class Model(object):
def __init__(self):
self.tick = 0
self.clock = Clock()
self.agentContainer = {'humanContainer': [], 'mosquitoContainer': [], 'habitatContainer': []}
self.fieldContainer = {'climate': None,'precipitation': None, 'temperature': None}
self.environment = Map(0,0,1250,1250)
self.options = {'graph': True, 'animation': True, 'saveOutput':True}
self.tracker = Tracker()
self.saveRaster = None
def createInstance(self, container, agentType, amount):
for i in xrange(amount):
container.append(agentType)
def run(self, ticks):
self.ticks = ticks
for tick in xrange(self.ticks):
# Enable time in model
self.clock.tick()
self.tick = tick
if self.tick % 100 == 0:
print self.agentContainer['habitatContainer'][0].getCarryingCapacity()
print self.tick
######## Environment part
self.fieldContainer['temperature'] = self.fieldContainer['climate'].loc[self.clock.month, 'h'+str(self.clock.hours) ]
self.fieldContainer['monthPrecipitation'] = self.fieldContainer['climate'].loc[self.clock.month, 'precipitation']
self.fieldContainer['rainyDays'] =self.fieldContainer['climate'].loc[self.clock.month, 'rainydays']
self.environment.rainToday = 0
if self.clock.hours == 6:
self.environment.rainToday = self.environment.rain( float(self.clock.daysPerMonth[self.clock.month]) , float(self.fieldContainer['rainyDays']) )
self.fieldContainer['hourlyPrecipitation'] =self.fieldContainer['monthPrecipitation'] / self.clock.daysPerMonth[self.clock.month] / 24.0
######## Habitat part
for habitat in self.agentContainer['habitatContainer']:
habitat.waterBalance(self.environment.rainToday)
#Calculate carrying capacity( m3 * 6.25) and biomass (non adult = 1) in a range of 25 meters for each habitat
carryingCapacity = int(habitat.getCarryingCapacity())
biomass = habitat.getBiomass(self.agentContainer['mosquitoContainer'])
if biomass > carryingCapacity:
# pick newest slice of non adult mosquios from the pool to simulate cannibalism
toBeRemoved = habitat.nonAdults[(carryingCapacity-(biomass-carryingCapacity)):carryingCapacity]
# Remove these eggs from the total container
for agent in toBeRemoved:
self.agentContainer['mosquitoContainer'].remove(agent)
######## Human immigration
rand = np.random.uniform(0,1)
if rand < 0.001:
### make this dependent on village contours?
human = Human(np.random.randint(500,800), np.random.randint(500,800), np.random.randint(20,50))
if rand <0.0005:
human.SEI.currentState = I()
self.agentContainer['humanContainer'].append(human)
####### Human emigration
rand3 = np.random.uniform(0,1)
if rand3 < 0.001:
rand2 = np.random.randint(0, len(self.agentContainer['humanContainer']))
self.agentContainer['humanContainer'].pop(rand2-1)
######## Human part
for human in self.agentContainer['humanContainer']:
#run SEI model
human.SEI.run_all()
####### Mosquito part
for mosquito in self.agentContainer['mosquitoContainer']:
#Calculate once per day if mosquito should die
if self.clock.hours == 6:
if mosquito.calcDeathchance():
self.agentContainer['mosquitoContainer'].remove(mosquito)
continue
#TO DO: Fix conversion formula
# Out of bounds check:
if self.environment.outOfBounds(mosquito):
#remove out of bounds mosquitos
self.agentContainer['mosquitoContainer'].remove(mosquito)
continue
# GENERAL MOZZIE FUNCTIONS
#Get older (runs age of mosquitos)
mosquito.development(self.fieldContainer['temperature'])
#run SEI model.
