mirror of
https://github.com/gsi-upm/soil
synced 2024-11-21 18:52:28 +00:00
WIP
This commit is contained in:
parent
1a8313e4f6
commit
6f7481769e
@ -36,13 +36,13 @@ def main():
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parser.add_argument('--module', '-m', type=str,
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help='file containing the code of any custom agents.')
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parser.add_argument('--dry-run', '--dry', action='store_true',
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help='Do not store the results of the simulation.')
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help='Do not store the results of the simulation to disk, show in terminal instead.')
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parser.add_argument('--pdb', action='store_true',
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help='Use a pdb console in case of exception.')
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parser.add_argument('--graph', '-g', action='store_true',
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help='Dump GEXF graph. Defaults to false.')
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help='Dump each trial\'s network topology as a GEXF graph. Defaults to false.')
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parser.add_argument('--csv', action='store_true',
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help='Dump history in CSV format. Defaults to false.')
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help='Dump all data collected in CSV format. Defaults to false.')
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parser.add_argument('--level', type=str,
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help='Logging level')
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parser.add_argument('--output', '-o', type=str, default="soil_output",
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@ -26,7 +26,14 @@ class DeadAgent(Exception):
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class BaseAgent(Agent):
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"""
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A special Agent that keeps track of its state history.
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A special type of Mesa Agent that:
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* Can be used as a dictionary to access its state.
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* Has logging built-in
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* Can be given default arguments through a defaults class attribute,
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which will be used on construction to initialize each agent's state
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Any attribute that is not preceded by an underscore (`_`) will also be added to its state.
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"""
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defaults = {}
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@ -61,6 +68,9 @@ class BaseAgent(Agent):
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for (k, v) in kwargs.items():
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setattr(self, k, v)
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for (k, v) in getattr(self, 'defaults', {}).items():
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if not hasattr(self, k) or getattr(self, k) is None:
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setattr(self, k, v)
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# TODO: refactor to clean up mesa compatibility
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@property
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@ -79,7 +89,6 @@ class BaseAgent(Agent):
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def state(self):
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'''
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Return the agent itself, which behaves as a dictionary.
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Changes made to `agent.state` will be reflected in the history.
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This method shouldn't be used, but is kept here for backwards compatibility.
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'''
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251
soil/config.py
Normal file
251
soil/config.py
Normal file
@ -0,0 +1,251 @@
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import yaml
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import os
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import sys
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import networkx as nx
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import collections.abc
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from . import serialization, utils, basestring, agents
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class Config(collections.abc.Mapping):
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"""
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1) agent type can be specified by name or by class.
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2) instead of just one type, a network agents distribution can be used.
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The distribution specifies the weight (or probability) of each
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agent type in the topology. This is an example distribution: ::
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[
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{'agent_type': 'agent_type_1',
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'weight': 0.2,
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'state': {
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'id': 0
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}
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},
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{'agent_type': 'agent_type_2',
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'weight': 0.8,
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'state': {
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'id': 1
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}
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}
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]
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In this example, 20% of the nodes will be marked as type
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'agent_type_1'.
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3) if no initial state is given, each node's state will be set
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to `{'id': 0}`.
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Parameters
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---------
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name : str, optional
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name of the Simulation
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group : str, optional
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a group name can be used to link simulations
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topology (optional): networkx.Graph instance or Node-Link topology as a dict or string (will be loaded with `json_graph.node_link_graph(topology`).
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network_params : dict
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parameters used to create a topology with networkx, if no topology is given
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network_agents : dict
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definition of agents to populate the topology with
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agent_type : NetworkAgent subclass, optional
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Default type of NetworkAgent to use for nodes not specified in network_agents
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states : list, optional
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List of initial states corresponding to the nodes in the topology. Basic form is a list of integers
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whose value indicates the state
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dir_path: str, optional
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Directory path to load simulation assets (files, modules...)
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seed : str, optional
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Seed to use for the random generator
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num_trials : int, optional
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Number of independent simulation runs
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max_time : int, optional
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Maximum step/time for each simulation
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environment_params : dict, optional
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Dictionary of globally-shared environmental parameters
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environment_agents: dict, optional
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Similar to network_agents. Distribution of Agents that control the environment
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environment_class: soil.environment.Environment subclass, optional
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Class for the environment. It defailts to soil.environment.Environment
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"""
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__slots__ = 'name', 'agent_type', 'group', 'network_agents', 'environment_agents', 'states', 'default_state', 'interval', 'network_params', 'seed', 'num_trials', 'max_time', 'topology', 'schedule', 'initial_time', 'environment_params', 'environment_class', 'dir_path', '_added_to_path'
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def __init__(self, name=None,
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group=None,
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agent_type='BaseAgent',
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network_agents=None,
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environment_agents=None,
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states=None,
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default_state=None,
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interval=1,
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network_params=None,
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seed=None,
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num_trials=1,
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max_time=None,
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topology=None,
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schedule=None,
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initial_time=0,
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environment_params={},
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environment_class='soil.Environment',
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dir_path=None):
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self.network_params = network_params
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self.name = name or 'Unnamed'
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self.seed = str(seed or name)
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self.group = group or ''
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self.num_trials = num_trials
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self.max_time = max_time
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self.default_state = default_state or {}
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self.dir_path = dir_path or os.getcwd()
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self.interval = interval
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self._added_to_path = list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
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sys.path += self._added_to_path
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self.topology = topology
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self.schedule = schedule
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self.initial_time = initial_time
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self.environment_class = environment_class
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self.environment_params = dict(environment_params)
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#TODO: Check agent distro vs fixed agents
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self.environment_agents = environment_agents or []
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self.agent_type = agent_type
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self.network_agents = network_agents or {}
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self.states = states or {}
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def validate(self):
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agents._validate_states(self.states,
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self._topology)
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def restore_path(self):
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for added in self._added_to_path:
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sys.path.remove(added)
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def to_yaml(self):
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return yaml.dump(self.to_dict())
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def dump_yaml(self, f=None, outdir=None):
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if not f and not outdir:
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raise ValueError('specify a file or an output directory')
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if not f:
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f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
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with utils.open_or_reuse(f, 'w') as f:
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f.write(self.to_yaml())
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def to_yaml(self):
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return yaml.dump(self.to_dict())
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# TODO: See note on getstate
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def to_dict(self):
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return self.__getstate__()
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def dump_yaml(self, f=None, outdir=None):
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if not f and not outdir:
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raise ValueError('specify a file or an output directory')
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if not f:
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f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
