def setUp(self):
self.D, self.nFES, self.nGEN = 10, 10, 10
self.t = StoppingTask(D=self.D, nFES=self.nFES, nGEN=self.nGEN, refValue=1, benchmark=MyBenchmark())
# encoding=utf8
# This is temporary fix to import module from parent folder
# It will be removed when package is published on PyPI
import sys
sys.path.append('../')
from NiaPy.algorithms.basic import MonarchButterflyOptimization
from NiaPy.task import StoppingTask
from NiaPy.benchmarks import Sphere
# we will run Monarch Butterfly Optimization algorithm for 5 independent runs
for i in range(5):
task = StoppingTask(D=10, nFES=10000, benchmark=Sphere())
algo = MonarchButterflyOptimization(NP=20, PAR=5.0 / 12.0, PER=1.2)
best = algo.run(task)
print('%s -> %s' % (best[0], best[1]))
def setUp(self):
self.D = 6
self.Lower, self.Upper = [2, 1, 1], [10, 10, 2]
self.task = StoppingTask(Lower=self.Lower, Upper=self.Upper, D=self.D)
class StoppingTaskTestCase(TestCase):
r"""Test case for testing `Task`, `StoppingTask` and `CountingTask` classes.
Date:
April 2019
Author:
Klemen Berkovič
See Also:
* :class:`NiaPy.util.Task`
* :class:`NiaPy.util.CountingTask`
* :class:`NiaPy.util.StoppingTask`
"""
def setUp(self):
self.D, self.nFES, self.nGEN = 10, 10, 10
self.t = StoppingTask(D=self.D, nFES=self.nFES, nGEN=self.nGEN, refValue=1, benchmark=MyBenchmark())
def test_isFeasible_fine(self):
x = full(self.D, 10)
self.assertTrue(self.t.isFeasible(x))
x = full(self.D, -10)
self.assertTrue(self.t.isFeasible(x))
x = rnd.uniform(-10, 10, self.D)
self.assertTrue(self.t.isFeasible(x))
x = full(self.D, -20)
self.assertFalse(self.t.isFeasible(x))
x = full(self.D, 20)
self.assertFalse(self.t.isFeasible(x))
def test_nextIter_fine(self):
for i in range(self.nGEN):
self.assertFalse(self.t.stopCond())
self.t.nextIter()
self.assertTrue(self.t.stopCond())
def test_stopCondI(self):
for i in range(self.nGEN):
self.assertFalse(self.t.stopCondI(), msg='Error at %s iteration!!!' % (i))
self.assertTrue(self.t.stopCondI())
def test_eval_fine(self):
x = full(self.D, 1.0)
for i in range(self.nFES):
self.assertAlmostEqual(self.t.eval(x), self.D, msg='Error at %s iteration!!!' % (i))
self.assertTrue(self.t.stopCond())
def test_eval_over_nFES_fine(self):
x = full(self.D, 1.0)
for i in range(self.nFES):
self.t.eval(x)
self.assertEqual(inf, self.t.eval(x))
self.assertTrue(self.t.stopCond())
def test_eval_over_nGEN_fine(self):
x = full(self.D, 1.0)
for i in range(self.nGEN):
self.t.nextIter()
self.assertEqual(inf, self.t.eval(x))
self.assertTrue(self.t.stopCond())
def test_nFES_count_fine(self):
x = full(self.D, 1.0)
for i in range(self.nFES):
self.t.eval(x)
self.assertEqual(self.t.Evals, i + 1, 'Error at %s. evaluation' % (i + 1))
def test_nGEN_count_fine(self):
x = full(self.D, 1.0)
for i in range(self.nGEN):
self.t.nextIter()
self.assertEqual(self.t.Iters, i + 1, 'Error at %s. iteration' % (i + 1))
def test_stopCond_evals_fine(self):
x = full(self.D, 1.0)
for i in range(self.nFES - 1):
self.t.eval(x)
self.assertFalse(self.t.stopCond())
self.t.eval(x)
self.assertTrue(self.t.stopCond())
def test_stopCond_iters_fine(self):
x = full(self.D, 1.0)
for i in range(self.nGEN - 1):
self.t.nextIter()
self.assertFalse(self.t.stopCond())
self.t.nextIter()
self.assertTrue(self.t.stopCond())
def test_stopCond_refValue_fine(self):
x = full(self.D, 1.0)
for i in range(self.nGEN - 5):
self.assertFalse(self.t.stopCond())
self.assertEqual(self.D, self.t.eval(x))
self.t.nextIter()
x = full(self.D, 0.0)
self.assertEqual(0, self.t.eval(x))
self.assertTrue(self.t.stopCond())
self.assertEqual(self.nGEN - 5, self.t.Iters)
# encoding=utf8
# This is temporary fix to import module from parent folder
# It will be removed when package is published on PyPI
from NiaPy.benchmarks import Sphere
from NiaPy.task import StoppingTask
from NiaPy.algorithms.basic import BeesAlgorithm
import sys
sys.path.append('../')
# we will run Bees Algorithm for 5 independent runs
for i in range(5):
task = StoppingTask(D=20, nGEN=2, benchmark=Sphere())
algo = BeesAlgorithm(NP=50, m=20, e=10, nep=20, nsp=15, ngh=7)
best = algo.run(task)
print('%s -> %s' % (best[0], best[1]))
class StoppingTaskBaseTestCase(TestCase):
r"""Test case for testing `Task`, `StoppingTask` and `CountingTask` classes.
