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 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)
