def evaluate_individual(self, genome):
""" Evaluate an individual solution.
Args:
genome: genome of the individual to evaluate
Returns:
fitness value of the individual
"""
global man, current_network, quadruped
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback,
stepsize=self.dt / self.n,
log_data=self.log_frames)
# Initialize the quadruped
quadruped = Quadruped(man=man)
# Load in the ANN from the population
self.current_network = NEAT.NeuralNetwork()
if not self.hyperNEAT:
genome.BuildPhenotype(self.current_network)
else:
genome.BuildHyperNEATPhenotype(self.current_network,
self.substrate)
# Conduct the evaluation
fit = self.physics_only_simulation()
#print(genome.GetID(), fit)
return fit, len(self.current_network.neurons), len(
self.current_network.connections)
def evaluate_individual(individual):
""" Wrapper to call Simulation which will evaluate an individual.
Args:
individual: arguments to pass to the simulation
Returns:
fitness of an individual
"""
log_frames = GlobalVarWorkaround.args.log_frames
run_num = GlobalVarWorkaround.args.run_num
eval_time = GlobalVarWorkaround.args.eval_time
dt = .02
n = 4
GlobalVarWorkaround.man = ODEManager(my_worm_simulation.near_callback,
stepsize=dt / n,
log_data=log_frames,
fluid_dynamics=1,
gravity=0)
GlobalVarWorkaround.worm = my_worm_simulation.Worm(
man=GlobalVarWorkaround.man,
morphology_genome=individual[1],
num_joints=7,
logging=log_frames)
simulation = my_worm_simulation.Simulation(eval_time,
dt=dt,
n=n,
man=GlobalVarWorkaround.man,
worm=GlobalVarWorkaround.worm)
return simulation.evaluate_individual(individual)
def validator(self, NEAT_file):
""" Validate a single run.
Args:
NEAT_File: file for the NEAT genome
"""
global man, quadruped
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback,
stepsize=self.dt / self.n,
log_data=self.log_frames,
run_num=self.run_num)
# Initialize the quadruped
quadruped = Quadruped(man=man)
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
if self.log_frames:
man.log_world_setup(self.eval_time, ind_num=self.run_num)
# Load in the best performing NEAT genome
genome = NEAT.Genome(NEAT_file)
self.current_network = NEAT.NeuralNetwork()
if not self.hyperNEAT:
genome.BuildPhenotype(self.current_network)
else:
genome.BuildHyperNEATPhenotype(self.current_network,
self.substrate)
fit = self.physics_only_simulation_validator()
print(fit)
def debug_validator(self):
""" Validate a single run. """
global man, worm
if self.aquatic:
grav = 0
fluid_dyn = 1
else:
grav = -9.81
fluid_dyn = 0
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback,
stepsize=self.dt / self.n,
log_data=self.log_frames,
run_num=self.run_num,
gravity=grav,
fluid_dynamics=fluid_dyn)
# Initialize the worm
worm = Worm(man=man, num_joints=self._num_joints)
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
if self.log_frames:
man.log_world_setup(self.eval_time, ind_num=self.run_num)
fit = self.physics_only_simulation_validator()
print(fit)
def __init__(self, log_frames=0, run_num=0, eval_time=10., dt=.02, n=4, con_type="single",hyperNEAT=False,substrate=False,periodic=True,sym_mus_mods=False):
""" Initialize the simulation class. """
global simulate
man = ODEManager(near_callback, stepsize=dt/n, log_data=log_frames, run_num=run_num)
# Settings for the simulation.
self.log_frames = log_frames
self.run_num = run_num
self.eval_time = eval_time
self.elapsed_time = 0.
self.dt = dt # Timestep for simulation.
self.n = n # How many timesteps to simulate per callback.
# Quadruped Specific Setup
quadruped = Quadruped(man=man)
self.current_network = 0
self.cur_mus_net = 0
self.hyperNEAT = True if hyperNEAT else False
self.substrate = substrate
self.ann_mus_mod_con_type = con_type
# Whether we include a periodic oscillating input signal.
self.periodic = periodic
# Whether the Muscle Models are symmetric (Same mus groups just mirrored left/right or not.)
self.sym_mus_mods = sym_mus_mods
def validator(self):
""" Validate a single run.