Date:
April 2019
Author:
Klemen Berkovič
See Also:
* :class:`NiaPy.util.Task`
* :class:`NiaPy.util.CountingTask`
* :class:`NiaPy.util.StoppingTask`
"""
def setUp(self):
self.D = 6
self.Lower, self.Upper = [2, 1, 1], [10, 10, 2]
self.task = StoppingTask(Lower=self.Lower, Upper=self.Upper, D=self.D)
def test_dim_ok(self):
self.assertEqual(self.D, self.task.D)
self.assertEqual(self.D, self.task.dim())
def test_lower(self):
self.assertTrue(array_equal(fullArray(self.Lower, self.D), self.task.Lower))
self.assertTrue(array_equal(fullArray(self.Lower, self.D), self.task.bcLower()))
def test_upper(self):
self.assertTrue(array_equal(fullArray(self.Upper, self.D), self.task.Upper))
self.assertTrue(array_equal(fullArray(self.Upper, self.D), self.task.bcUpper()))
def test_range(self):
self.assertTrue(array_equal(fullArray(self.Upper, self.D) - fullArray(self.Lower, self.D), self.task.bRange))
self.assertTrue(array_equal(fullArray(self.Upper, self.D) - fullArray(self.Lower, self.D), self.task.bcRange()))
def test_ngens(self):
self.assertEqual(inf, self.task.nGEN)
def test_nfess(self):
self.assertEqual(inf, self.task.nFES)
def test_stop_cond(self):
self.assertFalse(self.task.stopCond())
def test_stop_condi(self):
self.assertFalse(self.task.stopCondI())
def test_eval(self):
self.assertRaises(AttributeError, lambda: self.task.eval([]))
def test_evals(self):
self.assertEqual(0, self.task.evals())
def test_iters(self):
self.assertEqual(0, self.task.iters())
def test_next_iter(self):
self.assertEqual(None, self.task.nextIter())
def test_is_feasible(self):
self.assertFalse(self.task.isFeasible(fullArray([1, 2, 3], self.D)))
def _run(X, y, train_index, val_index, random_seed, optimizer, evaluator,
benchmark, optimizer_settings, nGENs, continue_opt, cut_type,
cutting_perc, j):
opt_settings = es.get_args(optimizer)
opt_settings.update(optimizer_settings)
X1 = X
cuted = [] # Which genes (features) are cutted
fitnesses = [] # Fitness values after every cutting
xb, fxb, benchm = None, -1, None
pop, fpop = None, None
for nGENp in nGENs: # Every interval before cutting
benchm = benchmark(X=X1,
y=y,
train_indices=train_index,
valid_indices=val_index,
random_seed=random_seed,
evaluator=evaluator)
task = StoppingTask(D=X1.shape[1],
nGEN=nGENp,
optType=OptimizationType.MINIMIZATION,
benchmark=benchm)
evo = optimizer(seed=random_seed, **opt_settings)
# Start new optimization. Continue on pop and give fitness of pop.
pop, fpop, xb, fxb = DynFeatureSelection.runTask(
evo, task, starting_pop=pop, starting_fpop=fpop)
if not isinstance(xb, np.ndarray):
xb = xb.x
xb = np.copy(xb)
# Cut genotype. Four different strategies
if cut_type == 'diff':
