def setUpClass(cls):
# Setup and run simulation data, single hosts on lattice with exponential kernel
cls._data_stub = os.path.join("testing", "spatial_sim_output")
cls._beta_val = 10
cls._scale_val = 0.3
cls._end_time = 10
size = (20, 20)
# Create host file
host_raster = raster_tools.RasterData(size, array=np.ones(size))
host_file = os.path.join("testing", "spatial_host_test_case.txt")
host_raster.to_file(host_file)
# Create initial conditions files
init_stub = os.path.join("testing", "spatial_init_test_case")
host_raster.array[int(size[0]/2), int(size[1]/2)] = 0
host_raster.to_file(init_stub + "_S.txt")
host_raster.array = np.zeros(size)
host_raster.array[int(size[0]/2), int(size[1]/2)] = 1
host_raster.to_file(init_stub + "_I.txt")
# Create kernel file
kernel_range = 20
kernel_size = (2*kernel_range+1, 2*kernel_range+1)
kernel_raster = raster_tools.RasterData(kernel_size, array=np.zeros(kernel_size))
for i in range(kernel_size[0]):
for j in range(kernel_size[1]):
row = i - kernel_range
col = j - kernel_range
distance = np.sqrt(row*row + col*col)
# kernel_raster.array[i, j] = np.exp(-distance/cls._scale_val) / (
# 2 * np.pi * cls._scale_val * cls._scale_val)
kernel_raster.array[i, j] = np.exp(-distance/cls._scale_val)
kernel_raster.to_file(init_stub + "_kernel.txt")
# Setup config file
config_filename = os.path.join("testing", "spatial_config.ini")
config_str = "\n[Epidemiology]\n"
config_str += "Model = SI\nInfRate = " + str(cls._beta_val)
config_str += "\nIAdvRate = 0.0\nKernelType = RASTER\n"
config_str += "\n[Simulation]\n"
config_str += "SimulationType = RASTER\nFinalTime = " + str(cls._end_time) +"\n"
config_str += "NIterations = 100\n"
config_str += "HostPosFile = " + host_file + "\nInitCondFile = " + init_stub + "\n"
config_str += "KernelFile = " + init_stub + "_kernel.txt" + "\n"
config_str += "VirtualSporulationStart = 3\nMaxHosts = 1"
config_str += "\n[Output]\n"
config_str += "SummaryOutputFreq = 0\nOutputFileStub = " + cls._data_stub
config_str += "\n[Optimisation]\n"
config_str += "SaveSetup = False\nRateStructure-Infection = ratetree"
with open(config_filename, "w") as outfile:
outfile.write(config_str)
cls._raster_header = host_raster.header_vals
# Run simulations
IndividualSimulator.main(configFile=config_filename)
def setUp(self):
