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Code Issues Releases Wiki Activity

All tests pass

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This commit is contained in:
J. Fernando Sánchez
2018-12-04 09:54:29 +01:00
parent 9165979b49
commit ff1df62eec
28 changed files with 81985 additions and 368 deletions
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36
soil/agents/SISaModel.py
View File

@@ -10,7 +10,7 @@ class SISaModel(FSM):
neutral_discontent_infected_prob
neutral_content_spong_prob
neutral_content_spon_prob
neutral_content_infected_prob
@@ -29,27 +29,27 @@ class SISaModel(FSM):
standard_variance
"""
def __init__(self, environment=None, agent_id=0, state=()):
def __init__(self, environment, agent_id=0, state=()):
super().__init__(environment=environment, agent_id=agent_id, state=state)
self.neutral_discontent_spon_prob = np.random.normal(environment.environment_params['neutral_discontent_spon_prob'],
environment.environment_params['standard_variance'])
self.neutral_discontent_infected_prob = np.random.normal(environment.environment_params['neutral_discontent_infected_prob'],
environment.environment_params['standard_variance'])
self.neutral_content_spon_prob = np.random.normal(environment.environment_params['neutral_content_spon_prob'],
environment.environment_params['standard_variance'])
self.neutral_content_infected_prob = np.random.normal(environment.environment_params['neutral_content_infected_prob'],
environment.environment_params['standard_variance'])
self.neutral_discontent_spon_prob = np.random.normal(self.env['neutral_discontent_spon_prob'],
self.env['standard_variance'])
self.neutral_discontent_infected_prob = np.random.normal(self.env['neutral_discontent_infected_prob'],
self.env['standard_variance'])
self.neutral_content_spon_prob = np.random.normal(self.env['neutral_content_spon_prob'],
self.env['standard_variance'])
self.neutral_content_infected_prob = np.random.normal(self.env['neutral_content_infected_prob'],
self.env['standard_variance'])
self.discontent_neutral = np.random.normal(environment.environment_params['discontent_neutral'],
environment.environment_params['standard_variance'])
self.discontent_content = np.random.normal(environment.environment_params['discontent_content'],
environment.environment_params['variance_d_c'])
self.discontent_neutral = np.random.normal(self.env['discontent_neutral'],
self.env['standard_variance'])
self.discontent_content = np.random.normal(self.env['discontent_content'],
self.env['variance_d_c'])
self.content_discontent = np.random.normal(environment.environment_params['content_discontent'],
environment.environment_params['variance_c_d'])
self.content_neutral = np.random.normal(environment.environment_params['content_neutral'],
environment.environment_params['standard_variance'])
self.content_discontent = np.random.normal(self.env['content_discontent'],
self.env['variance_c_d'])
self.content_neutral = np.random.normal(self.env['content_neutral'],
self.env['standard_variance'])
@state
def neutral(self):

69
soil/agents/__init__.py
View File

@@ -16,23 +16,15 @@ from functools import wraps
from .. import utils, history
agent_types = {}
class MetaAgent(type):
def __init__(cls, name, bases, nmspc):
super(MetaAgent, cls).__init__(name, bases, nmspc)
agent_types[name] = cls
class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
class BaseAgent(nxsim.BaseAgent):
"""
A special simpy BaseAgent that keeps track of its state history.
"""
defaults = {}
def __init__(self, environment=None, agent_id=None, state=None,
def __init__(self, environment, agent_id=None, state=None,
name='network_process', interval=None, **state_params):
# Check for REQUIRED arguments
assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. '
@@ -152,14 +144,18 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
def count_neighboring_agents(self, state_id=None):
return len(super().get_agents(state_id, limit_neighbors=True))
def get_agents(self, state_id=None, limit_neighbors=False, iterator=False, **kwargs):
def get_agents(self, state_id=None, agent_type=None, limit_neighbors=False, iterator=False, **kwargs):
agents = self.env.agents
if limit_neighbors:
agents = super().get_agents(state_id, limit_neighbors)
else:
agents = filter(lambda x: state_id is None or x.state.get('id', None) == state_id,
self.env.agents)
def matches_all(agent):
if state_id is not None:
if agent.state.get('id', None) != state_id:
return False
if agent_type is not None:
if type(agent) != agent_type:
return False
state = agent.state
for k, v in kwargs.items():
if state.get(k, None) != v:
@@ -219,7 +215,7 @@ def default_state(func):
return func
class MetaFSM(MetaAgent):
class MetaFSM(type):
def __init__(cls, name, bases, nmspc):
super(MetaFSM, cls).__init__(name, bases, nmspc)
states = {}
@@ -328,16 +324,42 @@ def calculate_distribution(network_agents=None,
return network_agents
def _serialize_distribution(network_agents):
d = _convert_agent_types(network_agents,
to_string=True)
def serialize_agent_type(agent_type):
if isinstance(agent_type, str):
return agent_type
type_name = agent_type.__name__
if type_name not in globals():
type_name = utils.name(agent_type)
return type_name
def serialize_distribution(network_agents):
'''
When serializing an agent distribution, remove the thresholds, in order
to avoid cluttering the YAML definition file.
'''
d = deepcopy(network_agents)
for v in d:
if 'threshold' in v:
del v['threshold']
v['agent_type'] = serialize_agent_type(v['agent_type'])
return d
def deserialize_type(agent_type, known_modules=[]):
if not isinstance(agent_type, str):
return agent_type
if agent_type in globals():
agent_type = globals()[agent_type]
else:
known = known_modules + ['soil.agents', 'soil.agents.custom' ]
agent_type = utils.deserializer(agent_type, known_modules=known)
return agent_type
def deserialize_distribution(ind):
d = deepcopy(ind)
for v in d:
v['agent_type'] = deserialize_type(v['agent_type'])
return d
@@ -354,14 +376,9 @@ def _validate_states(states, topology):
def _convert_agent_types(ind, to_string=False):
'''Convenience method to allow specifying agents by class or class name.'''
d = deepcopy(ind)
for v in d:
agent_type = v['agent_type']
if to_string and not isinstance(agent_type, str):
v['agent_type'] = str(agent_type.__name__)
elif not to_string and isinstance(agent_type, str):
v['agent_type'] = agent_types[agent_type]
return d
if to_string:
return serialize_distribution(ind)
return deserialize_distribution(ind)
def _agent_from_distribution(distribution, value=-1):