def DNAfill(self, Nucleotides):
" fills the DNA with given Nucleotides "
self.__dna = Nucleotides[:] # important: make a ground copy
if len(Nucleotides) > 0 and len(Nucleotides) != self.nb_nucleotides:
Tools.error('DNA: initialization','Provided genome length does not match gene map')
if len(Nucleotides) > 0 and not set(Nucleotides) <= set([0,1]):
Tools.error('DNA: initialization','Provided genome is not binary')
def nextNode(self, node, visited):
""" Finds next node from the node in argument """
if len(visited) > self.size: # the length of the trip before the last step cannot be greater than the number of nodes
ET.error('nextNode', 'Unexpected behavior')
return None
elif len(visited) == self.size: # the trip ends so we go to the first node
return visited[0]
else:
attractions = []
for n in self.nodes:
if n not in visited:
if Gbl.Parameter('PheromoneInfluence') > 0:
pheromoneInfluence = self.pheromones.getValue(node, n) ** Gbl.Parameter('PheromoneInfluence')
else:
pheromoneInfluence = 1
if Gbl.Parameter('DistanceInfluence') > 0:
distanceInfluence = self.distances.getValue(node, n) ** Gbl.Parameter('DistanceInfluence')
else:
distanceInfluence = 1
attractions.append((pheromoneInfluence / distanceInfluence, n))
return max(attractions)[1]
def __init__(self, Size=100, nbNodes=0):
#self.TestMessages = [] # Messages used to test the efficiency of the network
margin = 5 if Size > 20 else 0
self.nodes = []
self.currentLength = 0
if Gbl.Parameter('RandomNetwork') and nbNodes > 1:
self.nodes = [Node('N%d' % i, (random.randint(margin, Size-margin), random.randint(margin, Size-margin))) for i in range(nbNodes)]
else:
# loading network from file
# file format:
# Name1 x1 y1
# Name2 x2 y2
# ...
try:
for Line in open(Gbl.Parameter('NetworkFileName'), 'r', 1): # read one line at a time
NodeDef = Line.split()
self.nodes.append(Node(NodeDef[0], tuple(map(int, NodeDef[1:]))))
except IOError: ET.error('Unable to find Network description', Gbl.Parameter('NetworkFileName'))
self.size = len(self.nodes)
for n in self.nodes:
print "%s %d %d" % (n.name, n.getX(), n.getY())
self.distances = Distances(self.nodes)
self.pheromones = Pheromones(self.nodes)
def __init__(self, Size=100, NbNodes=0, NetworkFileName=None):
self.TestMessages = [
] # Messages used to test the efficiency of the network
margin = 5 if Size > 20 else 0
self.NodeNames = {}
self.Nodes = []
self.Links = []
if Gbl.Parameter('RandomNetwork') and NbNodes > 1:
self.Nodes = [
Node('N%d' % i, (random.randint(margin, Size - margin),
random.randint(margin, Size - margin)))
for i in range(NbNodes)
]
if NbNodes > 1:
for n in self.Nodes:
OtherNodes = self.Nodes[:]
OtherNodes.remove(n) # does not need to be efficient
if OtherNodes:
self.Links.append((n, random.choice(OtherNodes)))
self.Links.append((n, random.choice(OtherNodes)))
self.Links = list(set(self.Links)) # to remove duplicates
self.NodeNames = dict([(n.Name, n) for n in self.Nodes])
else: # loading network from file
# file format:
# Name1 x1 y1
# Name2 x2 y2
# ...
# Link NameA NameB C (C = capacity)
# ...
# ('Link' = keyword)
LinkDefinitions = []
try:
for Line in open(Gbl.Parameter('NetworkFileName'), 'r',
1): # read one line at a time
Link = re.match('(?i)link\s+(.*)', Line)
if Link is not None:
LinkDefinitions.append(Link.group(1).split())
elif Line:
NodeDef = Line.split()
self.Nodes.append(
Node(NodeDef[0], tuple(map(int, NodeDef[1:]))))
self.NodeNames[NodeDef[0]] = self.Nodes[-1]
except IOError:
ET.error('Unable to find Network description',
Gbl.Parameter('NetworkFileName'))
for L in LinkDefinitions:
self.Links.append((
self.NodeNames[L[0]],
self.NodeNames[L[1]],
))
for N in self.Nodes:
print(N)
self.Size = len(self.Nodes)
self.TestMessages = [Message('M1', self.Nodes[0], self.Nodes[1])]
# Creating routing tables
for n in self.Nodes:
n.CreateTable(self.Nodes, self.Neighbours(n))
def interaction(self, indiv, partner):
" Interaction between individuals "
PerceivedSignal = ET.noise_mult(partner.signal(), self['Noise'])
PartnerPerceivedSignal = ET.noise_mult(indiv.signal(), self['Noise'])
#indiv.get_friend(PerceivedSignal, partner, PartnerPerceivedSignal)
