def update_habitat_water_depth(h: Habitat, x=0):
"""
Simulate change in habitat's characteristics (water depth) over time
TODO: docs
"""
if h.id == C.LAGOON_ORANGE_SM:
h.props['w'] = -0.00002 * x**2 + 0.064 * x + 10.034
elif h.id == C.LAGOON_ORANGE_LG:
h.props['w'] = -0.0001 * x**2 + 0.0987 * x + 6.1176
elif h.id == C.LAGOON_BLUE:
h.props['w'] = -0.00003 * x**2 + 0.0636 * x + 34.114
elif h.id == C.LAGOON_GREEN:
h.props['w'] = -0.00005 * x**2 + 0.061 * x + 97.442
def __init__(self, env_x, env_y, env_size_x, env_size_y, habitat_side_length = 10, cell_side_length = 1):
self.env_x = env_x
self.env_y = env_y
self.env_size_x = env_size_x
self.env_size_y = env_size_y
self.habitat_side_length = habitat_side_length
self.cell_side_length = cell_side_length
row_hab_id = 0
col_hab_id = 0
self.habitat_cell_grid = []
self.habitat_array = []
for row in range(int(self.env_size_y) // int(self.cell_side_length)):
self.habitat_cell_grid.append([])
if row % (int(self.habitat_side_length) // int(self.cell_side_length)) == 0 and row != 0:
# inside a new habitat
row_hab_id = col_hab_id + 1
col_hab_id = row_hab_id
for col in range(int(self.env_size_x) // int(self.cell_side_length)):
hab_x = env_x + col * cell_side_length
hab_y = env_y + row * cell_side_length
if col % (int(self.habitat_side_length) // int(self.cell_side_length))== 0:
if col != 0:
# inside a new habitat
col_hab_id += 1
if row % (int(self.habitat_side_length) // int(self.cell_side_length)) == 0:
# need to add a new habitat into the habitat array
self.habitat_array.append(Habitat(hab_x, hab_y, col_hab_id, self.habitat_side_length))
self.habitat_cell_grid[row].append(HabitatCell(hab_x, hab_y, col_hab_id, side_length = self.cell_side_length))
def create_patches():
habitats = []
verts, props = C.DEFAULTS['verts'], C.DEFAULTS['props']
# prepare static patches (habitats and human settlements)
orange_sm = Habitat(C.LAGOON_ORANGE_SM, C.LAGOON_TYPE_ORANGE,
C.COLORS[C.LAGOON_ORANGE_SM])
orange_sm.verts = verts[C.LAGOON_ORANGE_SM]
orange_sm.props = props[C.LAGOON_ORANGE_SM]
orange_sm.label = C.LABELS[C.LAGOON_ORANGE_SM]
orange_sm.build()
habitats.append(orange_sm)
orange_lg = Habitat(C.LAGOON_ORANGE_LG, C.LAGOON_TYPE_ORANGE,
C.COLORS[C.LAGOON_ORANGE_LG])
orange_lg.verts = verts[C.LAGOON_ORANGE_LG]
orange_lg.props = props[C.LAGOON_ORANGE_LG]
orange_lg.label = C.LABELS[C.LAGOON_ORANGE_LG]
orange_lg.build()
habitats.append(orange_lg)
blue = Habitat(C.LAGOON_BLUE, C.LAGOON_TYPE_BLUE, C.COLORS[C.LAGOON_BLUE])
blue.verts = verts[C.LAGOON_BLUE]
blue.props = props[C.LAGOON_BLUE]
blue.label = C.LABELS[C.LAGOON_BLUE]
blue.build()
habitats.append(blue)
green = Habitat(C.LAGOON_GREEN, C.LAGOON_TYPE_GREEN,
C.COLORS[C.LAGOON_GREEN])
green.verts = verts[C.LAGOON_GREEN]
green.props = props[C.LAGOON_GREEN]
green.label = C.LABELS[C.LAGOON_GREEN]
green.build()
habitats.append(green)
human1 = Habitat(C.HUMAN_SETTLEMENT, C.HUMAN_SETTLEMENT,
C.COLORS[C.HUMAN_SETTLEMENT])
human1.verts = verts[C.HUMAN_SETTLEMENT + '1']
human1.label = C.LABELS[C.HUMAN_SETTLEMENT]
human1.build(fill=True)
habitats.append(human1)
human2 = Habitat(C.HUMAN_SETTLEMENT, C.HUMAN_SETTLEMENT,
C.COLORS[C.HUMAN_SETTLEMENT])
human2.verts = verts[C.HUMAN_SETTLEMENT + '2']
human2.label = C.LABELS[C.HUMAN_SETTLEMENT]
human2.build(fill=True)
habitats.append(human2)
human3 = Habitat(C.HUMAN_SETTLEMENT, C.HUMAN_SETTLEMENT,
C.COLORS[C.HUMAN_SETTLEMENT])
human3.verts = verts[C.HUMAN_SETTLEMENT + '3']
human3.label = C.LABELS[C.HUMAN_SETTLEMENT]
human3.build(fill=True)
habitats.append(human3)
return habitats
#### LOAD human locations
humans = fiona.open("C:\\Users\\Sjors\\Dropbox\\GIMAMasterThesis\\Data\\human_v2.shp")