# Best solutions say which features are most common, and worst solutions vote which features are most common.
# Difference between votes say which features will be cutted - those that are more coomon in worst solutions and
# least common in best features.
idx = DynFeatureSelection.cut_n_vote_diff(pop,
fpop,
cutting_perc,
benchm,
n=25)
elif cut_type == 'vote_all':
# Every solution votes which features are most common. Similar than best_vote worst, but every solution votes.
idx = DynFeatureSelection.cut_all_vote_for_worst(
pop, fpop, cutting_perc, benchm)
elif cut_type == 'best_vote_worst':
# Best solutions say which features are most common. Least common features are cutted.
idx = DynFeatureSelection.cut_n_vote(pop,
fpop,
cutting_perc,
benchm,
n=50)
elif cut_type == 'worst_vote_best':
# Worst solutions say which features are most common. Most common features are cutted.
idx = DynFeatureSelection.cut_n_vote(pop,
fpop,
cutting_perc,
benchm,
n=-50)
cuted.append(idx) # Log which genes are cutted
fitnesses.append(fxb) # Log fitenss value after the cutting
X1 = np.delete(X1, idx,
axis=1) # Delete columns (feature) from genotypes
# If we want the optimization to continue on genes not cutted
if continue_opt:
if isinstance(
pop[0],
np.ndarray): # If population is in shape of ndarray
pop = np.delete(pop, idx, 1)
else: # If population is in shape of individuals
for ind in pop:
ind.x = np.delete(ind.x, idx)
else: # If we want that after cutting, the solutions are reseted (random reinitialization)
pop = None
fpop = None
# Transform solutions to datasets with selected features
xb = benchmark.to_phenotype(xb, benchm.split)
# Remove not selected features
for i in range(len(cuted) - 2, -1, -1):
cut = np.sort(cuted[i])
for c in cut:
xb = np.insert(xb, c, False)
return xb, fxb
import sys
sys.path.append('../')
# End of fix
from NiaPy.algorithms.basic import GreyWolfOptimizer
from NiaPy.task import StoppingTask, OptimizationType
from NiaPy.benchmarks import Pinter
# initialize Pinter benchamrk with custom bound
pinterCustom = Pinter(-5, 5)
# we will run 10 repetitions of Grey Wolf Optimizer against Pinter benchmark function
for i in range(10):
# first parameter takes dimension of problem
# second parameter takes the number of function evaluations
# third parameter is benchmark optimization type
# forth parameter is benchmark function
task = StoppingTask(D=20,
nGEN=100,
optType=OptimizationType.MINIMIZATION,
benchmark=pinterCustom)
# parameter is population size
algo = GreyWolfOptimizer(NP=20)
# running algorithm returns best found minimum
best = algo.run(task)
# printing best minimum
print(best)
# This is temporary fix to import module from parent folder
# It will be removed when package is published on PyPI
import sys
sys.path.append('../')
# End of fix
from NiaPy.algorithms.basic import GreyWolfOptimizer
from NiaPy.task import StoppingTask
# we will run 10 repetitions of Grey Wolf Optimizer against Pinter benchmark function
for i in range(10):
task = StoppingTask(D=10, nFES=1000, benchmark='pinter')
algorithm = GreyWolfOptimizer(NP=20)
best = algorithm.run(task)
print(best[-1])
# encoding=utf8
# This is temporary fix to import module from parent folder
# It will be removed when package is published on PyPI
import sys
sys.path.append('../')
# End of fix
from NiaPy.task import StoppingTask
from NiaPy.benchmarks import Sphere
from NiaPy.algorithms.other import RandomSearch
for i in range(1):
task = StoppingTask(D=5, nGEN=5000, benchmark=Sphere())
algo = RandomSearch()
best = algo.run(task=task)
print(best)
# encoding=utf8
# This is temporary fix to import module from parent folder
# It will be removed when package is published on PyPI
import sys
sys.path.append('../')
# End of fix
from NiaPy.task import StoppingTask
from NiaPy.benchmarks import Sphere
from NiaPy.algorithms.basic import CatSwarmOptimization
task = StoppingTask(D=10, nFES=1000, logger=True, benchmark=Sphere())
algo = CatSwarmOptimization()
best = algo.run(task=task)
print('%s -> %s' % (best[0], best[1]))
#plot a convergence graph
task.plot()