# Suppression du gene Demande : bruit ???
#return
if PerceivedSignal >= indiv.demand() and PartnerPerceivedSignal >= partner.demand():
indiv.acquainted(partner)
def NextNode(self, Target, deterministic=False): " determines the most attractive neighbouring node when heading to Target" if len(self.Table): if deterministic: return max([(self.Table[Target][n], n) for n in self.Table[Target]])[1] return self.Table[Target].keys()[ET.fortune_wheel(self.Table[Target].values())] return None
def NextNode(self, Target, deterministic=False):
" determines the most attractive neighbouring node when heading to Target"
if len(self.Table):
if deterministic:
return max([(self.Table[Target][n], n)
for n in self.Table[Target]])[1]
return list(self.Table[Target].keys())[ET.fortune_wheel(
self.Table[Target].values())]
return None
def __init__(self, Size=100, NbNodes=0, NetworkFileName=None):
self.TestMessages = [] # Messages used to test the efficiency of the network
margin = 5 if Size > 20 else 0
self.NodeNames = {}
self.Nodes = []
self.Links = []
if Gbl.Parameter('RandomNetwork') and NbNodes > 1:
self.Nodes = [Node('N%d' % i, (random.randint(margin, Size-margin), random.randint(margin, Size-margin))) for i in range(NbNodes)]
if NbNodes > 1:
for n in self.Nodes:
OtherNodes = self.Nodes[:]
OtherNodes.remove(n) # does not need to be efficient
if OtherNodes:
self.Links.append((n, random.choice(OtherNodes)))
self.Links.append((n, random.choice(OtherNodes)))
self.Links = list(set(self.Links)) # to remove duplicates
self.NodeNames = dict([(n.Name, n) for n in self.Nodes])
else: # loading network from file
# file format:
# Name1 x1 y1
# Name2 x2 y2
# ...
# Link NameA NameB C (C = capacity)
# ...
# ('Link' = keyword)
LinkDefinitions = []
try:
for Line in open(Gbl.Parameter('NetworkFileName'), 'r', 1): # read one line at a time
Link = re.match('(?i)link\s+(.*)', Line)
if Link is not None: LinkDefinitions.append(Link.group(1).split())
elif Line:
NodeDef = Line.split()
self.Nodes.append(Node(NodeDef[0], tuple(map(int, NodeDef[1:]))))
self.NodeNames[NodeDef[0]] = self.Nodes[-1]
except IOError: ET.error('Unable to find Network description', Gbl.Parameter('NetworkFileName'))
for L in LinkDefinitions:
self.Links.append((self.NodeNames[L[0]],self.NodeNames[L[1]],))
for N in self.Nodes: print N
self.Size = len(self.Nodes)
self.TestMessages = [Message('M1', self.Nodes[0], self.Nodes[1])]
# Creating routing tables
for n in self.Nodes: n.CreateTable(self.Nodes, self.Neighbours(n))
def Sniff(self): " Looks for the next place to go " # The ant makes a biased choice of its next location # More probable links leading from neighbouring nodes to the ant's origin are more likely to be chosen Neighbours = self.location.Neighbours[:] if self.Origin in Neighbours: Neighbours.remove(self.Origin) Probabilities = [n.Table[self.Origin][self.location] for n in Neighbours] if Probabilities: NodeRank = ET.fortune_wheel(Probabilities) # chooses a neighbour based on probabilities return Neighbours[NodeRank] return None
def learning(self):
for agent in self.Pop: agent.assessment() # storing current scores (with possible cross-benefits)
# some agents learn
Learners = sample(self.Pop, ET.chances(self.Param('LearningProbability')/100.0, len(self.Pop)))
for agent in self.Pop:
agent.wins(agent.Points) # Stores points for learning
if agent in Learners:
if not agent.Learns(self.neighbours(agent), hot=self.Obs.hot_phase()):
# agent.update() # this is a newborn - update position for display
pass
agent.update() # update position for display
def learning(self):
for agent in self.Pop: agent.assessment() # storing current scores (with possible cross-benefits)