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with utils.open_or_reuse(f, 'w') as f:
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f.write(self.to_yaml())
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def __getitem__(self, key):
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return getattr(self, key)
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def __iter__(self):
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return (k for k in self.__slots__ if k[0] != '_')
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def __len__(self):
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return len(self.__slots__)
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def dump_pickle(self, f=None, outdir=None):
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if not outdir and not f:
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raise ValueError('specify a file or an output directory')
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if not f:
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f = os.path.join(outdir,
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'{}.simulation.pickle'.format(self.name))
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with utils.open_or_reuse(f, 'wb') as f:
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pickle.dump(self, f)
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# TODO: remove this. A config should be sendable regardless. Non-pickable objects could be computed via properties and the like
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# def __getstate__(self):
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# state={}
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# for k, v in self.__dict__.items():
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# if k[0] != '_':
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# state[k] = v
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# state['topology'] = json_graph.node_link_data(self.topology)
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# state['network_agents'] = agents.serialize_definition(self.network_agents,
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# known_modules = [])
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# state['environment_agents'] = agents.serialize_definition(self.environment_agents,
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# known_modules = [])
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# state['environment_class'] = serialization.serialize(self.environment_class,
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# known_modules=['soil.environment'])[1] # func, name
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# if state['load_module'] is None:
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# del state['load_module']
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# return state
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# # TODO: remove, same as __getstate__
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# def __setstate__(self, state):
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# self.__dict__ = state
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# self.load_module = getattr(self, 'load_module', None)
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# if self.dir_path not in sys.path:
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# sys.path += [self.dir_path, os.getcwd()]
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# self.topology = json_graph.node_link_graph(state['topology'])
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# self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
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# self.environment_agents = agents._convert_agent_types(self.environment_agents,
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# known_modules=[self.load_module])
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# self.environment_class = serialization.deserialize(self.environment_class,
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# known_modules=[self.load_module,
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# 'soil.environment', ]) # func, name
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class CalculatedConfig(Config):
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def __init__(self, config):
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"""
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Returns a configuration object that replaces some "plain" attributes (e.g., `environment_class` string) into
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a Python object (`soil.environment.Environment` class).
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"""
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self._config = config
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values = dict(config)
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values['environment_class'] = self._environment_class()
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values['environment_agents'] = self._environment_agents()
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values['topology'] = self._topology()
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values['network_agents'] = self._network_agents()
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values['agent_type'] = serialization.deserialize(self.agent_type, known_modules=['soil.agents'])
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return values
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def _topology(self):
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topology = self._config.topology
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if topology is None:
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topology = serialization.load_network(self._config.network_params,
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dir_path=self._config.dir_path)
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elif isinstance(topology, basestring) or isinstance(topology, dict):
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topology = json_graph.node_link_graph(topology)
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return nx.Graph(topology)
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def _environment_class(self):
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return serialization.deserialize(self._config.environment_class,
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known_modules=['soil.environment', ]) or Environment
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def _environment_agents(self):
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return agents._convert_agent_types(self._config.environment_agents)
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def _network_agents(self):
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distro = agents.calculate_distribution(self._config.network_agents,
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self._config.agent_type)
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return agents._convert_agent_types(distro)
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def _environment_class(self):
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return serialization.deserialize(self._config.environment_class,
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known_modules=['soil.environment', ]) # func, name
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@ -8,19 +8,17 @@ class SoilDataCollector(MDC):
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# Populate model and env reporters so they have a key per
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# So they can be shown in the web interface
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self.environment = environment
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raise NotImplementedError()
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@property
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def model_vars(self):
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pass
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raise NotImplementedError()
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@model_vars.setter
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def model_vars(self, value):
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pass
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raise NotImplementedError()
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@property
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def agent_reporters(self):
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self.model._history._
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pass
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raise NotImplementedError()
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@ -1,23 +1,20 @@
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from __future__ import annotations
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import os
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import sqlite3
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import csv
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import math
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import random
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import yaml
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import tempfile
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import logging
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import pandas as pd
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from time import time as current_time
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from copy import deepcopy
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from networkx.readwrite import json_graph
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import networkx as nx
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from tsih import History, NoHistory, Record, Key
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import networkx as nx
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from mesa import Model
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from . import serialization, agents, analysis, utils, time
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from tsih import Record
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from . import serialization, agents, analysis, utils, time, config
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# These properties will be copied when pickling/unpickling the environment
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_CONFIG_PROPS = [ 'name',
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@ -49,7 +46,6 @@ class Environment(Model):
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schedule=None,
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initial_time=0,
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environment_params=None,
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history=False,
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dir_path=None,
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**kwargs):
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@ -76,20 +72,11 @@ class Environment(Model):
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topology = nx.Graph()
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self.G = nx.Graph(topology)
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self.environment_params = environment_params or {}
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self.environment_params.update(kwargs)
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self._env_agents = {}
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self.interval = interval
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if history:
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history = History
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else:
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history = NoHistory
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self._history = history(name=self.name,
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backup=True)
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self['SEED'] = seed
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if network_agents:
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@ -106,6 +93,19 @@ class Environment(Model):
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self.logger = utils.logger.getChild(self.name)
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@staticmethod
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def from_config(conf: config.Config, trial_id, **kwargs) -> Environment:
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'''Create an environment for a trial of the simulation'''
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conf = config.Config(conf, **kwargs)
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conf.seed = '{}_{}'.format(conf.seed, trial_id)
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conf.name = '{}_trial_{}'.format(conf.name, trial_id).replace('.', '-')
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opts = conf.environment_params.copy()
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opts.update(conf)
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opts.update(kwargs)
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env = serialization.deserialize(conf.environment_class)(**opts)
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return env
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@property
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def now(self):
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if self.schedule:
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@ -212,11 +212,14 @@ class Environment(Model):
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return self.logger.log(level, message, extra=extra)
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def step(self):
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'''
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Advance one step in the simulation, and update the data collection and scheduler appropriately
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'''
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super().step()
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self.schedule.step()
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def run(self, until, *args, **kwargs):
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self._save_state()
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until = until or float('inf')
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while self.schedule.next_time < until:
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self.step()
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@ -252,14 +255,16 @@ class Environment(Model):
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def get(self, key, default=None):
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'''
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Get the value of an environment attribute in a
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given point in the simulation (history).