for feat in humans:
human = Human(feat['geometry']['coordinates'][0],feat['geometry']['coordinates'][1], feat['properties']['age'])
human.SEI.totalInfections = feat['properties']['prev_infec']
human.SEI.totalInfections = 0
if random.randint(1,2) == 2:
human.SEI.currentState = I()
myModel.agentContainer['humanContainer'].append(human)
#### LOAD HABITATS
habitats = fiona.open("C:\\Users\\Sjors\\Dropbox\\GIMAMasterThesis\\Data\\habitat.shp")
for feat in habitats:
habitat = Habitat(feat['geometry']['coordinates'][0],feat['geometry']['coordinates'][1])
habitat.size = 50
myModel.agentContainer['habitatContainer'].append(habitat)
# Create mosquitos
for i in xrange(500): #500 initial mozzies
myModel.agentContainer['mosquitoContainer'].append(Mosquito())
myModel.agentContainer['mosquitoContainer'][i].age = np.random.randint(0,40) #initial age between 0 and 40 days
myModel.agentContainer['mosquitoContainer'][i].x = np.random.randint(0,1250)
myModel.agentContainer['mosquitoContainer'][i].y = np.random.randint(0,1250)
if (i % 2) == 0:
myModel.agentContainer['mosquitoContainer'][i].SEI.currentState = I()
## Load in temperature data
myModel.fieldContainer['climate'] = read_csv('C:\\Users\\Sjors\\Dropbox\\GIMAMasterThesis\\OOMscripts\\climateBoboDioulassov2.csv', sep=';', index_col='name')
class Penguin(Walking, Swimming):
def __init__(self, name):
self.name = name
def run(self):
print(f"{self.name} the Penguin waddles")
if __name__ == "__main__":
# Create a penguin
bob = Penguin("Bob")
# Create a habitat
SeaWorld = Habitat("Jerry")
SeaWorld.add_animal(bob)
print(SeaWorld.animals)
class PaintedDog(Walking):
def __init__(self, name):
self.name = name
if __name__ == "__main__":
bob = Penguin("Bob")
ralph = PaintedDog("Ralph")
import sys
from habitat import Habitat
h = Habitat()
#h.test_feeder(1,1000,1,0)
h.start_experiment("test", "10_05", 5)
for i in range(4):
h.close_door(i)
for i in range(4):
r = h.open_door(i)
for i in range(4):
r = h.close_door(i)
for e in range(3):
print(h.feeder_reached(1))
for x in range(-20, 21):
print(h.track("mouse", x, 0))
print(h.feeder_reached(2))
print(h.finish_experiment())
print("ALL TEST FINISHED OK")
import unittest
from habitat import Habitat
try:
test_habitat = Habitat()
except NameError:
test_habitat = False
class Habitat_test(unittest.TestCase):
def test_habitat_is_defined(self):
"""
See if the object has been created
"""
self.assertTrue(test_habitat)
"""
See if created object is an instance of Habitat
"""
self.assertIsInstance(test_habitat, Habitat)
if __name__ == '__main__':
unittest.main()
def is_pangolin(self, animal):
Habitat()
return animal
# retrieving habitat data from characteristics at www.bfn.de
# retrieving contents of html page
hab_url = ''.join((URL_PREFIX, sitecode))
hab_conn = urllib2.urlopen(hab_url)
hab_doc = lxml.html.parse(hab_conn).getroot()
contents = hab_doc.get_element_by_id('content')
# finding name data (incl. sitecode, name, ...)
hab_name_data = contents.xpath('*/div/h2')[0].text_content().encode('utf-8')
match = re.search(NAME_REGEX, hab_name_data)
if match is not None:
hab_name = match.group(1)
# creating new habitat
hab = Habitat(sitecode, hab_name)
# find further habitat data
other_data = contents.findall('div/div/p')
# containing administrative area
fed_state = other_data[0].text_content().encode('utf-8')
try:
nuts_code = NUTS_CODES[fed_state]
except:
nuts_code = ''
# biogreophical region and size
region = other_data[1].text_content().encode('utf-8')
# separating region and size
region_size_match = re.search(REGION_SIZE_REGEX, region)
if region_size_match is not None: