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Added explicit exception to selTournamentDCD so that if individuals l…
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…ength isn't a multiple of 4 it gives a useful error
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tzr committed May 15, 2018
1 parent f141d3f commit af1ae05
Showing 1 changed file with 61 additions and 57 deletions.
118 changes: 61 additions & 57 deletions deap/tools/emo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,12 @@ def selNSGA2(individuals, k, nd='standard'):
than sorting the population according to their front rank. The
list returned contains references to the input *individuals*. For more
details on the NSGA-II operator see [Deb2002]_.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param nd: Specify the non-dominated algorithm to use: 'standard' or 'log'.
:returns: A list of selected individuals.
.. [Deb2002] Deb, Pratab, Agarwal, and Meyarivan, "A fast elitist
non-dominated sorting genetic algorithm for multi-objective
optimization: NSGA-II", 2002.
Expand All @@ -39,27 +39,27 @@ def selNSGA2(individuals, k, nd='standard'):

for front in pareto_fronts:
assignCrowdingDist(front)

chosen = list(chain(*pareto_fronts[:-1]))
k = k - len(chosen)
if k > 0:
sorted_front = sorted(pareto_fronts[-1], key=attrgetter("fitness.crowding_dist"), reverse=True)
chosen.extend(sorted_front[:k])

return chosen

def sortNondominated(individuals, k, first_front_only=False):
"""Sort the first *k* *individuals* into different nondomination levels
"""Sort the first *k* *individuals* into different nondomination levels
using the "Fast Nondominated Sorting Approach" proposed by Deb et al.,
see [Deb2002]_. This algorithm has a time complexity of :math:`O(MN^2)`,
where :math:`M` is the number of objectives and :math:`N` the number of
see [Deb2002]_. This algorithm has a time complexity of :math:`O(MN^2)`,
where :math:`M` is the number of objectives and :math:`N` the number of
individuals.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param first_front_only: If :obj:`True` sort only the first front and
exit.
:returns: A list of Pareto fronts (lists), the first list includes
:returns: A list of Pareto fronts (lists), the first list includes
nondominated individuals.
.. [Deb2002] Deb, Pratab, Agarwal, and Meyarivan, "A fast elitist
Expand All @@ -73,12 +73,12 @@ def sortNondominated(individuals, k, first_front_only=False):
for ind in individuals:
map_fit_ind[ind.fitness].append(ind)
fits = map_fit_ind.keys()

current_front = []
next_front = []
dominating_fits = defaultdict(int)
dominated_fits = defaultdict(list)

# Rank first Pareto front
for i, fit_i in enumerate(fits):
for fit_j in fits[i+1:]:
Expand All @@ -90,13 +90,13 @@ def sortNondominated(individuals, k, first_front_only=False):
dominated_fits[fit_j].append(fit_i)
if dominating_fits[fit_i] == 0:
current_front.append(fit_i)

fronts = [[]]
for fit in current_front:
fronts[-1].extend(map_fit_ind[fit])
pareto_sorted = len(fronts[-1])

# Rank the next front until all individuals are sorted or
# Rank the next front until all individuals are sorted or
# the given number of individual are sorted.
if not first_front_only:
N = min(len(individuals), k)
Expand All @@ -111,22 +111,22 @@ def sortNondominated(individuals, k, first_front_only=False):
fronts[-1].extend(map_fit_ind[fit_d])
current_front = next_front
next_front = []

return fronts

def assignCrowdingDist(individuals):
"""Assign a crowding distance to each individual's fitness. The
crowding distance can be retrieve via the :attr:`crowding_dist`
"""Assign a crowding distance to each individual's fitness. The
crowding distance can be retrieve via the :attr:`crowding_dist`
attribute of each individual's fitness.
"""
if len(individuals) == 0:
return

distances = [0.0] * len(individuals)
crowd = [(ind.fitness.values, i) for i, ind in enumerate(individuals)]

nobj = len(individuals[0].fitness.values)

for i in xrange(nobj):
crowd.sort(key=lambda element: element[0][i])
distances[crowd[0][1]] = float("inf")
Expand All @@ -148,14 +148,18 @@ def selTournamentDCD(individuals, k):
individuals, two consecutive individuals will be different (assuming all
individuals in the input list are unique). Each individual from the input
list won't be selected more than twice.
This selection requires the individuals to have a :attr:`crowding_dist`
attribute, which can be set by the :func:`assignCrowdingDist` function.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:returns: A list of selected individuals.
"""

if len(individuals)%4 !=0:
raise Exception("selTournamentDCD: individuals length must be a multiple of 4")

def tourn(ind1, ind2):
if ind1.fitness.dominates(ind2.fitness):
return ind1
Expand Down Expand Up @@ -194,7 +198,7 @@ def identity(obj):

def isDominated(wvalues1, wvalues2):
"""Returns whether or not *wvalues1* dominates *wvalues2*.
:param wvalues1: The weighted fitness values that would be dominated.
:param wvalues2: The weighted fitness values of the dominant.
:returns: :obj:`True` if wvalues2 dominates wvalues1, :obj:`False`
Expand All @@ -209,8 +213,8 @@ def isDominated(wvalues1, wvalues2):
return not_equal

def median(seq, key=identity):
"""Returns the median of *seq* - the numeric value separating the higher
half of a sample from the lower half. If there is an even number of
"""Returns the median of *seq* - the numeric value separating the higher
half of a sample from the lower half. If there is an even number of
elements in *seq*, it returns the mean of the two middle values.
"""
sseq = sorted(seq, key=key)
Expand All @@ -224,28 +228,28 @@ def sortLogNondominated(individuals, k, first_front_only=False):
"""Sort *individuals* in pareto non-dominated fronts using the Generalized
Reduced Run-Time Complexity Non-Dominated Sorting Algorithm presented by
Fortin et al. (2013).
:param individuals: A list of individuals to select from.
:returns: A list of Pareto fronts (lists), with the first list being the
true Pareto front.
"""
if k == 0:
return []

#Separate individuals according to unique fitnesses
unique_fits = defaultdict(list)
for i, ind in enumerate(individuals):
unique_fits[ind.fitness.wvalues].append(ind)

#Launch the sorting algorithm
obj = len(individuals[0].fitness.wvalues)-1
fitnesses = unique_fits.keys()
front = dict.fromkeys(fitnesses, 0)

# Sort the fitnesses lexicographically.
fitnesses.sort(reverse=True)
sortNDHelperA(fitnesses, obj, front)
sortNDHelperA(fitnesses, obj, front)

#Extract individuals from front list here
nbfronts = max(front.values())+1
pareto_fronts = [[] for i in range(nbfronts)]
Expand Down Expand Up @@ -318,7 +322,7 @@ def sweepA(fitnesses, front):
to the first two objectives using a geometric sweep procedure.
"""
stairs = [-fitnesses[0][1]]
fstairs = [fitnesses[0]]
fstairs = [fitnesses[0]]
for fit in fitnesses[1:]:
idx = bisect.bisect_right(stairs, -fit[1])
if 0 < idx <= len(stairs):
Expand All @@ -333,11 +337,11 @@ def sweepA(fitnesses, front):
fstairs.insert(idx, fit)

def sortNDHelperB(best, worst, obj, front):
"""Assign front numbers to the solutions in H according to the solutions
in L. The solutions in L are assumed to have correct front numbers and the
solutions in H are not compared with each other, as this is supposed to
"""Assign front numbers to the solutions in H according to the solutions
in L. The solutions in L are assumed to have correct front numbers and the
solutions in H are not compared with each other, as this is supposed to
happen after sortNDHelperB is called."""
key = itemgetter(obj)
key = itemgetter(obj)
if len(worst) == 0 or len(best) == 0:
#One of the lists is empty: nothing to do
return
Expand All @@ -351,7 +355,7 @@ def sortNDHelperB(best, worst, obj, front):
sweepB(best, worst, front)
elif key(min(best, key=key)) >= key(max(worst, key=key)):
#All individuals from L dominate H for objective M:
#Also supports the case where every individuals in L and H
#Also supports the case where every individuals in L and H
#has the same value for the current objective
#Skip to objective M-1
sortNDHelperB(best, worst, obj-1, front)
Expand All @@ -364,7 +368,7 @@ def sortNDHelperB(best, worst, obj, front):
def splitB(best, worst, obj):
"""Split both best individual and worst sets of fitnesses according
to the median of objective *obj* computed on the set containing the
most elements. The values equal to the median are attributed so as
most elements. The values equal to the median are attributed so as
to balance the four resulting sets as much as possible.
"""
median_ = median(best if len(best) > len(worst) else worst, itemgetter(obj))
Expand All @@ -379,8 +383,8 @@ def splitB(best, worst, obj):
else:
best1_a.append(fit)
best2_b.append(fit)
worst1_a, worst2_a, worst1_b, worst2_b = [], [], [], []

worst1_a, worst2_a, worst1_b, worst2_b = [], [], [], []
for fit in worst:
if fit[obj] > median_:
worst1_a.append(fit)
Expand All @@ -391,7 +395,7 @@ def splitB(best, worst, obj):
else:
worst1_a.append(fit)
worst2_b.append(fit)

balance_a = abs(len(best1_a) - len(best2_a) + len(worst1_a) - len(worst2_a))
balance_b = abs(len(best1_b) - len(best2_b) + len(worst1_b) - len(worst2_b))

Expand Down Expand Up @@ -441,11 +445,11 @@ def selSPEA2(individuals, k):
than sorting the population according to a strength Pareto scheme. The
list returned contains references to the input *individuals*. For more
details on the SPEA-II operator see [Zitzler2001]_.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:returns: A list of selected individuals.
.. [Zitzler2001] Zitzler, Laumanns and Thiele, "SPEA 2: Improving the
strength Pareto evolutionary algorithm", 2001.
"""
Expand All @@ -455,7 +459,7 @@ def selSPEA2(individuals, k):
strength_fits = [0] * N
fits = [0] * N
dominating_inds = [list() for i in xrange(N)]

for i, ind_i in enumerate(individuals):
for j, ind_j in enumerate(individuals[i+1:], i+1):
if ind_i.fitness.dominates(ind_j.fitness):
Expand All @@ -464,14 +468,14 @@ def selSPEA2(individuals, k):
elif ind_j.fitness.dominates(ind_i.fitness):
strength_fits[j] += 1
dominating_inds[i].append(j)

for i in xrange(N):
for j in dominating_inds[i]:
fits[i] += strength_fits[j]

# Choose all non-dominated individuals
chosen_indices = [i for i in xrange(N) if fits[i] < 1]

if len(chosen_indices) < k: # The archive is too small
for i in xrange(N):
distances = [0.0] * N
Expand All @@ -485,13 +489,13 @@ def selSPEA2(individuals, k):
kth_dist = _randomizedSelect(distances, 0, N - 1, K)
density = 1.0 / (kth_dist + 2.0)
fits[i] += density

next_indices = [(fits[i], i) for i in xrange(N)
if not i in chosen_indices]
next_indices.sort()
#print next_indices
chosen_indices += [i for _, i in next_indices[:k - len(chosen_indices)]]

elif len(chosen_indices) > k: # The archive is too large
N = len(chosen_indices)
distances = [[0.0] * N for i in xrange(N)]
Expand All @@ -506,7 +510,7 @@ def selSPEA2(individuals, k):
distances[i][j] = dist
distances[j][i] = dist
distances[i][i] = -1

# Insert sort is faster than quick sort for short arrays
for i in xrange(N):
for j in xrange(1, N):
Expand All @@ -515,7 +519,7 @@ def selSPEA2(individuals, k):
sorted_indices[i][l] = sorted_indices[i][l - 1]
l -= 1
sorted_indices[i][l] = j

size = N
to_remove = []
while size > k:
Expand All @@ -525,32 +529,32 @@ def selSPEA2(individuals, k):
for j in xrange(1, size):
dist_i_sorted_j = distances[i][sorted_indices[i][j]]
dist_min_sorted_j = distances[min_pos][sorted_indices[min_pos][j]]

if dist_i_sorted_j < dist_min_sorted_j:
min_pos = i
break
elif dist_i_sorted_j > dist_min_sorted_j:
break

# Remove minimal distance from sorted_indices
for i in xrange(N):
distances[i][min_pos] = float("inf")
distances[min_pos][i] = float("inf")

for j in xrange(1, size - 1):
if sorted_indices[i][j] == min_pos:
sorted_indices[i][j] = sorted_indices[i][j + 1]
sorted_indices[i][j + 1] = min_pos

# Remove corresponding individual from chosen_indices
to_remove.append(min_pos)
size -= 1

for index in reversed(sorted(to_remove)):
del chosen_indices[index]

return [individuals[i] for i in chosen_indices]

def _randomizedSelect(array, begin, end, i):
"""Allows to select the ith smallest element from array without sorting it.
Runtime is expected to be O(n).
Expand All @@ -568,7 +572,7 @@ def _randomizedPartition(array, begin, end):
i = random.randint(begin, end)
array[begin], array[i] = array[i], array[begin]
return _partition(array, begin, end)

def _partition(array, begin, end):
x = array[begin]
i = begin - 1
Expand Down

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