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If key is an attribute name, this method returns
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the current value.
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To get values at other times, use a
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:meth: `soil.history.Key` tuple.
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Get the value of an environment attribute.
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Return `default` if the value is not set.
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'''
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return self[key] if key in self else default
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return self.environment_params.get(key, default)
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def __getitem__(self, key):
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return self.environment_params.get(key)
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def __setitem__(self, key, value):
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return self.environment_params.__setitem__(key, value)
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def get_agent(self, agent_id):
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return self.G.nodes[agent_id]['agent']
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@ -269,112 +274,31 @@ class Environment(Model):
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return self.agents
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return (self.G.nodes[i]['agent'] for i in nodes)
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def dump_csv(self, f):
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with utils.open_or_reuse(f, 'w') as f:
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cr = csv.writer(f)
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cr.writerow(('agent_id', 't_step', 'key', 'value'))
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for i in self.history_to_tuples():
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cr.writerow(i)
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def dump_gexf(self, f):
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G = self.history_to_graph()
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# Workaround for geometric models
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# See soil/soil#4
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for node in G.nodes():
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if 'pos' in G.nodes[node]:
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G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
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del (G.nodes[node]['pos'])
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nx.write_gexf(G, f, version="1.2draft")
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def dump(self, *args, formats=None, **kwargs):
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if not formats:
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return
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functions = {
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'csv': self.dump_csv,
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'gexf': self.dump_gexf
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}
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for f in formats:
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if f in functions:
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functions[f](*args, **kwargs)
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else:
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raise ValueError('Unknown format: {}'.format(f))
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def df(self):
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return self._history[None, None, None].df()
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|
||||
def dump_sqlite(self, f):
|
||||
return self._history.dump(f)
|
||||
|
||||
def state_to_tuples(self, now=None):
|
||||
def _agent_to_tuples(self, agent, now=None):
|
||||
if now is None:
|
||||
now = self.now
|
||||
for k, v in agent.state.items():
|
||||
yield Record(dict_id=agent.id,
|
||||
t_step=now,
|
||||
key=k,
|
||||
value=v)
|
||||
|
||||
def state_to_tuples(self, agent_id=None, now=None):
|
||||
if now is None:
|
||||
now = self.now
|
||||
|
||||
if agent_id:
|
||||
agent = self.get_agent(agent_id)
|
||||
yield from self._agent_to_tuples(agent, now)
|
||||
return
|
||||
|
||||
for k, v in self.environment_params.items():
|
||||
yield Record(dict_id='env',
|
||||
t_step=now,
|
||||
key=k,
|
||||
value=v)
|
||||
for agent in self.agents:
|
||||
for k, v in agent.state.items():
|
||||
yield Record(dict_id=agent.id,