# some agents learn
Learners = sample(self.Pop, ET.chances(self.Param('LearningProbability')/100.0, len(self.Pop)))
for agent in self.Pop:
agent.wins(agent.Points) # Stores points for learning
if agent in Learners:
if not agent.Learns(self.neighbours(agent), hot=self.Obs.hot_phase()):
# agent.update() # this is a newborn - update position for display
pass
agent.update() # update position for display
def mutate(self, mutation_rate = -1):
" computing the expected number of mutations "
if mutation_rate < 0: mutation_rate = self.Scenario.Parameter('MutationRate')
mutation_number = Tools.chances(mutation_rate/1000.0, self.nb_nucleotides)
## mutation_number = (mutation_rate * self.nb_nucleotides) / 1000
## if randint(1,1000) < 1 + ((mutation_rate * self.nb_nucleotides) % 1000) :
## mutation_number += 1
# performing mutations
for mutation in range(mutation_number):
pos = random.randint(0, self.nb_nucleotides - 1)
self.__dna[pos] = 1 - self.__dna[pos]
return mutation_number
def Sniff(self):
" Looks for the next place to go "
# The ant makes a biased choice of its next location
# More probable links leading from neighbouring nodes to the ant's origin are more likely to be chosen
Neighbours = self.location.Neighbours[:]
if self.Origin in Neighbours: Neighbours.remove(self.Origin)
Probabilities = [
n.Table[self.Origin][self.location] for n in Neighbours
]
if Probabilities:
NodeRank = ET.fortune_wheel(
Probabilities) # chooses a neighbour based on probabilities
return Neighbours[NodeRank]
return None
def read_DNA(self, start, end, coding = None):
" reads a chunk of DNA "
if coding == None: coding = self.Scenario.Parameter('GeneCoding')
if coding in range(-1,3):
# old numeric designation of coding
coding = ['NoCoding', 'Weighted', 'Unweighted', 'Gray'][coding+1]
value = 0
if coding == 'NoCoding':
return 0
if coding not in ['Weighted', 'Unweighted', 'Gray']:
Tools.error("DNA", 'unknown binary coding mode')
try:
for pos in range(start,end):
if coding == 'Unweighted':
value += self.__dna[pos]
else: # Weighted or Gray
## value += self.__dna[pos]* 2 ** (end - 1 - pos)
value += (self.__dna[pos] << (end - 1 - pos))
if coding == 'Gray':
value = Tools.GrayTable.Gray2Int(value)
return(value)
except IndexError:
Tools.error("DNA", "reading outside the DNA")
def Sniff(self):
" Looks for the next place to go "
DirectionToTarget = cmath.phase(t2c(self.Target) - t2c(self.location)) # argument
DirectionToTarget = ET.noise_add(DirectionToTarget, 0.02*cmath.pi * Gbl.Parameter('Noise'))
# Distance0 = abs(DirectionToTarget)
Neighbourhood = list(Land.neighbours(self.location, Gbl.Parameter('SniffingDistance')))
random.shuffle(Neighbourhood) # to avoid anisotropy
acceptable = None
best = -Gbl.Parameter('Saturation') # best == pheromone balance found so far
for NewPos in Neighbourhood:
if NewPos == self.location: continue
# Target attractiveness
Direction = cmath.phase(t2c(NewPos) - t2c(self.location))
Value = Gbl.Parameter('TargetAttractiveness') * abs(cmath.pi - abs(DirectionToTarget - Direction))
# looking for position with pheromone
# attractiveness of pheromone
Value += Gbl.Parameter('PheromoneAttractiveness') * float(Land.pheromone(NewPos)) / Gbl.Parameter('Saturation')
# Value += Gbl.Parameter('PheromoneAttractiveness') * (Land.pheromone(NewPos))
# aversion to climbing
Value -= Gbl.Parameter('SlopeAversion') * abs(Land.Altitude(NewPos) - Land.Altitude(self.location))
if Value > best:
acceptable = NewPos
best = Value
return acceptable
def Sniff(self):
" Looks for the next place to go "