mosquito.SEI.run_all()
#run mosquito movement
mosquito.newMove(self.clock, self.agentContainer['humanContainer'], self.agentContainer['habitatContainer'], self.agentContainer['mosquitoContainer'])
#### DATA SAVE###
## save module
#Save data every month
if self.tick % (30*24) == 0:
self.save()
########Visualisation engine########
if self.options['graph']:
self.graphPlotter()
if self.options['animation']:
self.animationPlotter()
def animationPlotter(self):
if self.tick == 0:
plt.ion()
## plotting module
if self.clock.isNight:
#Plot all mosquitos, humans and mosquitos
mozziex, mozziey = [mosquito.x for mosquito in self.agentContainer['mosquitoContainer']], [mosquito.y for mosquito in self.agentContainer['mosquitoContainer']]
humanx, humany = [human.x for human in self.agentContainer['humanContainer']], [human.y for human in self.agentContainer['humanContainer']]
habitatx, habitaty = [habitat.x for habitat in self.agentContainer['habitatContainer']], [habitat.y for habitat in self.agentContainer['habitatContainer']]
plt.plot(mozziex, mozziey, 'o', color = 'blue')
plt.plot(humanx, humany, 'x', color = 'red')
plt.plot(habitatx, habitaty, 'x', color = 'green')
plt.ylim([self.environment.lowerY, self.environment.upperY])
plt.xlim([self.environment.lowerX, self.environment.upperX])
plt.draw()
plt.pause(0.0001)
plt.clf()
def graphPlotter(self):
#put initial settings here
if self.tick == 0:
#Create lists to keep track of total values
self.tracker.totalMosquitosInfected = []
self.tracker.totalHumansInfected =[]
self.tracker.adultMosquitos = []
self.tracker.totalHumans = []
# Calc totals
infHumans = [human for human in myModel.agentContainer['humanContainer'] if isinstance(human.SEI.currentState, I)]
infMosquitos = [mosquito for mosquito in self.agentContainer['mosquitoContainer'] if isinstance(mosquito.SEI.currentState, I)]
adultMosquitos = [mosquito for mosquito in self.agentContainer['mosquitoContainer'] if mosquito.state == 'adult']
# Append totals to list
self.tracker.tick.append(self.tick)
self.tracker.totalMosquitos.append(len(self.agentContainer['mosquitoContainer']))
self.tracker.totalMosquitosInfected.append(len(infMosquitos))
self.tracker.totalHumansInfected.append(len(infHumans))
self.tracker.adultMosquitos.append(len(adultMosquitos))
self.tracker.totalHumans.append(len(self.agentContainer['humanContainer']))
# Show list at final tick
if self.tick == (self.ticks-1):
plt.plot(self.tracker.totalHumans, 'r--', self.tracker.adultMosquitos, 'b--', self.tracker.totalMosquitosInfected, 'g', self.tracker.totalHumansInfected, 'y')
plt.show()
plt.savefig(outputFolder+'graph.png')
def save(self):
# Open raster file that serves as blueprint for saving data.
with fiona.open('C:/Users/Sjors/Dropbox/GIMAMasterThesis/OOMscripts/mold.shp', 'r') as blueprint:
blueprintRaster = list(blueprint)
schema = blueprint.schema
# Create copy of container
mosquitos = self.agentContainer['mosquitoContainer']
humans= self.agentContainer['humanContainer']
for square in blueprintRaster:
#Replace geometry dictionary with shapely polygon object
square['geometry'] = shape(square['geometry'])
#Get list of mosquitos inside geometry of square
mosquitoInSquare = [mosquito for mosquito in mosquitos if square['geometry'].contains(shapely.geometry.Point(mosquito.x, mosquito.y))]
#Get list of humans inside geometry of square
humanInSquare = [human for human in humans if square['geometry'].contains(shapely.geometry.Point(human.x, human.y))]
#Mosquito total
square['properties']['mtotal'] = len(mosquitoInSquare)
#Mosquito adult total
square['properties']['madult'] = len([mosquito for mosquito in mosquitoInSquare if mosquito.state == 'adult'])
#Mosquito infected total
square['properties']['minfect'] = len([mosquito for mosquito in mosquitoInSquare if isinstance(mosquito.SEI.currentState, (I,E))])
#Human total
square['properties']['htotal'] = len(humanInSquare)
#Human infected total
square['properties']['hinfect'] = len([human for human in humanInSquare if isinstance(human.SEI.currentState, (I, E))])
# Remove mosquitos and humans that are already found from the list to be searched
mosquitos = [mosquito for mosquito in mosquitos if mosquito not in mosquitoInSquare]
humans = [human for human in humans if human not in humanInSquare]
## Write data to file
with fiona.open(outputFolder+str(self.tick)+'.shp', 'w', 'ESRI Shapefile', schema) as output:
for square in blueprintRaster:
## Write output in file, filename has tick as name
output.write({
'geometry': mapping(square['geometry']),
'properties': square['properties']
})