|
||||
t_step=now,
|
||||
key=k,
|
||||
value=v)
|
||||
|
||||
def history_to_tuples(self, agent_id=None):
|
||||
if isinstance(self._history, NoHistory):
|
||||
tuples = self.state_to_tuples()
|
||||
else:
|
||||
tuples = self._history.to_tuples()
|
||||
if agent_id is None:
|
||||
return tuples
|
||||
return filter(lambda x: str(x[0]) == str(agent_id), tuples)
|
||||
|
||||
def history_to_graph(self):
|
||||
G = nx.Graph(self.G)
|
||||
|
||||
for agent in self.network_agents:
|
||||
|
||||
attributes = {'agent': str(agent.__class__)}
|
||||
lastattributes = {}
|
||||
spells = []
|
||||
lastvisible = False
|
||||
laststep = None
|
||||
history = sorted(list(self.history_to_tuples(agent_id=agent.id)))
|
||||
if not history:
|
||||
continue
|
||||
for _, t_step, attribute, value in history:
|
||||
if attribute == 'visible':
|
||||
nowvisible = value
|
||||
if nowvisible and not lastvisible:
|
||||
laststep = t_step
|
||||
if not nowvisible and lastvisible:
|
||||
spells.append((laststep, t_step))
|
||||
|
||||
lastvisible = nowvisible
|
||||
continue
|
||||
key = 'attr_' + attribute
|
||||
if key not in attributes:
|
||||
attributes[key] = list()
|
||||
if key not in lastattributes:
|
||||
lastattributes[key] = (value, t_step)
|
||||
elif lastattributes[key][0] != value:
|
||||
last_value, laststep = lastattributes[key]
|
||||
commit_value = (last_value, laststep, t_step)
|
||||
if key not in attributes:
|
||||
attributes[key] = list()
|
||||
attributes[key].append(commit_value)
|
||||
lastattributes[key] = (value, t_step)
|
||||
for k, v in lastattributes.items():
|
||||
attributes[k].append((v[0], v[1], None))
|
||||
if lastvisible:
|
||||
spells.append((laststep, None))
|
||||
if spells:
|
||||
G.add_node(agent.id, spells=spells, **attributes)
|
||||
else:
|
||||
G.add_node(agent.id, **attributes)
|
||||
|
||||
return G
|
||||
yield from self._agent_to_tuples(agent, now)
|
||||
|
||||
def __getstate__(self):
|
||||
state = {}
|
||||
@ -382,7 +306,6 @@ class Environment(Model):
|
||||
state[prop] = self.__dict__[prop]
|
||||
state['G'] = json_graph.node_link_data(self.G)
|
||||
state['environment_agents'] = self._env_agents
|
||||
state['history'] = self._history
|
||||
state['schedule'] = self.schedule
|
||||
return state
|
||||
|
||||
@ -391,7 +314,6 @@ class Environment(Model):
|
||||
self.__dict__[prop] = state[prop]
|
||||
self._env_agents = state['environment_agents']
|
||||
self.G = json_graph.node_link_graph(state['G'])
|
||||
self._history = state['history']
|
||||
# self._env = None
|
||||
self.schedule = state['schedule']
|
||||
self._queue = []
|
||||
|
@ -48,20 +48,24 @@ class Exporter:
|
||||
self.simulation = simulation
|
||||
outdir = outdir or os.path.join(os.getcwd(), 'soil_output')
|
||||
self.outdir = os.path.join(outdir,
|
||||
simulation.group or '',
|
||||
simulation.name)
|
||||
simulation.config.group or '',
|
||||
simulation.config.name)
|
||||
self.dry_run = dry_run
|
||||
self.copy_to = copy_to
|
||||
|
||||
def start(self):
|
||||
def sim_start(self):
|
||||
'''Method to call when the simulation starts'''
|
||||
pass
|
||||
|
||||
def end(self, stats):
|
||||
def sim_end(self, stats):
|
||||
'''Method to call when the simulation ends'''
|
||||
pass
|
||||
|
||||
def trial(self, env, stats):
|
||||
def trial_start(self, env):
|
||||
'''Method to call when a trial start'''
|
||||
pass
|
||||
|
||||
def trial_end(self, env, stats):
|
||||
'''Method to call when a trial ends'''
|
||||
pass
|
||||
|
||||
@ -80,21 +84,21 @@ class Exporter:
|
||||
class default(Exporter):
|
||||
'''Default exporter. Writes sqlite results, as well as the simulation YAML'''
|
||||
|
||||
def start(self):
|
||||
def sim_start(self):
|
||||
if not self.dry_run:
|
||||
logger.info('Dumping results to %s', self.outdir)
|
||||
self.simulation.dump_yaml(outdir=self.outdir)
|
||||
else:
|
||||
logger.info('NOT dumping results')
|
||||
|
||||
def trial(self, env, stats):
|
||||
def trial_start(self, env, stats):
|
||||
if not self.dry_run:
|
||||
with timer('Dumping simulation {} trial {}'.format(self.simulation.name,
|
||||
env.name)):
|
||||
with self.output('{}.sqlite'.format(env.name), mode='wb') as f:
|
||||
env.dump_sqlite(f)
|
||||
|
||||
def end(self, stats):
|
||||
def sim_end(self, stats):
|
||||
with timer('Dumping simulation {}\'s stats'.format(self.simulation.name)):
|
||||
with self.output('{}.sqlite'.format(self.simulation.name), mode='wb') as f:
|
||||
self.simulation.dump_sqlite(f)
|
||||
@ -102,15 +106,14 @@ class default(Exporter):
|
||||
|
||||
|
||||
class csv(Exporter):
|
||||
|
||||
'''Export the state of each environment (and its agents) in a separate CSV file'''
|
||||
def trial(self, env, stats):
|
||||
def trial_end(self, env, stats):
|
||||
with timer('[CSV] Dumping simulation {} trial {} @ dir {}'.format(self.simulation.name,
