def main():
#directory containing simulation output files (relative or absolute path)
directory = 'exampleSimulation'
filenames = "SIR"
plotStates = True #set to False if you only want the visualisation
animate = True #set to False if you only want the plotting
# Parameters for plotting of system states
# define those states you wish to appear on the plot,
# along with their colour and label
statesToMonitor = [INFECTED, SUSCEPTIBLE]
colours = ["r", "g"]
labels = ["Infected", "Susceptible"]
titlePlot = "Simulation of agent-based simple SIR"
# Parameters for animated visualisations
# define a mapping from state to colour
# define the specific trial you wish to visualise. Default=0, first trial
mapping = {SUSCEPTIBLE: "w", INFECTED: "r", RECOVERED: "0.4"}
titleVisual = "Simulation of agent-based simple SIR"
trialToVisualise = 0
if animate: #run visualisation
visualiser = AnimationCreator(directory,
filenames,
titleVisual,
mapping,
trial=trialToVisualise)
visualiser.create_gif(verbose=True)
if plotStates: #plot results
p = PlotCreator(directory, filenames, titlePlot, statesToMonitor,
colours, labels)
p.plotSimulation(show=False)
def main(nodes=30):
# Model parameters
directory = 'test'
globalSharedParameters = {}
globalSharedParameters['infection_rate'] = 0.3
globalSharedParameters['inf_dur'] = "self.r.gauss(7, 2)"
# Output Parameters
statesToMonitor = [INFECTED, SUSCEPTIBLE, RECOVERED]
colours = ["r", "--g", ":k"]
mapping = {SUSCEPTIBLE: "w", INFECTED: "r", RECOVERED: "0.4"}
labels = ["Infected", "Susceptible", "Recovered"]
name = "SIR_scale_free"
titlePlot = "Simulation on scale free graph, %i trials, %i%% infection prob" \
% (TRIALS, 100 * globalSharedParameters['infection_rate'])
titleVisual = ""
# Network
G = nx.scale_free_graph(nodes)
states = [SUSCEPTIBLE for n in G.nodes()]
# run simulation
simulation = NetworkSimulation(G, states, agentClass, directory,
MAX_SIMULATION_TIME, TRIALS,
environmentAgent, **globalSharedParameters)
simulation.runSimulation()
# run visualisation
gif = AnimationCreator(directory, name, titleVisual, mapping)
gif.create_gif()
# plot results
p = PlotCreator(directory, name, titlePlot, statesToMonitor, colours,
labels)
p.plotSimulation()
def main():
#directory containing simulation output files (relative or absolute path)
directory = 'exampleSimulation'
filenames = "SIR"
plotStates = True #set to False if you only want the visualisation
animate = True #set to False if you only want the plotting
# Parameters for plotting of system states
# define those states you wish to appear on the plot,
# along with their colour and label
statesToMonitor = [INFECTED, SUSCEPTIBLE]
colours = ["r", "g"]
labels = ["Infected", "Susceptible"]
titlePlot = "Simulation of agent-based simple SIR"
# Parameters for animated visualisations
# define a mapping from state to colour
# define the specific trial you wish to visualise. Default=0, first trial
mapping = {SUSCEPTIBLE:"w", INFECTED:"r", RECOVERED:"0.4"}
titleVisual = "Simulation of agent-based simple SIR"
trialToVisualise = 0
if animate: #run visualisation
visualiser = AnimationCreator(directory, filenames, titleVisual, mapping, trial=trialToVisualise)
visualiser.create_gif(verbose=True)
if plotStates: #plot results
p = PlotCreator(directory, filenames, titlePlot, statesToMonitor, colours, labels)
p.plotSimulation(show=False)
def simulate(**kwargs):
# Model parameters
directory = kwargs.get("directory", 'skype')
agentClass = kwargs.get("agentClass", Skype)
environmentAgent = kwargs.get("environmentAgent", crash)