Args:
NEAT_File: file for the NEAT genome
"""
global man, test_setup
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback,
gravity=0,
stepsize=self.dt / self.n,
log_data=self.log_frames,
run_num=self.run_num)
# Initialize the quadruped
test_setup = Test_Setup(man=man)
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
if self.log_frames:
man.log_world_setup(self.eval_time, ind_num=self.run_num)
fit = self.physics_only_simulation_validator()
print(fit)
def __init__(self,
log_frames=0,
run_num=0,
eval_time=10.,
dt=.02,
n=4,
con_type="single",
hyperNEAT=False,
substrate=False,
periodic=True,
num_joints=1,
aquatic=False):
""" Initialize the simulation class. """
global simulate
# Whether or not we simulate in the aquatic environment or not.
self.aquatic = aquatic
if self.aquatic:
grav = 0
fluid_dyn = 1
else:
grav = -9.81
fluid_dyn = 0
man = ODEManager(near_callback,
stepsize=dt / n,
log_data=log_frames,
run_num=run_num,
gravity=grav,
fluid_dynamics=fluid_dyn)
# Settings for the simulation.
self.log_frames = log_frames
self.run_num = run_num
self.eval_time = eval_time
self.elapsed_time = 0.
self.dt = dt # Timestep for simulation.
self.n = n # How many timesteps to simulate per callback.
self._num_joints = num_joints
# Worm Specific Setup
worm = ""
self.current_network = 0
self.hyperNEAT = True if hyperNEAT else False
self.substrate = substrate
# Whether we include a periodic oscillating input signal.
self.periodic = periodic
# Check for explosions
self.exploded = False
def eval_ribbot(individual):
"""Evaluate Ribbot for distance traveled.
"""
log_frames = False
dt = .02
n = 4
run_num = GlobalVarWorkaround.args.run_num
eval_time = GlobalVarWorkaround.args.eval_time
num_joints = GlobalVarWorkaround.args.num_joints
AMP, FRQ, PHS = 0, 1, 2
# Extract genes
amps = individual[AMP] #individual[AMP:AMP + NUM_JOINTS]
frqs = individual[FRQ] #individual[FRQ:FRQ + NUM_JOINTS]
phss = individual[PHS] #individual[PHS:]
bias = 0 #[0] * NUM_JOINTS
GlobalVarWorkaround.man = ODEManager(simulation.near_callback,
stepsize=dt / n,
log_data=log_frames,
fluid_dynamics=1,
gravity=0,
run_num=run_num)
GlobalVarWorkaround.worm = simulation.Worm(man=GlobalVarWorkaround.man,
num_joints=num_joints,
logging=log_frames)
print '--amps:' + str(amps) + ' frqs:' + str(frqs) + ' phss:' + str(phss)
jointctrlers = [
simulation.JointActuationController(amplitude=amps,
frequency=frqs,
phaseshift=phss,
offset=bias)
for i in range(num_joints - 8)
]
simulationobj = simulation.Simulation(eval_time,
dt=dt,
n=n,
man=GlobalVarWorkaround.man,
worm=GlobalVarWorkaround.worm,
jointctrlers=jointctrlers)
fit = simulationobj.evaluate_individual()
print '--fit=' + str(fit)
fitness = fit[0] # reward only distance traveled in positive x direction
return fitness,
def validator(NEAT_file, Morph_file, log_frames, run_num, eval_time, dt, n,
num_joints, output_path, gennumber, eucquad):
genome = [0, {}]
# Load in the best performing NEAT genome
genome[0] = NEAT.Genome(NEAT_file)
# Load the morphology
with open(Morph_file, "r") as f:
line = f.readline()
line = line.strip().split(',')
genome[1][0] = float(line[0]) # read frequency
GlobalVarWorkaround.man = ODEManager(near_callback,
stepsize=dt / n,
log_data=log_frames,
fluid_dynamics=1,
gravity=0,
run_num=run_num)
GlobalVarWorkaround.worm = Worm(man=GlobalVarWorkaround.man,
morphology_genome=genome[1],
num_joints=num_joints,
logging=log_frames,
log_path=output_path,
logfileprefix='rep' + str(run_num) +
'_gen' + str(gennumber))
GlobalVarWorkaround.foodenv = FoodEnvironment(man=GlobalVarWorkaround.man,
square_size=40,
eucquadrant=eucquad)
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
# Must be placed after creating the quadruped.
if log_frames:
GlobalVarWorkaround.man.log_world_setup(eval_time, ind_num=run_num)
simulation = Simulation(eval_time,
dt=dt,
n=n,
man=GlobalVarWorkaround.man,
worm=GlobalVarWorkaround.worm)
#simulation.current_network = NEAT.NeuralNetwork()
#genome[0].BuildPhenotype(simulation.current_network)
fit = simulation.evaluate_individual(genome)
print(fit)
def debug_validator(self):
""" Validate a single run. """
global man, quadruped
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback, stepsize=self.dt/self.n, log_data=self.log_frames, run_num=self.run_num)
# Initialize the quadruped
quadruped = Quadruped(man=man)
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
if self.log_frames:
man.log_world_setup(self.eval_time,ind_num=self.run_num)
fit = self.physics_only_simulation_validator()
print(fit)
def __init__(self, log_frames=0, run_num=0, eval_time=10., dt=.002, n=4):
""" Initialize the simulation class. """
global simulate
man = ODEManager(near_callback,
stepsize=dt / n,
log_data=log_frames,
run_num=run_num)
# Settings for the simulation.
self.log_frames = log_frames
self.run_num = run_num
self.eval_time = eval_time
self.elapsed_time = 0.
self.dt = dt # Timestep for simulation.
self.n = n # How many timesteps to simulate per callback.