|
||||
env.name,
|
||||
self.outdir)):
|
||||
with self.output('{}.csv'.format(env.name)) as f:
|
||||
env.dump_csv(f)
|
||||
|
||||
with self.output('{}.stats.csv'.format(env.name)) as f:
|
||||
with self.output('{}.stats.{}.csv'.format(env.name, stats.name)) as f:
|
||||
statwriter = csvlib.writer(f, delimiter='\t', quotechar='"', quoting=csvlib.QUOTE_ALL)
|
||||
|
||||
for stat in stats:
|
||||
@ -118,7 +121,7 @@ class csv(Exporter):
|
||||
|
||||
|
||||
class gexf(Exporter):
|
||||
def trial(self, env, stats):
|
||||
def trial_end(self, env, stats):
|
||||
if self.dry_run:
|
||||
logger.info('Not dumping GEXF in dry_run mode')
|
||||
return
|
||||
@ -126,22 +129,32 @@ class gexf(Exporter):
|
||||
with timer('[GEXF] Dumping simulation {} trial {}'.format(self.simulation.name,
|
||||
env.name)):
|
||||
with self.output('{}.gexf'.format(env.name), mode='wb') as f:
|
||||
env.dump_gexf(f)
|
||||
self.dump_gexf(env, f)
|
||||
|
||||
def dump_gexf(self, env, f):
|
||||
G = env.history_to_graph()
|
||||
# Workaround for geometric models
|
||||
# See soil/soil#4
|
||||
for node in G.nodes():
|
||||
if 'pos' in G.nodes[node]:
|
||||
G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
|
||||
del (G.nodes[node]['pos'])
|
||||
|
||||
nx.write_gexf(G, f, version="1.2draft")
|
||||
|
||||
class dummy(Exporter):
|
||||
|
||||
def start(self):
|
||||
def sim_start(self):
|
||||
with self.output('dummy', 'w') as f:
|
||||
f.write('simulation started @ {}\n'.format(current_time()))
|
||||
|
||||
def trial(self, env, stats):
|
||||
def trial_end(self, env, stats):
|
||||
with self.output('dummy', 'w') as f:
|
||||
for i in env.history_to_tuples():
|
||||
for i in stats:
|
||||
f.write(','.join(map(str, i)))
|
||||
f.write('\n')
|
||||
|
||||
def sim(self, stats):
|
||||
def sim_end(self, stats):
|
||||
with self.output('dummy', 'a') as f:
|
||||
f.write('simulation ended @ {}\n'.format(current_time()))
|
||||
|
||||
@ -149,10 +162,57 @@ class dummy(Exporter):
|
||||
|
||||
class graphdrawing(Exporter):
|
||||
|
||||
def trial(self, env, stats):
|
||||
def trial_end(self, env, stats):
|
||||
# Outside effects
|
||||
f = plt.figure()
|
||||
nx.draw(env.G, node_size=10, width=0.2, pos=nx.spring_layout(env.G, scale=100), ax=f.add_subplot(111))
|
||||
with open('graph-{}.png'.format(env.name)) as f:
|
||||
f.savefig(f)
|
||||
|
||||
'''
|
||||
Convert an environment into a NetworkX graph
|
||||
'''
|
||||
def env_to_graph(env, history=None):
|
||||
G = nx.Graph(env.G)
|
||||
|
||||
for agent in env.network_agents:
|
||||
|
||||
attributes = {'agent': str(agent.__class__)}
|
||||
lastattributes = {}
|
||||
spells = []
|
||||
lastvisible = False
|
||||
laststep = None
|
||||
if not history:
|
||||
history = sorted(list(env.state_to_tuples()))
|
||||
for _, t_step, attribute, value in history:
|
||||
if attribute == 'visible':
|
||||
nowvisible = value
|
||||
if nowvisible and not lastvisible:
|
||||
laststep = t_step
|
||||
if not nowvisible and lastvisible:
|
||||
spells.append((laststep, t_step))
|
||||
|
||||
lastvisible = nowvisible
|
||||
continue
|
||||
key = 'attr_' + attribute
|
||||
if key not in attributes:
|
||||
attributes[key] = list()
|
||||
if key not in lastattributes:
|
||||
lastattributes[key] = (value, t_step)
|
||||
elif lastattributes[key][0] != value:
|
||||
last_value, laststep = lastattributes[key]
|
||||
commit_value = (last_value, laststep, t_step)
|
||||
if key not in attributes:
|
||||
attributes[key] = list()
|
||||
attributes[key].append(commit_value)
|
||||
lastattributes[key] = (value, t_step)
|
||||
for k, v in lastattributes.items():
|
||||
attributes[k].append((v[0], v[1], None))
|
||||
if lastvisible:
|
||||
spells.append((laststep, None))
|
||||
if spells:
|
||||
G.add_node(agent.id, spells=spells, **attributes)
|
||||
else:
|
||||
G.add_node(agent.id, **attributes)
|
||||
|
||||
return G
|
||||
|
@ -2,6 +2,7 @@ import os
|
||||
import logging
|
||||
import ast
|
||||
import sys
|
||||
import re
|
||||
import importlib
|
||||
from glob import glob
|
||||
from itertools import product, chain
|
||||
@ -18,6 +19,9 @@ logger = logging.getLogger('soil')
|
||||
def load_network(network_params, dir_path=None):
|
||||
G = nx.Graph()
|
||||
|
||||
if not network_params:
|
||||
return G
|
||||
|
||||
if 'path' in network_params:
|
||||
path = network_params['path']
|
||||
if dir_path and not os.path.isabs(path):
|
||||
@ -169,6 +173,9 @@ def serialize(v, known_modules=[]):
|
||||
func = serializer(tname)
|
||||
return func(v), tname
|
||||
|
||||
|
||||
IS_CLASS = re.compile(r"<class '(.*)'>")
|
||||
|
||||
def deserializer(type_, known_modules=[]):
|
||||
if type(type_) != str: # Already deserialized
|
||||
return type_
|
||||
@ -179,6 +186,13 @@ def deserializer(type_, known_modules=[]):