# Setup and run simulation data, single infected hosts on lattice with non-spatial kernel.
self._full_lambda = full_lambda
self._data_stub = os.path.join("testing",
"cont_intervention_sim_output")
size = (100, 100)
kernel_size = (3, 3)
kernel_centre = [int(x / 2) for x in kernel_size]
# Create host file
host_raster = raster_tools.RasterData(size, array=np.ones(size))
host_file = os.path.join("testing",
"cont_intervention_host_test_case.txt")
host_raster.to_file(host_file)
# Create initial conditions files
init_stub = os.path.join("testing", "cont_intervention_init_test_case")
host_raster.to_file(init_stub + "_I.txt")
host_raster.array = np.zeros(size)
host_raster.to_file(init_stub + "_S.txt")
host_raster.to_file(init_stub + "_R.txt")
# Create kernel file
kernel_raster = raster_tools.RasterData(kernel_size,
array=np.full(
kernel_size, 1.0))
kernel_raster.array[kernel_centre[0], kernel_centre[1]] = 0
kernel_raster.to_file(init_stub + "_kernel.txt")
self._kernel = kernel_raster.array
self._size = size
# Setup config file
self.config_filename = os.path.join("testing",
"cont_intervention_config.ini")
config_str = "\n[Epidemiology]\n"
config_str += "Model = SIR\nInfRate = 0"
config_str += "\nIAdvRate = " + str(
self._full_lambda / 2) + "\nKernelType = RASTER\n"
config_str += "\n[Simulation]\n"
config_str += "SimulationType = RASTER\nFinalTime = 1000\nNIterations = 1\n"
config_str += "HostPosFile = " + host_file + "\nInitCondFile = " + init_stub + "\n"
config_str += "KernelFile = " + init_stub + "_kernel.txt" + "\n"
config_str += "VirtualSporulationStart = None"
config_str += "\n[Output]\n"
config_str += "SummaryOutputFreq = 0\nOutputFileStub = " + self._data_stub
config_str += "\n[Optimisation]\n"
config_str += "SaveSetup = False"
config_str += "\n[Interventions]\n"
config_str += "InterventionUpdateFrequencies = None\n"
config_str += "UpdateOnAllEvents = True\n"
with open(self.config_filename, "w") as outfile:
outfile.write(config_str)
def create_initial_conditions(host_array,
out_stub="InitialConditions",
seed_inf_cell=(0, 0),
host_numbers=False,
prop_infected=1.0):
init_s_array = np.zeros(
(host_array.header_vals['nrows'], host_array.header_vals['ncols']))
init_i_array = np.zeros(
(host_array.header_vals['nrows'], host_array.header_vals['ncols']))
init_r_array = np.zeros(
(host_array.header_vals['nrows'], host_array.header_vals['ncols']))
for row in range(host_array.header_vals['nrows']):
for col in range(host_array.header_vals['ncols']):
if host_array.array[row, col] > 0:
if (row, col) != seed_inf_cell:
if host_numbers:
init_s_array[row, col] = host_array.array[row, col]
else:
init_s_array[row, col] = 1.0
else:
if host_numbers:
init_i_array[row, col] = int(
np.ceil(prop_infected *
host_array.array[row, col]))
init_s_array[row, col] = int(
np.floor((1 - prop_infected) *
host_array.array[row, col]))
else:
init_i_array[row, col] = prop_infected
init_s_array[row, col] = 1 - prop_infected
init_s_raster = raster_tools.RasterData(
array=init_s_array,
cellsize=host_array.header_vals['cellsize'],
shape=init_s_array.shape,
llcorner=(host_array.header_vals['xllcorner'],
host_array.header_vals['yllcorner']))
init_i_raster = raster_tools.RasterData(
array=init_i_array,
cellsize=host_array.header_vals['cellsize'],
shape=init_i_array.shape,
llcorner=(host_array.header_vals['xllcorner'],
host_array.header_vals['yllcorner']))
init_r_raster = raster_tools.RasterData(
array=init_r_array,
cellsize=host_array.header_vals['cellsize'],
shape=init_r_array.shape,
llcorner=(host_array.header_vals['xllcorner'],
host_array.header_vals['yllcorner']))
init_s_raster.to_file(os.path.join("GeneratedData", out_stub + "_S.txt"))
init_i_raster.to_file(os.path.join("GeneratedData", out_stub + "_I.txt"))
init_r_raster.to_file(os.path.join("GeneratedData", out_stub + "_R.txt"))
def setUp(cls):
# Setup and run simulation data, single hosts on lattice with exponential kernel
cls._data_stub = os.path.join("testing", "VS_rates_sim_output")
cls._beta_val = 10e3
cls._scale_val = 1
size = (21, 21)
kernel_size = (43, 43)
kernel_centre = [int(x / 2) for x in kernel_size]
# Create host file
host_raster = raster_tools.RasterData(size, array=np.ones(size))
host_file = os.path.join("testing", "VS_rates_host_test_case.txt")
host_raster.to_file(host_file)
# Create initial conditions files
init_stub = os.path.join("testing", "VS_rates_init_test_case")
host_raster.array[int(size[0] / 2), int(size[1] / 2)] = 0
host_raster.to_file(init_stub + "_E.txt")
host_raster.array = np.zeros(size)
host_raster.to_file(init_stub + "_S.txt")
host_raster.array[int(size[0] / 2), int(size[1] / 2)] = 1
host_raster.to_file(init_stub + "_I.txt")
# Create kernel file
kernel_raster = raster_tools.RasterData(kernel_size,
array=np.full(
kernel_size, 1.0))
kernel_raster.array[kernel_centre[0], kernel_centre[1]] = 0
kernel_raster.to_file(init_stub + "_kernel.txt")
cls._kernel = kernel_raster.array
cls._size = size
# Setup config file
config_filename = os.path.join("testing", "VS_rates_config.ini")
config_str = "\n[Epidemiology]\n"
config_str += "Model = SEI\nInfRate = " + str(cls._beta_val)
config_str += "\nEAdvRate = 0.0\nIAdvRate = 0.0\nKernelType = RASTER\n"
config_str += "\n[Simulation]\n"
config_str += "SimulationType = RASTER\nFinalTime = 1\nNIterations = 1\n"
config_str += "HostPosFile = " + host_file + "\nInitCondFile = " + init_stub + "\n"
config_str += "KernelFile = " + init_stub + "_kernel.txt" + "\n"
config_str += "VirtualSporulationStart = 1"
config_str += "\n[Output]\n"
config_str += "SummaryOutputFreq = 0\nOutputFileStub = " + cls._data_stub
config_str += "\n[Optimisation]\n"
config_str += "SaveSetup = False"
with open(config_filename, "w") as outfile:
outfile.write(config_str)
cls._simulator = simulator.Simulator(config_file=config_filename)
cls._simulator.setup()
def average_mask(target_header):
"""Average weather and forest type mask over full 18 years of data for given target."""
analysis_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..")
weather_stub = os.path.join(analysis_path, "InputData", "weather",
"gis_m_c_")
llcorner = (target_header['xllcorner'], target_header['yllcorner'])
urcorner = (target_header['xllcorner'] +
(target_header['ncols']) * target_header['cellsize'] - 125,
target_header['yllcorner'] +
(target_header['nrows']) * target_header['cellsize'] - 125)
forest_mask = raster_tools.extract_raster(
os.path.join(analysis_path, "InputData", "forestType_Map.txt"),
llcorner, urcorner)
forest_mask.array[forest_mask.array == -9999] = np.nan
average_array = raster_tools.RasterData(
shape=(target_header['nrows'], target_header['ncols']),
llcorner=(target_header['xllcorner'], target_header['yllcorner']),
cellsize=target_header['cellsize'],
NODATA_value=target_header['NODATA_value'],
array=np.zeros((target_header['nrows'], target_header['ncols'])))
for year in range(1990, 2008):
for week in range(1, 29):
# Extract correct region of weather file
weather_raster = raster_tools.extract_raster(
weather_stub + str(year) + "_" + str(week) + ".txt", llcorner,
urcorner)
weather_raster.array[weather_raster.array == -9999] = np.nan
if week < 7:
weather_raster.array[forest_mask.array == 2] = 0
if target_header['cellsize'] == weather_raster.header_vals[
'cellsize']:
average_array.array += np.square(weather_raster.array)
else:
weather_raster.array = np.square(weather_raster.array)
averaged_weather_array = raster_tools.extract_raster(
weather_raster,
llcorner,
urcorner,
resolution=target_header['cellsize'])
averaged_weather_array.array[averaged_weather_array.array ==
-9999] = 0
average_array.array += averaged_weather_array.array
average_array.array /= (28 * 18)
average_array.array = np.sqrt(average_array.array)
logging.info("Overall mean mask: %f", np.nanmean(average_array.array))
average_array.array[np.where(np.isnan(
average_array.array))] = average_array.header_vals['NODATA_value']
return average_array
def read_sus_inf_files(all_cells,
header,
sus_file,
inf_file,
sim_type="INDIVIDUAL"):
"""Read all files associated with host susceptibility and infectiousness."""
if sim_type == "INDIVIDUAL":
return
if sim_type == "RASTER":
if isinstance(sus_file, raster_tools.RasterData):
sus_raster = sus_file
else:
try:
sus_raster = raster_tools.RasterData.from_file(sus_file)
except (FileNotFoundError, TypeError):
sus_raster = raster_tools.RasterData(
shape=(header['nrows'], header['ncols']),
llcorner=(header['xllcorner'], header['yllcorner']),
cellsize=header['cellsize'],
NODATA_value=header['NODATA_value'],
array=np.ones((header['nrows'], header['ncols'])))
if isinstance(inf_file, raster_tools.RasterData):
inf_raster = inf_file
else:
try:
inf_raster = raster_tools.RasterData.from_file(inf_file)
except (FileNotFoundError, TypeError):
inf_raster = raster_tools.RasterData(
shape=(header['nrows'], header['ncols']),
llcorner=(header['xllcorner'], header['yllcorner']),
cellsize=header['cellsize'],
NODATA_value=header['NODATA_value'],
array=np.ones((header['nrows'], header['ncols'])))
for cell in all_cells:
row, col = cell.cell_position
cell.susceptibility = sus_raster.array[row, col]
cell.infectiousness = inf_raster.array[row, col]
def setUpClass(cls):
# Setup and run simulation data, multiple hosts in single cell to make non-spatial
cls._data_stub = os.path.join("testing", "nonspatial_sim_output")
cls._beta_val = 0.0007
# Create host file
host_raster = raster_tools.RasterData((1, 1), array=np.array([[1000]], dtype=float))
host_file = os.path.join("testing", "nonspatial_host_test_case.txt")
host_raster.to_file(host_file)
# Create simulation initial conditions files
init_stub = os.path.join("testing", "nonspatial_init_test_case")
host_raster.array[0, 0] = 995
host_raster.to_file(init_stub + "_S.txt")
host_raster.array[0, 0] = 5
host_raster.to_file(init_stub + "_I.txt")
# Create raster model initial conditions files
host_raster.array[0, 0] = 1
host_raster.to_file(init_stub + "_host_density.txt")
host_raster.array[0, 0] = 0.995
host_raster.to_file(init_stub + "_S_density.txt")
host_raster.array[0, 0] = 0.005
host_raster.to_file(init_stub + "_I_density.txt")
# Create kernel file
host_raster.array[0, 0] = 1
host_raster.to_file(init_stub + "_kernel.txt")
# Setup config file
config_filename = os.path.join("testing", "nonspatial_config.ini")
config_str = "\n[Epidemiology]\n"
config_str += "Model = SI\nInfRate = " + str(cls._beta_val)
config_str += "\nIAdvRate = 0.0\nKernelType = RASTER\n"
config_str += "\n[Simulation]\n"
config_str += "SimulationType = RASTER\nFinalTime = 10.0\nNIterations = 100\n"
config_str += "HostPosFile = " + host_file + "\nInitCondFile = " + init_stub + "\n"
config_str += "KernelFile = " + init_stub + "_kernel.txt" + "\n"
config_str += "VirtualSporulationStart = 1\nMaxHosts = 1000"
config_str += "\n[Output]\n"
config_str += "SummaryOutputFreq = 0\nOutputFileStub = " + cls._data_stub
config_str += "\n[Optimisation]\n"
config_str += "SaveSetup = False\nRateStructure-Infection = ratetree"
with open(config_filename, "w") as outfile:
outfile.write(config_str)
cls._raster_header = host_raster.header_vals
cls._init_stub = init_stub
# Run simulations
IndividualSimulator.main(configFile=config_filename, silent=True)
def setUpClass(cls):
# Setup fake simulation data
cls._data_stub = os.path.join("testing", "quick_sim_output")
# Create host file
host_raster = raster_tools.RasterData((2, 2), array=np.ones((2, 2)))
host_file = os.path.join("testing", "host_test_case.txt")
host_raster.to_file(host_file)
# Create initial conditions files
init_stub = os.path.join("testing", "init_test_case")
host_raster.array[1, 1] = 0
host_raster.to_file(init_stub + "_S.txt")
host_raster.array = np.zeros((2, 2))
host_raster.array[1, 1] = 1
host_raster.to_file(init_stub + "_I.txt")
# Create log file
log_str = "Configuration File Used\n" + "#" * 20 + "\n"
log_str += "\n[Epidemiology]\n"
log_str += "Model = SI\nInfRate = 0.8\nKernelType = RASTER\n"
log_str += "\n[Simulation]\n"
log_str += "SimulationType = RASTER\nFinalTime = 10.0\nNIterations = 2\n"
log_str += "HostPosFile = " + host_file + "\nInitCondFile = " + init_stub + "\n"
log_str += "\n[Output]\n"
log_str += "SummaryOutputFreq = 0\nOutputFileStub = " + cls._data_stub
with open(cls._data_stub + ".log", "w") as outfile:
outfile.write(log_str)
# Create host data files
host_data_dict = {
"posX": np.tile(np.arange(0.5, 2.5), 2),
"posY": np.repeat(np.arange(1.5, -0.5, -1), 2),
"hostID": list(range(4)),
"initial_state": ["S"] * 3 + ["I"]
}
host_data = pd.DataFrame(host_data_dict)
for i in range(2):
filename = cls._data_stub + "_hosts_" + str(i) + ".csv"
host_data.to_csv(filename, index=False)
# Create event data files
cls._inf_hosts = np.array([[0, 1, 2], [1, 2, 0]])
for i in range(2):
event_data_dict = {"time": [2, 4, 6], "hostID": cls._inf_hosts[i]}
event_data = pd.DataFrame(event_data_dict)
filename = cls._data_stub + "_events_" + str(i) + ".csv"
event_data.to_csv(filename, index=False)
cls._raster_header = host_raster.header_vals
def make_np_mask(target_header):
"""Generate mask of cells that are in Redwood National Park"""
rdr = Reader(os.path.join("InputData", "nps_boundary", "nps_boundary.shp"))
redw_records = []
for x in rdr.records():
if 'Redwood' in x.attributes['UNIT_NAME']:
redw_records.append(x)
redw_shape_nps = redw_records[0].geometry[0]
NAD83_Cali_Albers = pyproj.Proj("+init=EPSG:3310")
nps_proj = pyproj.Proj("+init=EPSG:4269")
project = partial(pyproj.transform, nps_proj, NAD83_Cali_Albers)
redw_shape = transform(project, redw_shape_nps)
lower_x = np.array([
target_header['xllcorner'] + i * target_header['cellsize']
for i in range(target_header['ncols'])
])
upper_x = lower_x + target_header['cellsize']
lower_y = np.array([
target_header['yllcorner'] + i * target_header['cellsize']
for i in range(target_header['nrows'])
])[::-1]
upper_y = lower_y + target_header['cellsize']
np_array = np.zeros((target_header['nrows'], target_header['ncols']))
for i in range(target_header['nrows']):
for j in range(target_header['ncols']):
points = [[lower_x[j], lower_y[i]], [upper_x[j], lower_y[i]],
[upper_x[j], upper_y[i]], [lower_x[j], upper_y[i]]]
cell = geometry.Polygon(points)
intersection_area = redw_shape.intersection(cell).area / (
target_header['cellsize'] * target_header['cellsize'])
np_array[i, j] = intersection_area
np_raster = raster_tools.RasterData(
(target_header['nrows'], target_header['ncols']),
(target_header['xllcorner'], target_header['yllcorner']),
target_header['cellsize'],
array=np_array)
return np_raster
def output_raster_data(parent_sim, time=None, iteration=None, states=None):
"""Output current state raster"""
all_cells = parent_sim.all_cells
header = parent_sim.params['header']
if states is None:
states = list(parent_sim.params['Model']) + ["Culled"]
output_stub = parent_sim.params['RasterFileStub']
if iteration is not None:
iterstub = "_" + str(iteration)
else:
iterstub = ""
if time is not None:
timestub = "_" + str(time)
else:
timestub = ""
for state in states:
cell_state = np.full((header['nrows'], header['ncols']),
header['NODATA_value'])
for row in range(header['nrows']):
for col in range(header['ncols']):
cell_id = parent_sim.params['cell_map'].get((row, col), None)
if cell_id is not None:
cell_state[row, col] = all_cells[cell_id].states[state]
cell_state = cell_state.reshape((header['nrows'], header['ncols']))
raster = raster_tools.RasterData(shape=(header['nrows'],
header['ncols']),
llcorner=(header['xllcorner'],
header['yllcorner']),
cellsize=header['cellsize'],
NODATA_value=header['NODATA_value'],
array=cell_state)
raster.to_file(output_stub + iterstub + "_" + state + timestub +
".txt")
def setUpClass(cls):
# Setup and run simulation data, single hosts on lattice with exponential kernel
cls._data_stub = os.path.join("testing", "target_sim_output")
cls._beta_val = 6
cls._scale_val = 0.9
cls._end_time = 10.0
cls._size = (21, 21)
# Create host file
motif = np.zeros((3, 3))
motif[1, 1] = 1
host_array = np.tile(motif, cls._size)
# host_array = host_array * np.random.randint(1, 4, host_array.shape)
host_raster = raster_tools.RasterData([3*x for x in cls._size], array=host_array)
host_file = os.path.join("testing", "target_host_test_case.txt")
host_raster.to_file(host_file)
# Create initial conditions files
centre_host = tuple(3*int(x/2) + 1 for x in cls._size)
init_stub = os.path.join("testing", "target_init_test_case")
n_init_inf = host_raster.array[centre_host]
host_raster.array[centre_host] = 0
host_raster.to_file(init_stub + "_S.txt")
host_raster.array = np.zeros_like(host_array)
host_raster.array[centre_host] = n_init_inf
host_raster.to_file(init_stub + "_I.txt")
# TODO think about kernel normalisation
# Create kernel file
kernel_range = max(cls._size)*3
kernel_size = (2*kernel_range+1, 2*kernel_range+1)
kernel_raster = raster_tools.RasterData(kernel_size, array=np.zeros(kernel_size))
for i in range(kernel_size[0]):
for j in range(kernel_size[1]):
row = i - kernel_range
col = j - kernel_range
distance = np.sqrt(row*row + col*col)
# host_raster.array[i, j] = np.exp(-distance/cls._scale_val) / (
# 2 * np.pi * cls._scale_val * cls._scale_val)
if row % 3 == 0 and col % 3 == 0:
kernel_raster.array[i, j] = np.exp(-distance/cls._scale_val)
kernel_raster.to_file(init_stub + "_kernel.txt")
# Setup config file
config_filename = os.path.join("testing", "target_config.ini")
config_str = "\n[Epidemiology]\n"
config_str += "Model = SI\nInfRate = " + str(cls._beta_val)
config_str += "\nIAdvRate = 0.0\nKernelType = RASTER\n"
config_str += "\n[Simulation]\n"
config_str += "SimulationType = RASTER\nFinalTime = " + str(cls._end_time) + "\n"
config_str += "NIterations = 200\n"
config_str += "HostPosFile = " + host_file + "\nInitCondFile = " + init_stub + "\n"
config_str += "KernelFile = " + init_stub + "_kernel.txt" + "\n"
config_str += "VirtualSporulationStart = 3\nMaxHosts = 1"
config_str += "\n[Output]\n"
config_str += "SummaryOutputFreq = 0\nOutputFileStub = " + cls._data_stub
config_str += "\n[Optimisation]\n"
config_str += "SaveSetup = False\nRateStructure-Infection = ratetree"
with open(config_filename, "w") as outfile:
outfile.write(config_str)
# Run simulations
IndividualSimulator.main(configFile=config_filename)
