From 68ae32eff8416d13fdcf5b890976790934cc22b8 Mon Sep 17 00:00:00 2001
From: Giuseppe Chindemi <giuseppe.chindemi@epfl.ch>
Date: Mon, 9 May 2016 11:07:47 +0200
Subject: [PATCH] Added support for elitism

---
 bluepyopt/deapext/algorithms.py    | 14 +++++++++++++-
 bluepyopt/deapext/optimisations.py |  9 +++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/bluepyopt/deapext/algorithms.py b/bluepyopt/deapext/algorithms.py
index bd247a2..e4f5f3f 100644
--- a/bluepyopt/deapext/algorithms.py
+++ b/bluepyopt/deapext/algorithms.py
@@ -28,6 +28,7 @@
 import deap.algorithms
 import deap.tools
 import pickle
+import numpy
 
 logger = logging.getLogger('__main__')
 
@@ -69,6 +70,14 @@ def _get_offspring(parents, toolbox, cxpb, mutpb):
     return deap.algorithms.varAnd(parents, toolbox, cxpb, mutpb)
 
 
+def _get_elite(halloffame, nelite):
+    if nelite > 0 and halloffame is not None:
+        normsorted_idx = numpy.argsort([ind.fitness.norm for ind in halloffame])
+        # Return nelite best individuals
+        return [halloffame[idx] for idx in normsorted_idx[:nelite]]
+    return list()
+
+
 def eaAlphaMuPlusLambdaCheckpoint(
         population,
         toolbox,
@@ -78,6 +87,7 @@ def eaAlphaMuPlusLambdaCheckpoint(
         ngen,
         stats=None,
         halloffame=None,
+        nelite=0,
         cp_frequency=1,
         cp_filename=None,
         continue_cp=False):
@@ -92,6 +102,8 @@ def eaAlphaMuPlusLambdaCheckpoint(
         ngen(int): Total number of generation to run
         stats(deap.tools.Statistics): generation of statistics
         halloffame(deap.tools.HallOfFame): hall of fame
+        nelite(int): Total number of individuals added to population at every
+                     generation from hall of fame
         cp_frequency(int): generations between checkpoints
         cp_filename(string): path to checkpoint filename
         continue_cp(bool): whether to continue
@@ -131,7 +143,7 @@ def eaAlphaMuPlusLambdaCheckpoint(
         _record_stats(stats, logbook, gen, population, invalid_count)
 
         # Select the next generation parents
-        parents = toolbox.select(population, mu)
+        parents = toolbox.select(population + _get_elite(halloffame, nelite), mu)
 
         logger.info(logbook.stream)
 
diff --git a/bluepyopt/deapext/optimisations.py b/bluepyopt/deapext/optimisations.py
index 3985ef6..f17625c 100644
--- a/bluepyopt/deapext/optimisations.py
+++ b/bluepyopt/deapext/optimisations.py
@@ -25,6 +25,7 @@
 import random
 import logging
 import functools
+import numpy
 
 import deap
 import deap.base
@@ -62,6 +63,11 @@ def sum(self):
         """Weighted sum of values"""
         return sum(self.values)
 
+    @property
+    def norm(self):
+        """Frobenius norm of values"""
+        return numpy.linalg.norm(self.values)
+
     def __le__(self, other):
         return self.weighted_sum <= other.weighted_sum
 
@@ -96,6 +102,7 @@ def __init__(self, evaluator=None,
                  use_scoop=False,
                  seed=1,
                  offspring_size=10,
+                 elite_size=0,
                  eta=10,
                  mutpb=1.0,
                  cxpb=1.0,
@@ -107,6 +114,7 @@ def __init__(self, evaluator=None,
         self.use_scoop = use_scoop
         self.seed = seed
         self.offspring_size = offspring_size
+        self.elite_size = elite_size
         self.eta = eta
         self.cxpb = cxpb
         self.mutpb = mutpb
@@ -254,6 +262,7 @@ def run(self,
             max_ngen,
             stats=stats,
             halloffame=hof,
+            nelite=self.elite_size,
             cp_frequency=cp_frequency,
             continue_cp=continue_cp,
             cp_filename=cp_filename)