NUMBER_SUPERNODES = kwargs.get("supernodes", 90)
NUMBER_NODES = kwargs.get("nodes", 600)
NUMBER_PERMANENT_SUPERNODES = kwargs.get("permanent_supernodes", 1)
globalSharedParameters = {}
globalSharedParameters['supernodes'] = list(range(NUMBER_SUPERNODES))
globalSharedParameters['permanent_supernodes'] = list(range(NUMBER_PERMANENT_SUPERNODES))
globalSharedParameters['threshold'] = kwargs.get("threshold", 12)
globalSharedParameters['cache_size'] = kwargs.get("cache_size", 20)
globalSharedParameters['kills'] = kwargs.get("kills", 30)
globalSharedParameters['restart_time'] = kwargs.get('restart_time', "4.0")
# Output Parameters
statesToMonitor = [ENABLED, ENABLED_S]
colours = ["g", "^b", "0.5"]
mapping = {ENABLED:"g", ENABLED_S: "b", DISABLED:"0.2", DISABLED_S: "0.4"}
labels = ["Online nodes", "Online supernodes", "Offline"]
name = "skype"
titlePlot = "Skype simulation, %i trials, threshold=%i, cacheSize=%i \n supernode_restart_distr=%s" % \
(TRIALS, globalSharedParameters['threshold'], globalSharedParameters['cache_size'],
str(globalSharedParameters['restart_time']))
titleVisual = "Skype visualisation"
#####topology####
G = nx.Graph(nx.complete_graph(NUMBER_SUPERNODES))
G.add_nodes_from(range(NUMBER_SUPERNODES,NUMBER_NODES+NUMBER_SUPERNODES))
states = [DISABLED for node in G.nodes_iter()]
# run simulation
simulation = NetworkSimulation(G,
states,
agentClass,
directory,
MAX_SIMULATION_TIME,
TRIALS,
environmentAgent,
**globalSharedParameters)
simulation.runSimulation()
# # run visualisation
# gif = AnimationCreator(directory, name, titleVisual, mapping)
# gif.create_gif()
# plot results
p = PlotCreator(directory, name, titlePlot, statesToMonitor,
colours, labels)
p.plotSimulation()
def simulate(**kwargs):
# Model parameters
directory = kwargs.get("directory", 'skype')
agentClass = kwargs.get("agentClass", Skype)
environmentAgent = kwargs.get("environmentAgent", crash)
NUMBER_SUPERNODES = kwargs.get("supernodes", 90)
NUMBER_NODES = kwargs.get("nodes", 600)
NUMBER_PERMANENT_SUPERNODES = kwargs.get("permanent_supernodes", 1)
globalSharedParameters = {}
globalSharedParameters['supernodes'] = range(NUMBER_SUPERNODES)
globalSharedParameters['permanent_supernodes'] = range(NUMBER_PERMANENT_SUPERNODES)
globalSharedParameters['threshold'] = kwargs.get("threshold", 12)
globalSharedParameters['cache_size'] = kwargs.get("cache_size", 20)
globalSharedParameters['kills'] = kwargs.get("kills", 30)
globalSharedParameters['restart_time'] = kwargs.get('restart_time', "4.0")
# Output Parameters
statesToMonitor = [ENABLED, ENABLED_S]
colours = ["g", "^b", "0.5"]
mapping = {ENABLED:"g", ENABLED_S: "b", DISABLED:"0.2", DISABLED_S: "0.4"}
labels = ["Online nodes", "Online supernodes", "Offline"]
name = "skype"
titlePlot = "Skype simulation, %i trials, threshold=%i, cacheSize=%i \n supernode_restart_distr=%s" % \
(TRIALS, globalSharedParameters['threshold'], globalSharedParameters['cache_size'],
str(globalSharedParameters['restart_time']))
titleVisual = "Skype visualisation"
#####topology####
G = nx.Graph(nx.complete_graph(NUMBER_SUPERNODES))
G.add_nodes_from(xrange(NUMBER_SUPERNODES,NUMBER_NODES+NUMBER_SUPERNODES))
states = [DISABLED for node in G.nodes_iter()]
# run simulation
simulation = NetworkSimulation(G,
states,
agentClass,
directory,
MAX_SIMULATION_TIME,
TRIALS,
environmentAgent,
**globalSharedParameters)
simulation.runSimulation()
# # run visualisation
# gif = AnimationCreator(directory, name, titleVisual, mapping)
# gif.create_gif()
# plot results
p = PlotCreator(directory, name, titlePlot, statesToMonitor,
colours, labels)