# Quadruped Specific Setup
test_setup = Test_Setup(man=man)
def validator(self,NEAT_file,Morph_file):
""" Validate a single run.
Args:
NEAT_File: file for the NEAT genome
Morph_file: file for the morphology components
"""
global man, quadruped
self.validating = True
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback, stepsize=self.dt/self.n, log_data=self.log_frames, run_num=self.run_num,erp=0.5,cfm=1E-2)
genome = [0,{}]
if NEAT_file:
# Load in the best performing NEAT genome
genome[0] = NEAT.Genome(NEAT_file)
self.current_network = NEAT.NeuralNetwork()
if not self.hyperNEAT:
genome[0].BuildPhenotype(self.current_network)
else:
genome[0].BuildHyperNEATPhenotype(self.current_network,self.substrate)
if Morph_file:
with open(Morph_file,"r") as f:
line = f.readline()
line = line.strip().split(',')
genome[1]['erp'] = float(line[0])
genome[1]['cfm'] = float(line[1])
# Initialize the quadruped
quadruped = Quadruped(man=man,morphology_genome={'erp':genome[1]['erp'],'cfm':genome[1]['cfm']})
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
# Must be placed after creating the quadruped.
if self.log_frames:
man.log_world_setup(self.eval_time,ind_num=self.run_num)
fit = self.physics_only_simulation_validator()
return self.ann_activations,self.joint_feedback
def evaluate_individual(self, genome):
""" Evaluate an individual solution.
Args:
genome: genome of the individual to evaluate
Returns:
fitness value of the individual
"""
global man, current_network, worm
if self.aquatic:
grav = 0
fluid_dyn = 1
else:
grav = -9.81
fluid_dyn = 0
# Initialize the manager to be unique to the process.
man = ODEManager(near_callback,
stepsize=self.dt / self.n,
log_data=self.log_frames,
gravity=grav,
fluid_dynamics=fluid_dyn)
# Initialize the worm
worm = Worm(man=man, num_joints=self._num_joints)
# Load in the ANN from the population
self.current_network = NEAT.NeuralNetwork()
if not self.hyperNEAT:
genome.BuildPhenotype(self.current_network)
else:
genome.BuildHyperNEATPhenotype(self.current_network,
self.substrate)
# Conduct the evaluation
fit = self.physics_only_simulation()
return fit
def __init__(self,
log_frames=0,
run_num=0,
eval_time=10.,
dt=.02,
n=4,
con_type="single",
hyperNEAT=False,
substrate=False,
periodic=True):
""" Initialize the simulation class. """
global simulate
man = ODEManager(near_callback,
stepsize=dt / n,
log_data=log_frames,
run_num=run_num)
# Settings for the simulation.
self.log_frames = log_frames
self.run_num = run_num
self.eval_time = eval_time
self.elapsed_time = 0.
self.dt = dt # Timestep for simulation.
self.n = n # How many timesteps to simulate per callback.
# Quadruped Specific Setup
quadruped = Quadruped(man=man)
self.current_network = 0
self.hyperNEAT = True if hyperNEAT else False
self.substrate = substrate
# Whether we include a periodic oscillating input signal.
self.periodic = periodic
default=10.,
help="Apply force till a certain time")
args = parser.parse_args()
print args
log_frames = args.log_frames
eval_time = args.eval_time
run_num = args.run_num
dt = .02
n = 4
forcetill = args.applyforcetill_time
GlobalVarWorkaround.man = ODEManager(box_simu.near_callback,
stepsize=dt / n,
log_data=log_frames,
fluid_dynamics=1,
gravity=0,
run_num=run_num)
box = box_simu.Box(man=GlobalVarWorkaround.man,
desnsity=50.,
base_pos=[.0, 1., .0])
# If logging the output, tell manager to write the body type, dimensions, and position to the logging file.
# Must be placed after creating the quadruped.
if log_frames:
GlobalVarWorkaround.man.log_world_setup(eval_time, ind_num=run_num)
simulation = box_simu.Simulation(eval_time,
dt=dt,
n=n,
print args
log_frames = args.log_frames
eval_time = args.eval_time
run_num = args.run_num
output_path = args.output_path
dt = .02
n = 4
numofjoints = args.numofjoints
length = args.length
GlobalVarWorkaround.man = ODEManager(
ribosomalrobot_ctrl_simu_stop.near_callback,
stepsize=dt / n,
log_data=log_frames,
fluid_dynamics=1,
gravity=0,
run_num=run_num)
density = args.rdensity
GlobalVarWorkaround.worm = ribosomalrobot_ctrl_simu_stop.Worm(
man=GlobalVarWorkaround.man,
num_joints=numofjoints,
morphology={
'density': density,
'xlength': length
},
logging=log_frames,
log_path=output_path,
logfileprefix='rep' + str(run_num))