DirectionToTarget = cmath.phase(t2c(self.Target) - t2c(self.location)) # argument
DirectionToTarget = ET.noise_add(DirectionToTarget, 0.02*cmath.pi * Gbl.Parameter('Noise'))
# Distance0 = abs(DirectionToTarget)
Neighbourhood = Land.neighbours(self.location, Gbl.Parameter('SniffingDistance'))
random.shuffle(Neighbourhood) # to avoid anisotropy
acceptable = None
best = -Gbl.Parameter('Saturation') # best == pheromone balance found so far
for NewPos in Neighbourhood:
if NewPos == self.location: continue
# Target attractiveness
Direction = cmath.phase(t2c(NewPos) - t2c(self.location))
Value = Gbl.Parameter('TargetAttractiveness') * abs(cmath.pi - abs(DirectionToTarget - Direction))
# looking for position with pheromone
# attractiveness of pheromone
Value += Gbl.Parameter('PheromoneAttractiveness') * float(Land.pheromone(NewPos)) / Gbl.Parameter('Saturation')
# Value += Gbl.Parameter('PheromoneAttractiveness') * (Land.pheromone(NewPos))
# aversion to climbing
Value -= Gbl.Parameter('SlopeAversion') * abs(Land.Altitude(NewPos) - Land.Altitude(self.location))
if Value > best:
acceptable = NewPos
best = Value
return acceptable
import sys
from time import sleep
import random
sys.path.append('..')
sys.path.append('../../..')
import Evolife.Scenarii.Parameters as EPar
import Evolife.Ecology.Observer as EO
import Evolife.Ecology.Individual as EI
import Evolife.Ecology.Group as EG
import Evolife.Ecology.Population as EP
import Evolife.QtGraphics.Evolife_Window as EW
import Evolife.Tools.Tools as ET
print(ET.boost()) # significantly accelerates python on some platforms
from Antnet import Antnet_Observer, Node, Network, Ant, Group, Population
#################################################
# Aspect of ants, food and pheromons on display
#################################################
LinkAspect = ('green5', 2) # 2 = thickness
AntAspect = ('black', 5) # 4 = size
AntAspectWhenOld = ('red5', 4) # 4 = size
PPAspect = (17, 2) # 17th colour
class City(Node):
def __init__(self, Name, Location):
Node.__init__(self, Name, Location)
# -------------------------------------------------------------------------- #
# License: Creative Commons BY-NC-SA #
##############################################################################
""" 2D Cellular Automaton with coloring mutation:
Modified by Cybill Clerger
"""
import sys
sys.path.append('../../..')
import Evolife.Ecology.Observer as EO
import Evolife.QtGraphics.Evolife_Window as EW
import Evolife.Tools.Tools as ET
import Evolife.Scenarii.Parameters as EPar
print ET.boost(
) # A technical trick that sometimes provides impressive speeding up
import random
import math
class Rule:
" defines all possible automaton rules "
def __init__(self, RuleNumber):
" convert the rule number into a list of bits "
# For each configuration number (9-bit for nine-cell neighbourhood --> 512 configurations),
# the rule gives the new binary state of the cell.
self.Rule = [int(b) for b in list(bin(RuleNumber)[2:].rjust(512, '0'))]
self.Rule.reverse()
# if this configuration is absent at the beginning, an all-0 state emerges.
Evolife.QtGraphics.Evolife_Batch.Start(Population.One_Run, Observer)
# writing header to result file
open(Observer.get_info('ResultFile')+'.res','w').write(Observer.get_info('ResultHeader'))
return
####################
# Interactive mode
####################
print __doc__
" launching window "
# Evolife.QtGraphics.Evolife_Window.Start(Pop.One_Run, Observer, Capabilities='FNCP', Options=[('BackGround','grey')])
Evolife.QtGraphics.Evolife_Window.Start(Population.One_Run, Observer, Capabilities='FNCP', Options=[('BackGround','lightblue')])
print "Bye......."