p.plotSimulation()
def main(nodes=30):
# Model parameters
directory = 'test'
globalSharedParameters = {}
globalSharedParameters['infection_rate'] = 0.3
globalSharedParameters['inf_dur'] = "self.r.gauss(7, 2)"
# Output Parameters
statesToMonitor = [INFECTED, SUSCEPTIBLE, RECOVERED]
colours = ["r", "--g", ":k"]
mapping = {SUSCEPTIBLE:"w", INFECTED:"r", RECOVERED:"0.4"}
labels = ["Infected", "Susceptible", "Recovered"]
name = "SIR_scale_free"
titlePlot = "Simulation on scale free graph, %i trials, %i%% infection prob" \
% (TRIALS, 100 * globalSharedParameters['infection_rate'])
titleVisual = ""
# Network
G = nx.scale_free_graph(nodes)
states = [SUSCEPTIBLE for n in G.nodes()]
# run simulation
simulation = NetworkSimulation(G,
states,
agentClass,
directory,
MAX_SIMULATION_TIME,
TRIALS,
environmentAgent,
**globalSharedParameters)
simulation.runSimulation()
# run visualisation
gif = AnimationCreator(directory, name, titleVisual, mapping)
gif.create_gif()
# plot results
p = PlotCreator(directory, name, titlePlot, statesToMonitor,
colours, labels)
p.plotSimulation()
Complete code file only from ComplexNetworkSim's "getting started" documentation section, for visualising a simulation. For explanations refer to the documentation page.
Current link: http://complexnetworksim.0sites.net/start.html (documentation hosting may change place - see the PyPi index page.)
@author: Joe Schaul <*****@*****.**>
'''
from ComplexNetworkSim import PlotCreator, AnimationCreator
directory = 'test' #location of simulation result files
myName = "SIR" #name that you wish to give your image output files
title = "Simulation of agent-based simple SIR"
#define three simulation-specific constants:
SUSCEPTIBLE = 0
INFECTED = 1
RECOVERED = 2
statesToMonitor = [INFECTED, SUSCEPTIBLE] #even if we have states 0,1,2,3,... plot only 1 and 0
colours = ["r", "g"] #state 1 in red, state 0 in green
labels = ["Infected", "Susceptible"] #state 1 named 'Infected', 0 named 'Susceptible'
mapping = {SUSCEPTIBLE:"w", INFECTED:"r", RECOVERED:"0.4"}
trialToVisualise = 0
p = PlotCreator(directory, myName, title, statesToMonitor, colours, labels)
p.plotSimulation(show=False)
#show=True shows the graph directly,
#otherwise only a png file is created in the directory defined above.
visualiser = AnimationCreator(directory, myName, title, mapping, trial=trialToVisualise)
#gif speed can be changed by giving a parameter 'delay' (default=100) to AnimationCreator
visualiser.create_gif(verbose=True)
from ComplexNetworkSim import PlotCreator, AnimationCreator
directory = 'test' #location of simulation result files
myName = "SIR" #name that you wish to give your image output files
title = "Simulation of agent-based simple SIR"
#define three simulation-specific constants:
SUSCEPTIBLE = 0
INFECTED = 1
RECOVERED = 2
statesToMonitor = [INFECTED, SUSCEPTIBLE
] #even if we have states 0,1,2,3,... plot only 1 and 0
colours = ["r", "g"] #state 1 in red, state 0 in green
labels = ["Infected",
"Susceptible"] #state 1 named 'Infected', 0 named 'Susceptible'
mapping = {SUSCEPTIBLE: "w", INFECTED: "r", RECOVERED: "0.4"}
trialToVisualise = 0
p = PlotCreator(directory, myName, title, statesToMonitor, colours, labels)
p.plotSimulation(show=False)
#show=True shows the graph directly,
#otherwise only a png file is created in the directory defined above.
visualiser = AnimationCreator(directory,
myName,
title,
mapping,
trial=trialToVisualise)
#gif speed can be changed by giving a parameter 'delay' (default=100) to AnimationCreator
visualiser.create_gif(verbose=True)