|
||||
if hasattr(builtins, type_): # Check if it's a builtin type
|
||||
cls = getattr(builtins, type_)
|
||||
return lambda x=None: ast.literal_eval(x) if x is not None else cls()
|
||||
match = IS_CLASS.match(type_)
|
||||
if match:
|
||||
modname, tname = match.group(1).rsplit(".", 1)
|
||||
module = importlib.import_module(modname)
|
||||
cls = getattr(module, tname)
|
||||
return getattr(cls, 'deserialize', cls)
|
||||
|
||||
# Otherwise, see if we can find the module and the class
|
||||
modules = known_modules or []
|
||||
options = []
|
||||
@ -189,7 +203,7 @@ def deserializer(type_, known_modules=[]):
|
||||
|
||||
if '.' in type_: # Fully qualified module
|
||||
module, type_ = type_.rsplit(".", 1)
|
||||
options.append ((module, type_))
|
||||
options.append((module, type_))
|
||||
|
||||
errors = []
|
||||
for modname, tname in options:
|
||||
@ -213,10 +227,10 @@ def deserialize(type_, value=None, **kwargs):
|
||||
|
||||
|
||||
def deserialize_all(names, *args, known_modules=['soil'], **kwargs):
|
||||
'''Return the set of exporters for a simulation, given the exporter names'''
|
||||
exporters = []
|
||||
'''Return the list of deserialized objects'''
|
||||
objects = []
|
||||
for name in names:
|
||||
mod = deserialize(name, known_modules=known_modules)
|
||||
exporters.append(mod(*args, **kwargs))
|
||||
return exporters
|
||||
objects.append(mod(*args, **kwargs))
|
||||
return objects
|
||||
|
||||
|
@ -10,8 +10,6 @@ import networkx as nx
|
||||
from networkx.readwrite import json_graph
|
||||
from multiprocessing import Pool
|
||||
from functools import partial
|
||||
from tsih import History
|
||||
|
||||
import pickle
|
||||
|
||||
from . import serialization, utils, basestring, agents
|
||||
@ -20,127 +18,34 @@ from .utils import logger
|
||||
from .exporters import default
|
||||
from .stats import defaultStats
|
||||
|
||||
from .config import Config
|
||||
|
||||
|
||||
#TODO: change documentation for simulation
|
||||
|
||||
class Simulation:
|
||||
"""
|
||||
Similar to nsim.NetworkSimulation with three main differences:
|
||||
1) agent type can be specified by name or by class.
|
||||
2) instead of just one type, a network agents distribution can be used.
|
||||
The distribution specifies the weight (or probability) of each
|
||||
agent type in the topology. This is an example distribution: ::
|
||||
|
||||
[
|
||||
{'agent_type': 'agent_type_1',
|
||||
'weight': 0.2,
|
||||
'state': {
|
||||
'id': 0
|
||||
}
|
||||
},
|
||||
{'agent_type': 'agent_type_2',
|
||||
'weight': 0.8,
|
||||
'state': {
|
||||
'id': 1
|
||||
}
|
||||
}
|
||||
]
|
||||
|
||||
In this example, 20% of the nodes will be marked as type
|
||||
'agent_type_1'.
|
||||
3) if no initial state is given, each node's state will be set
|
||||
to `{'id': 0}`.
|
||||
|
||||
Parameters
|
||||
---------
|
||||
name : str, optional
|
||||
config (optional): :class:`config.Config`
|
||||
name of the Simulation
|
||||
group : str, optional
|
||||
a group name can be used to link simulations
|
||||
topology : networkx.Graph instance, optional
|
||||
network_params : dict
|
||||
parameters used to create a topology with networkx, if no topology is given
|
||||
network_agents : dict
|
||||
definition of agents to populate the topology with
|
||||
agent_type : NetworkAgent subclass, optional
|
||||
Default type of NetworkAgent to use for nodes not specified in network_agents
|
||||
states : list, optional
|
||||
List of initial states corresponding to the nodes in the topology. Basic form is a list of integers
|
||||
whose value indicates the state
|
||||
dir_path: str, optional
|
||||
Directory path to load simulation assets (files, modules...)
|
||||
seed : str, optional
|
||||
Seed to use for the random generator
|
||||
num_trials : int, optional
|
||||
Number of independent simulation runs
|
||||
max_time : int, optional
|
||||
Time how long the simulation should run
|
||||
environment_params : dict, optional
|
||||
Dictionary of globally-shared environmental parameters
|
||||
environment_agents: dict, optional
|
||||
Similar to network_agents. Distribution of Agents that control the environment
|
||||
environment_class: soil.environment.Environment subclass, optional
|
||||
Class for the environment. It defailts to soil.environment.Environment
|
||||
load_module : str, module name, deprecated
|
||||
If specified, soil will load the content of this module under 'soil.agents.custom'
|
||||
history: tsih.History subclass, optional
|
||||
Class to use to store the history of the simulation (and environments). It defailts to tsih.History
|
||||
If set to True, tsih.History will be used. If set to False or None, tsih.NoHistory will be used.
|
||||
|
||||
kwargs: parameters to use to initialize a new configuration, if one has not been provided.
|
||||
"""
|
||||
|
||||
def __init__(self, name=None, group=None, topology=None, network_params=None,
|
||||
network_agents=None, agent_type=None, states=None,
|
||||
default_state=None, interval=1, num_trials=1,
|
||||
max_time=100, load_module=None, seed=None,
|
||||
dir_path=None, environment_agents=None,
|
||||
environment_params=None, environment_class=None,
|
||||
history=History, **kwargs):
|
||||
def __init__(self, config=None,
|
||||
**kwargs):
|
||||
|
||||
self.load_module = load_module
|
||||
self.network_params = network_params
|
||||
self.name = name or 'Unnamed'
|
||||
self.seed = str(seed or name)
|
||||
self._id = '{}_{}'.format(self.name, strftime("%Y-%m-%d_%H.%M.%S"))
|
||||
self.group = group or ''
|
||||
self.num_trials = num_trials
|
||||
self.max_time = max_time
|
||||
self.default_state = default_state or {}
|
||||
self.dir_path = dir_path or os.getcwd()
|
||||
self.interval = interval
|
||||
if bool(config) == bool(kwargs):
|
||||
raise ValueError("Specify either a configuration or the parameters to initialize a configuration")
|
||||
|
||||
sys.path += list(x for x in [os.getcwd(), self.dir_path] if x not in sys.path)
|
||||
if kwargs:
|
||||
config = Config(**kwargs)
|
||||
|
||||
if topology is None:
|
||||
topology = serialization.load_network(network_params,
|
||||
dir_path=self.dir_path)
|
||||
elif isinstance(topology, basestring) or isinstance(topology, dict):
|
||||
topology = json_graph.node_link_graph(topology)
|
||||
self.topology = nx.Graph(topology)
|
||||
self.config = config
|
||||
|
||||
|
||||
self.environment_params = environment_params or {}
|
||||
self.environment_class = serialization.deserialize(environment_class,
|
||||
known_modules=['soil.environment', ]) or Environment
|
||||
|
||||
environment_agents = environment_agents or []
|
||||
self.environment_agents = agents._convert_agent_types(environment_agents,
|
||||
known_modules=[self.load_module])
|
||||
|
||||
distro = agents.calculate_distribution(network_agents,
|
||||
agent_type)
|
||||
self.network_agents = agents._convert_agent_types(distro,
|
||||
known_modules=[self.load_module])
|
||||
|
||||
self.states = agents._validate_states(states,
|
||||
self.topology)
|
||||
|
||||
if history == True:
|
||||
history = History
|
||||
elif not history:
|
||||
history = NoHistory
|
||||
|
||||
self._history = history(name=self.name,
|
||||
backup=False)
|
||||
@property
|
||||
def name(self) -> str:
|
||||
return self.config.name
|
||||
|
||||
def run_simulation(self, *args, **kwargs):
|
||||
return self.run(*args, **kwargs)
|
||||
@ -153,13 +58,13 @@ class Simulation:
|
||||
if parallel and not os.environ.get('SENPY_DEBUG', None):
|
||||
p = Pool()
|
||||
func = partial(self.run_trial_exceptions, **kwargs)
|
||||
for i in p.imap_unordered(func, range(self.num_trials)):
|
||||
for i in p.imap_unordered(func, range(self.config.num_trials)):
|
||||
if isinstance(i, Exception):
|
||||
logger.error('Trial failed:\n\t%s', i.message)
|
||||
continue
|
||||
yield i
|
||||
else:
|
||||
for i in range(self.num_trials):
|
||||
for i in range(self.config.num_trials):
|
||||
yield self.run_trial(trial_id=i,
|
||||
**kwargs)
|
||||
|
||||
@ -179,50 +84,47 @@ class Simulation:
|
||||
outdir=outdir,
|
||||
**exporter_params)
|
||||
stats = serialization.deserialize_all(simulation=self,
|
||||
names=stats,
|
||||
known_modules=['soil.stats',],
|
||||
**stats_params)
|
||||
names=stats,
|
||||
known_modules=['soil.stats',],
|
||||
**stats_params)
|
||||
|
||||
with utils.timer('simulation {}'.format(self.name)):
|
||||
with utils.timer('simulation {}'.format(self.config.name)):
|
||||
for stat in stats:
|
||||
stat.start()
|
||||
stat.sim_start()
|
||||
|
||||
for exporter in exporters:
|
||||
exporter.start()
|
||||
|
||||
for env in self._run_sync_or_async(parallel=parallel,
|
||||
log_level=log_level,
|
||||
**kwargs):
|
||||
|
||||
collected = list(stat.trial(env) for stat in stats)
|
||||
for exporter in exporters:
|
||||
exporter.trial_start(env)
|
||||
|
||||
saved = self.save_stats(collected, t_step=env.now, trial_id=env.name)
|
||||
collected = list(stat.trial_end(env) for stat in stats)
|
||||
|
||||
saved = self._update_stats(collected, t_step=env.now, trial_id=env.name)
|
||||
|
||||
for exporter in exporters:
|
||||
exporter.trial(env, saved)
|
||||
exporter.trial_end(env, saved)
|
||||
|
||||
yield env
|
||||
|
||||
|
||||
collected = list(stat.end() for stat in stats)
|
||||
saved = self.save_stats(collected)
|
||||
saved = self._update_stats(collected)
|
||||
|
||||
for exporter in exporters:
|
||||
exporter.end(saved)
|
||||
exporter.sim_end(saved)
|
||||
|
||||
|
||||
def save_stats(self, collection, **kwargs):
|
||||
def _update_stats(self, collection, **kwargs):
|
||||
stats = dict(kwargs)
|
||||
for stat in collection:
|
||||
stats.update(stat)
|
||||
self._history.save_stats(utils.flatten_dict(stats))
|
||||
return stats
|
||||
|
||||
def get_stats(self, **kwargs):
|
||||
return self._history.get_stats(**kwargs)
|
||||
|
||||
def log_stats(self, stats):
|
||||
logger.info('Stats: \n{}'.format(yaml.dump(stats, default_flow_style=False)))
|
||||
|
||||
|
||||
def get_env(self, trial_id=0, **kwargs):
|
||||
'''Create an environment for a trial of the simulation'''
|
