def add_objective(self,
name,
maximize,
tag,
node_func=None,
output_node_name=None,
logging_only=False):
"""Add an optimization objective to the dictionary.
Objectives must be added in order of importance, however fitness is fixed to be the most important.
The keys of an ObjectiveDict correspond to the objective's rank or importance. The ranks are set via the order
in which objectives are added (fitness will auto-correct to rank 0).
For each rank key, starting with 0, the corresponding value is another dictionary with three components:
name, maximized, tag.
Parameters
----------
name : str
The associated individual-level attribute name
maximize : bool
Whether superior individuals maximized (True) or minimize (False) the objective.
tag : str or None
The tag used in parsing the resulting output from a VoxCad simulation.
If this is None then the attribute is calculated outside of VoxCad (in Python only).
node_func : function
If tag is None then the objective is not computed in VoxCad and is instead calculated on an output of a
network.
output_node_name : str
The output node which node_func operates on.
logging_only : bool
If True then don't use as objective, only to track statistics from the simulation.
"""
curr_rank = self.max_rank
# if fitness is not added first, shift every other objective "down" in importance
if name == "fitness" and self.max_rank > 0:
curr_rank = 0 # change the key to rank 0
for rank in reversed(range(len(self))):
self[rank + 1] = self[rank]
super(ObjectiveDict, self).__setitem__(
curr_rank,
{
"name": name,
"maximize": maximize,
"tag": xml_format(tag) if tag is not None else None,
"worst_value": -10e6 if maximize else 10e6,
#"worst_value": 0,
"node_func": node_func,
"output_node_name": output_node_name,
"logging_only": logging_only
})
# TODO: logging_only 'objectives' should be a separate 'SimStats' class
self.max_rank += 1
def add_map(self, name, tag, func=sigmoid, output_type=float, dependency_order=None, params=None, param_tags=None,
env_kws=None, logging_stats=np.mean):
"""Add an association between a genotype output and a VoxCad parameter.
Parameters
----------
name : str
A network output node name from the genotype.
tag : str
The tag used in parsing the resulting output from a VoxCad simulation.
If this is None then the attribute is calculated outside of VoxCad (in Python only).
func : func
Specifies relationship between attributes and xml tag.
output_type : type
The output type
dependency_order : list
Order of operations
params : list
Constants dictating parameters of the mapping
param_tags : list
Tags for any constants associated with the mapping
env_kws : dict
Specifies which function of the output state to use (on top of func) to set an Env attribute
logging_stats : func or list
One or more functions (statistics) of the output to be logged as additional column(s) in logging
"""
if (dependency_order is not None) and not isinstance(dependency_order, list):
dependency_order = [dependency_order]
if params is not None:
assert (param_tags is not None)
if not isinstance(params, list):
params = [params]
if param_tags is not None:
assert (params is not None)
if not isinstance(param_tags, list):
param_tags = [param_tags]
param_tags = [xml_format(t) for t in param_tags]
if (env_kws is not None) and not isinstance(env_kws, dict):
env_kws = {env_kws: np.mean}
if (logging_stats is not None) and not isinstance(logging_stats, list):
logging_stats = [logging_stats]
if tag is not None:
tag = xml_format(tag)
self.mapping[name] = {"tag": tag,
"func": func,
"dependency_order": dependency_order,
"state": None,
"old_state": None,
"output_type": output_type,
"params": params,
"param_tags": param_tags,
"env_kws": env_kws,
"logging_stats": logging_stats}
def add_param(self, name, val, tag):
setattr(self, name, val)
self.new_param_tag_dict[name] = xml_format(tag)
def add_map(self, name, tag, func=sigmoid, output_type=float, dependency_order=None, params=None, param_tags=None,
env_kws=None, logging_stats=np.mean, age_zero_overwrite=None, switch_proportion=0, switch_name=None):
"""Add an association between a genotype output and a VoxCad parameter.
Parameters
----------
name : str
A network output node name from the genotype.
tag : str
The tag used in parsing the resulting output from a VoxCad simulation.
If this is None then the attribute is calculated outside of VoxCad (in Python only).
func : func
Specifies relationship between attributes and xml tag.
output_type : type
The output type
dependency_order : list
Order of operations
params : list
Constants dictating parameters of the mapping
param_tags : list
Tags for any constants associated with the mapping
env_kws : dict
Specifies which function of the output state to use (on top of func) to set an Env attribute
logging_stats : func or list
One or more functions (statistics) of the output to be logged as additional column(s) in logging
age_zero_overwrite : str
Evaluate this network with this placeholder at birth (age=0) instead of actual values.
switch_proportion : float
Switches are non-inheritable portions of genotype (Hinton & Nowlan, 1987).
switch_name : str
Network name containing switch values
"""
if (dependency_order is not None) and not isinstance(dependency_order, list):
dependency_order = [dependency_order]
if params is not None:
assert (param_tags is not None)
if not isinstance(params, list):
params = [params]
if param_tags is not None:
assert (params is not None)
if not isinstance(param_tags, list):
param_tags = [param_tags]
param_tags = [xml_format(t) for t in param_tags]
if (env_kws is not None) and not isinstance(env_kws, dict):
env_kws = {env_kws: np.mean}
if (logging_stats is not None) and not isinstance(logging_stats, list):
logging_stats = [logging_stats]
if tag is not None:
tag = xml_format(tag)
self.mapping[name] = {"tag": tag,
"func": func,
"dependency_order": dependency_order,
"state": None,
"oldstate": None, #daniel: was old_state before
"output_type": output_type,
"params": params,
"param_tags": param_tags,
"env_kws": env_kws,
"logging_stats": logging_stats,
"age_zero_overwrite": age_zero_overwrite,
"switch_proportion": switch_proportion,
"switch_name": switch_name}