sleep(2.1)
return
if __name__ == "__main__":
ET.boost() # A technical trick that sometimes provides impressive speeding up with Python up to 2.6
Observer = Social_Observer(Gbl.Parameters) # Observer contains statistics
Observer.setOutputDir('___Results')
Observer.recordInfo('DefaultViews', ['Field', 'Network']) # Evolife should start with that window open
Pop = Population(Gbl.Param('NbAgents'), Observer) # population of agents
Start(BatchMode=Gbl.Param('BatchMode'))
__author__ = 'Dessalles'
def recordChanges(self, Info, Slot='Positions'):
# stores current changes
# Info is a couple (InfoName, Position) and Position == (x,y) or a longer tuple
if Slot == 'Positions': self.Positions.append(Info)
elif Slot == 'Trajectories': self.Trajectories.append(Info)
else: ET.error('Antnet Observer', 'unknown slot')
def recordChanges(self, Info, Slot='Positions'):
# stores current changes
# Info is a couple (InfoName, Position) and Position == (x,y) or a longer tuple
if Slot == 'Positions': self.Positions.append(Info)
elif Slot == 'Trajectories': self.Trajectories.append(Info)
else: ET.error('Antnet Observer', 'unknown slot')
""" Cellular Automaton:
"""
import sys
sys.path.append('../../..')
import Evolife.Ecology.Observer as EO
import Evolife.QtGraphics.Evolife_Window as EW
import Evolife.Tools.Tools as ET
import Evolife.Scenarii.Parameters as EPar
print ET.boost() # A technical trick that sometimes provides impressive speeding up
import random
class Rule:
" defines all possible automaton rules "
def __init__(self, RuleNumber):
" convert the rule number into a list of bits "
# For each configuration number (3-bit for three-cell neighbourhood --> 8 configurations),
# the rule gives the new binary state of the cell.
# Attention: the following line is only valid for 8 configurations
self.Rule = [int(b) for b in list(bin(RuleNumber)[2:].rjust(8,'0'))]
# example: rule 32 --> 00100000
self.Rule.reverse()
# example: rule 32 --> 00000100
def Neighbours(self, Node):
if not Node in self.Nodes: ET.error('Network', 'Non existing node has no neighbours')
return [n for n in self.Nodes if (Node, n) in self.Links]
for M in Ntwrk.TestMessages:
for link in M.erase():
Observer.recordChanges(
link, Slot='Trajectories') # display of message route
Route = M.draw(MaxPath=Ntwrk.Size)
self.Observer.MsgLength[M] = len(Route)
for link in Route:
Observer.recordChanges(
link, Slot='Trajectories') # display of message route
# print (year, self.AllMoved, Moves),
return self.SimulationEnd > 0 # stops the simulation when True
if __name__ == "__main__":
print(__doc__)
print(ET.boost()) # significantly accelerates python on some platforms
#############################
# Global objects #
#############################
Gbl = EPar.Parameters('_Params.evo') # Loading global parameter values
Observer = Antnet_Observer(Gbl) # Observer contains statistics
Ntwrk = Network(Size=Gbl.Parameter('DisplaySize'),
NbNodes=Gbl.Parameter('NumberOfNodes'))
Pop = AntPopulation(Gbl, Observer, Ntwrk.nodes()) # Ant colony
# Initial draw
Observer.recordInfo('FieldWallpaper', 'yellow')
Observer.recordInfo('TrajectoriesWallpaper', 'lightblue')
Observer.recordInfo('DefaultViews', ['Field', 'Trajectories'])
Observer.recordChanges(
from time import sleep
import random
import cmath
sys.path.append('..')
sys.path.append('../../..')
import Evolife.Scenarii.Parameters as EPar
import Evolife.Ecology.Observer as EO
import Evolife.Ecology.Individual as EI
import Evolife.Ecology.Group as EG
import Evolife.Ecology.Population as EP
import Evolife.QtGraphics.Evolife_Window as EW
import Evolife.Tools.Tools as ET
import Landscapes
print ET.boost() # significWalkerly accelerates python on some platforms
# two functions to convert from complex numbers into (x,y) coordinates
c2t = lambda c: (int(round(c.real)),int(round(c.imag))) # converts a complex into a couple
t2c = lambda (x,y): complex(x,y) # converts a couple into a complex
#################################################
# Aspect of Walkers and pheromone on display
#################################################
# WalkerAspect = ('black', 6)
# PheromonAspect = (17, 2)
WalkerAspect = ('white', 1)
PheromonAspect = ('white', 4)
