kwargs)
parse_doc_string(Radviz.__init__)
return_random_if_equal=True)
# otherwise just select random
else:
S[i] = random.choice([a, b])
return S[:, None].astype(np.int)
# =========================================================================================================
# Interface
# =========================================================================================================
def unsga3(**kwargs):
"""
This is an implementation of the Unified NSGA3 algorithm :cite:`unsga3`. The same options as for
:class:`pymoo.algorithms.nsga3.nsga3` are available.
Returns
-------
unsga3 : :class:`~pymoo.model.algorithm.Algorithm`
Returns an UNSGA3 algorithm object.
"""
return NSGA3(selection=TournamentSelection(func_comp=comp_by_rank_and_ref_line_dist), **kwargs)
parse_doc_string(unsga3)
X = np.array(X)
self.send_array_to_yield = X.ndim > 1
X = np.atleast_2d(X)
# evaluate the population
self.pop = Population.new("X", X)
self.evaluator.eval(self.problem, self.pop, algorithm=self)
# set infeasible individual's objective values to np.nan - then CMAES can handle it
for ind in self.pop:
if not ind.feasible[0]:
ind.F[0] = np.nan
def _set_optimum(self):
val = self.pop
if self.opt is not None:
val = Population.merge(val, self.opt)
self.opt = filter_optimum(val, least_infeasible=True)
def __getstate__(self):
state = self.__dict__.copy()
del state["es"]
return state
def __setstate__(self, state):
self.__dict__.update(state)
self.ers = None
parse_doc_string(CMAES.__init__)
return self
def plot(self, ax, _type, F, **kwargs):
is_3d = F.shape[1] == 3
if _type is None:
_type = "scatter"
if _type == "scatter":
if is_3d:
ax.scatter(F[:, 0], F[:, 1], F[:, 2], **kwargs)
else:
ax.scatter(F[:, 0], F[:, 1], **kwargs)
else:
if is_3d:
ax.plot_trisurf(F[:, 0], F[:, 1], F[:, 2], **kwargs)
else:
ax.plot(F[:, 0], F[:, 1], **kwargs)
def set_labels(self, ax, labels, is_3d):
# set the labels for each axis
ax.set_xlabel(labels[0])
ax.set_ylabel(labels[1])
if is_3d:
ax.set_zlabel(labels[2])
parse_doc_string(Scatter.__init__)
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
selection : {selection}
crossover : {crossover}
mutation : {mutation}
eliminate_duplicates : {eliminate_duplicates}
n_offsprings : {n_offsprings}
Returns
-------
nsganet : :class:`~pymoo.model.algorithm.Algorithm`
Returns an NSGANet algorithm object.
"""
return NSGANet(pop_size=pop_size,
sampling=sampling,
selection=selection,
crossover=crossover,
mutation=mutation,
survival=RankAndCrowdingSurvival(),
eliminate_duplicates=eliminate_duplicates,
n_offsprings=n_offsprings,
**kwargs)
parse_doc_string(nsganet)
if self.show_bounds:
self.ax.text(i - margin_left, bottom,
self.func_number_to_text(bounds[0][i]))
self.ax.text(i - margin_left, top,
self.func_number_to_text(bounds[1][i]))
if self.n_ticks is not None:
n_length = 0.03
for y in np.linspace(0, 1, self.n_ticks):
self.ax.hlines(y, i - n_length, i + n_length,
**self.axis_style)
# if bounds are shown, then move them to the bottom
if self.show_bounds:
self.ax.tick_params(axis='x', which='major', pad=25)
self.ax.spines['right'].set_visible(False)
self.ax.spines['left'].set_visible(False)
self.ax.set_yticklabels([])
self.ax.set_yticks([])
self.ax.set_ylim((-0.05, 1.05))
self.ax.set_xticks(np.arange(self.n_dim))
self.ax.set_xticklabels(self.get_labels())
return self
parse_doc_string(PCP.__init__)
self.pop = self.pc_pop.copy(deep=True)
def _replace(self, i, off):
npc_pop = self.npc_pop
pop_size = len(self.ref_dirs)
nr = math.ceil(pop_size / 100)
# calculate the decomposed values for each neighbor
N = self.neighbors[i]
FV = self.decomp.do(npc_pop[N].get("F"),
weights=self.ref_dirs[N, :],
ideal_point=self.ideal)
off_FV = self.decomp.do(off.get("F"),
weights=self.ref_dirs[N, :],
ideal_point=self.ideal)
# get the absolute index in F where offspring is better than the current F (decomposed space)
I = np.where(off_FV < FV)[0]
if len(I) > 0:
npc_pop[N[I[:nr]]] = off[0]
return npc_pop
parse_doc_string(BCEMOEAD.__init__)
label="particle")
X, F, CV = pop.get("X", "F", "CV")
plt.scatter(X[:, 0],
X[:, 1],
color="blue",
marker="o",
s=30,
alpha=0.5)
opt = algorithm.opt
X, F, CV = opt.get("X", "F", "CV")
plt.scatter(X[:, 0],
X[:, 1],
color="black",
marker="x",
s=100,
label="gbest")
xl, xu = problem.bounds()
plt.xlim(xl[0], xu[0])
plt.ylim(xl[1], xu[1])
plt.title(f"Generation: %s \nf: %.5E" % (algorithm.n_gen, opt[0].F[0]))
plt.legend()
self.last_pop = off.copy(deep=True)
parse_doc_string(PSO.__init__)
else:
IC = (Ci + 1e-6) / (CV + 1e-6)
CVF = np.max(np.maximum(Fi, F) / np.minimum(Fi, F), axis=1)
val = np.log(np.maximum(CVF, IC))
indicator[:, i] = val
indicator[i, i] = np.inf
feas = np.where(CV <= 0)[0]
if len(feas) <= self.pop_size:
self.archive = pop[np.argsort(CV)[:self.pop_size]]
else:
feas_F = pop[feas].get("F") - self.norm.ideal(
only_feas=True) + 1e-6
I = Selection_Operator_of_PREA(feas_F, indicator[feas][:, feas],
self.pop_size)
self.archive = pop[feas[I]]
I = Indicator_based_CHT(F, indicator, self.ref_dirs, self.pop_size)
self.pop = pop[I]
self.Ra = 1 - self.n_gen / self.termination.n_max_gen
def _set_optimum(self, **kwargs):
self.opt = filter_optimum(self.archive, least_infeasible=True)
parse_doc_string(ICMA.__init__)
ref_points : {ref_points}
pop_per_ref_point : int
Size of the population used for each reference point.
mu : float
Defines the scaling of the reference lines used during survival selection. Increasing mu will result
having solutions with a larger spread.
Other Parameters
-------
n_offsprings : {n_offsprings}
sampling : {sampling}
selection : {selection}
crossover : {crossover}
mutation : {mutation}
eliminate_duplicates : {eliminate_duplicates}
Returns
-------
nsga3 : :class:`~pymoo.model.algorithm.Algorithm`
Returns an NSGA3 algorithm object.
"""
return RNSGA3(ref_points, pop_per_ref_point, mu, **kwargs)
parse_doc_string(rnsga3)
