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Code Issues Releases Wiki Activity

WIP

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This commit is contained in:
J. Fernando Sánchez
2022-04-04 16:00:54 +02:00
parent 1a8313e4f6
commit 6f7481769e
9 changed files with 467 additions and 362 deletions
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174
soil/environment.py
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@@ -1,23 +1,20 @@
from __future__ import annotations
import os
import sqlite3
import csv
import math
import random
import yaml
import tempfile
import logging
import pandas as pd
from time import time as current_time
from copy import deepcopy
from networkx.readwrite import json_graph
import networkx as nx
from tsih import History, NoHistory, Record, Key
import networkx as nx
from mesa import Model
from . import serialization, agents, analysis, utils, time
from tsih import Record
from . import serialization, agents, analysis, utils, time, config
# These properties will be copied when pickling/unpickling the environment
_CONFIG_PROPS = [ 'name',
@@ -49,7 +46,6 @@ class Environment(Model):
schedule=None,
initial_time=0,
environment_params=None,
history=False,
dir_path=None,
**kwargs):
@@ -76,20 +72,11 @@ class Environment(Model):
topology = nx.Graph()
self.G = nx.Graph(topology)
self.environment_params = environment_params or {}
self.environment_params.update(kwargs)
self._env_agents = {}
self.interval = interval
if history:
history = History
else:
history = NoHistory
self._history = history(name=self.name,
backup=True)
self['SEED'] = seed
if network_agents:
@@ -106,6 +93,19 @@ class Environment(Model):
self.logger = utils.logger.getChild(self.name)
@staticmethod
def from_config(conf: config.Config, trial_id, **kwargs) -> Environment:
'''Create an environment for a trial of the simulation'''
conf = config.Config(conf, **kwargs)
conf.seed = '{}_{}'.format(conf.seed, trial_id)
conf.name = '{}_trial_{}'.format(conf.name, trial_id).replace('.', '-')
opts = conf.environment_params.copy()
opts.update(conf)
opts.update(kwargs)
env = serialization.deserialize(conf.environment_class)(**opts)
return env
@property
def now(self):
if self.schedule:
@@ -212,11 +212,14 @@ class Environment(Model):
return self.logger.log(level, message, extra=extra)
def step(self):
'''
Advance one step in the simulation, and update the data collection and scheduler appropriately
'''
super().step()
self.schedule.step()
def run(self, until, *args, **kwargs):
self._save_state()
until = until or float('inf')
while self.schedule.next_time < until:
self.step()
@@ -252,14 +255,16 @@ class Environment(Model):
def get(self, key, default=None):
'''
Get the value of an environment attribute in a
given point in the simulation (history).
If key is an attribute name, this method returns
the current value.
To get values at other times, use a
:meth: `soil.history.Key` tuple.
Get the value of an environment attribute.
Return `default` if the value is not set.
'''
return self[key] if key in self else default
return self.environment_params.get(key, default)
def __getitem__(self, key):
return self.environment_params.get(key)
def __setitem__(self, key, value):
return self.environment_params.__setitem__(key, value)
def get_agent(self, agent_id):
return self.G.nodes[agent_id]['agent']
@@ -269,112 +274,31 @@ class Environment(Model):
return self.agents
return (self.G.nodes[i]['agent'] for i in nodes)
def dump_csv(self, f):
with utils.open_or_reuse(f, 'w') as f:
cr = csv.writer(f)
cr.writerow(('agent_id', 't_step', 'key', 'value'))
for i in self.history_to_tuples():
cr.writerow(i)
def dump_gexf(self, f):
G = self.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")
def dump(self, *args, formats=None, **kwargs):
if not formats:
return
functions = {
'csv': self.dump_csv,
'gexf': self.dump_gexf
}
for f in formats:
if f in functions:
functions[f](*args, **kwargs)
else:
raise ValueError('Unknown format: {}'.format(f))
def df(self):
return self._history[None, None, None].df()
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 = []