||||
@ -246,18 +148,20 @@ class Simulation:
|
||||
env = self.environment_class(**opts)
|
||||
return env
|
||||
|
||||
def run_trial(self, trial_id=0, until=None, log_level=logging.INFO, **opts):
|
||||
def run_trial(self, trial_id=None, until=None, log_level=logging.INFO, **opts):
|
||||
"""
|
||||
Run a single trial of the simulation
|
||||
|
||||
"""
|
||||
trial_id = trial_id if trial_id is not None else current_time()
|
||||
if log_level:
|
||||
logger.setLevel(log_level)
|
||||
# Set-up trial environment and graph
|
||||
until = until or self.max_time
|
||||
env = self.get_env(trial_id=trial_id, **opts)
|
||||
until = until or self.config.max_time
|
||||
|
||||
env = Environment.from_config(self.config, trial_id=trial_id)
|
||||
# Set up agents on nodes
|
||||
with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
|
||||
with utils.timer('Simulation {} trial {}'.format(self.config.name, trial_id)):
|
||||
env.run(until)
|
||||
return env
|
||||
|
||||
@ -274,64 +178,6 @@ class Simulation:
|
||||
ex.message = ''.join(traceback.format_exception(type(ex), ex, ex.__traceback__)[:])
|
||||
return ex
|
||||
|
||||
def to_dict(self):
|
||||
return self.__getstate__()
|
||||
|
||||
def to_yaml(self):
|
||||
return yaml.dump(self.to_dict())
|
||||
|
||||
|
||||
def dump_yaml(self, f=None, outdir=None):
|
||||
if not f and not outdir:
|
||||
raise ValueError('specify a file or an output directory')
|
||||
|
||||
if not f:
|
||||
f = os.path.join(outdir, '{}.dumped.yml'.format(self.name))
|
||||
|
||||
with utils.open_or_reuse(f, 'w') as f:
|
||||
f.write(self.to_yaml())
|
||||
|
||||
def dump_pickle(self, f=None, outdir=None):
|
||||
if not outdir and not f:
|
||||
raise ValueError('specify a file or an output directory')
|
||||
|
||||
if not f:
|
||||
f = os.path.join(outdir,
|
||||
'{}.simulation.pickle'.format(self.name))
|
||||
with utils.open_or_reuse(f, 'wb') as f:
|
||||
pickle.dump(self, f)
|
||||
|
||||
def dump_sqlite(self, f):
|
||||
return self._history.dump(f)
|
||||
|
||||
def __getstate__(self):
|
||||
state={}
|
||||
for k, v in self.__dict__.items():
|
||||
if k[0] != '_':
|
||||
state[k] = v
|
||||
state['topology'] = json_graph.node_link_data(self.topology)
|
||||
state['network_agents'] = agents.serialize_definition(self.network_agents,
|
||||
known_modules = [])
|
||||
state['environment_agents'] = agents.serialize_definition(self.environment_agents,
|
||||
known_modules = [])
|
||||
state['environment_class'] = serialization.serialize(self.environment_class,
|
||||
known_modules=['soil.environment'])[1] # func, name
|
||||
if state['load_module'] is None:
|
||||
del state['load_module']
|
||||
return state
|
||||
|
||||
def __setstate__(self, state):
|
||||
self.__dict__ = state
|
||||
self.load_module = getattr(self, 'load_module', None)
|
||||
if self.dir_path not in sys.path:
|
||||
sys.path += [self.dir_path, os.getcwd()]
|
||||
self.topology = json_graph.node_link_graph(state['topology'])
|
||||
self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
|
||||
self.environment_agents = agents._convert_agent_types(self.environment_agents,
|
||||
known_modules=[self.load_module])
|
||||
self.environment_class = serialization.deserialize(self.environment_class,
|
||||
known_modules=[self.load_module, 'soil.environment', ]) # func, name
|
||||
|
||||
|
||||
def all_from_config(config):
|
||||
configs = list(serialization.load_config(config))
|
||||
|
@ -8,18 +8,23 @@ class Stats:
|
||||
if you don't plan to implement all the methods.
|
||||
'''
|
||||
|
||||
def __init__(self, simulation):
|
||||
def __init__(self, simulation, name=None):
|
||||
self.name = name or type(self).__name__
|
||||
self.simulation = simulation
|
||||
|
||||
def start(self):
|
||||
def sim_start(self):
|
||||
'''Method to call when the simulation starts'''
|
||||
pass
|
||||
|
||||
def end(self):
|
||||
def sim_end(self):
|
||||
'''Method to call when the simulation ends'''
|
||||
return {}
|
||||
|
||||
def trial(self, env):
|
||||
def trial_start(self, env):
|
||||
'''Method to call when a trial starts'''
|
||||
return {}
|
||||
|
||||
def trial_end(self, env):
|
||||
'''Method to call when a trial ends'''
|
||||
return {}
|
||||
|
||||
@ -30,12 +35,12 @@ class distribution(Stats):
|
||||
the mean value, and its deviation.
|
||||
'''
|
||||
|
||||
def start(self):
|
||||
def sim_start(self):
|
||||
self.means = []
|
||||
self.counts = []
|
||||
|
||||
def trial(self, env):
|
||||
df = env.df()
|
||||
def trial_end(self, env):
|
||||
df = pd.DataFrame(env.state_to_tuples())
|
||||
df = df.drop('SEED', axis=1)
|
||||
ix = df.index[-1]
|
||||
attrs = df.columns.get_level_values(0)
|
||||
@ -60,7 +65,7 @@ class distribution(Stats):
|
||||
|
||||
return stats
|
||||
|
||||
def end(self):
|
||||
def sim_end(self):
|
||||
dfm = pd.DataFrame(self.means, columns=['metric', 'key', 'value'])
|
||||
dfc = pd.DataFrame(self.counts, columns=['metric', 'key', 'value', 'count'])
|
||||
|
||||
@ -87,7 +92,7 @@ class distribution(Stats):
|
||||
|
||||
class defaultStats(Stats):
|
||||
|
||||
def trial(self, env):
|
||||
def trial_end(self, env):
|
||||
c = Counter()
|
||||
c.update(a.__class__.__name__ for a in env.network_agents)
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user