def test_surface_water_more_absorption():
# First get a benchmark
rainfall = 1.4
plant_biomass = 90.0
surface_water = 3.0
frac_available = 0.1
bare_soil_infilt = 0.15
infilt_saturation = 5
change_1 = PG.calc_surface_water_change(
surface_water,
plant_biomass,
rainfall,
frac_available,
bare_soil_infilt,
infilt_saturation,
)
# now increase soil absorption
bare_soil_infilt = 0.2
change_2 = PG.calc_surface_water_change(
surface_water,
plant_biomass,
rainfall,
frac_available,
bare_soil_infilt,
infilt_saturation,
)
assert change_2 < change_1
def test_plant_increases():
# first get a benchmark
plant_biomass = 90.0
soil_water = 0
grazing_loss = 0.3
senescence = 0.1
growth_constant = 0.05
uptake = 10.0
uptake_saturation = 3.0
change_1 = PG.calc_plant_change(
plant_biomass,
soil_water,
uptake,
uptake_saturation,
growth_constant,
senescence,
grazing_loss,
)
# now increase the soil water
soil_water = 3.0
change_2 = PG.calc_plant_change(
plant_biomass,
soil_water,
uptake,
uptake_saturation,
growth_constant,
senescence,
grazing_loss,
)
assert change_2 > change_1
def test_plant_decreases():
# first get a benchmark
plant_biomass = 90.
soil_water = 0
grazing_loss = 0.3
senescence = 0.1
growth_constant = 0.05
uptake = 10.
uptake_saturation = 3.
change_1 = PG.calc_plant_change(plant_biomass, soil_water, uptake,
uptake_saturation, growth_constant,
senescence, grazing_loss)
# now increase grazing_loss
grazing_loss = 0.5
change_2 = PG.calc_plant_change(plant_biomass, soil_water, uptake,
uptake_saturation, growth_constant,
senescence, grazing_loss)
assert (change_1 > change_2)
# now increase senescence
senescence = 0.2
change_3 = PG.calc_plant_change(plant_biomass, soil_water, uptake,
uptake_saturation, growth_constant,
senescence, grazing_loss)
assert (change_2 > change_3)
def test_surface_water_more_rain():
# First get a benchmark
rainfall = 0.
plant_biomass = 90.
surface_water = 0.
frac_available = 0.1
bare_soil_infilt = 0.15
infilt_saturation = 5
change_1 = PG.calc_surface_water_change(surface_water, plant_biomass,
rainfall, frac_available,
bare_soil_infilt,
infilt_saturation)
# now increase rainfall
rainfall = 1.4
change_2 = PG.calc_surface_water_change(surface_water, plant_biomass,
rainfall, frac_available,
bare_soil_infilt,
infilt_saturation)
assert (change_2 > change_1)
def test_plant_change_zero():
plant_biomass = 0.
soil_water = 0
grazing_loss = 0.3
senescence = 0.1
growth_constant = 0.05
uptake = 10.
uptake_saturation = 3.
assert (PG.calc_plant_change(plant_biomass, soil_water, uptake,
uptake_saturation, growth_constant,
senescence, grazing_loss) == 0)
def test_plant_growth_quantitative():
# create a PG object and check results against expected
pg = PG()
pg.set_rainfall(1.0)
starting_pattern_filename = os.path.join(os.path.dirname(__file__), "..",
"testdata",
"binary_labyrinths_50.csv")
pg.set_starting_pattern_from_file(starting_pattern_filename)
pg.initial_conditions()
pg.evolve_pattern(100)
expected = np.loadtxt(os.path.join(os.path.dirname(__file__), "..",
"testdata", "PG-1mm-100iterations.csv"),
delimiter=",")
assert ((pg.plant_biomass.round(1) == expected.round(1)).all()
) # agreement to two decimal places
def test_surface_water_zero():
# zero rainfall, zero starting water
rainfall = 0.
plant_biomass = 90.
surface_water = 0.
frac_available = 0.1
bare_soil_infilt = 0.15
infilt_saturation = 5
change = PG.calc_surface_water_change(surface_water, plant_biomass,
rainfall, frac_available,
bare_soil_infilt, infilt_saturation)
assert (change == 0)
def test_soil_water_change_zero():
#no surface water, no plants, no evaporation
plant_biomass = 0
soil_water = 3.0
surface_water = 0
frac_available = 0.1
bare_soil_infilt = 0.15
infilt_saturation = 5.
plant_growth = 0.
soil_water_evap = 0.
uptake_saturation = 3.
change = PG.calc_soil_water_change(soil_water, surface_water,
plant_biomass, frac_available,
bare_soil_infilt, infilt_saturation,
plant_growth, soil_water_evap,
uptake_saturation)
assert (change == 0)
def main():
parser = argparse.ArgumentParser(
description="Generate vegetation patterns")
parser.add_argument("--rainfall",
help="rainfall in mm",
type=float,
default=1.0)
parser.add_argument("--input_config",
help="input config JSON filename",
type=str)
parser.add_argument("--input_csv",
help="starting pattern CSV filename",
type=str)
parser.add_argument("--steps",
help="number of time steps to run",
type=int,
default=1000)
parser.add_argument("--transpose",
help="rotate image (useful for comparing to matlab",
action="store_true")
parser.add_argument("--make_binary",
help="threshold the plant_biomass member",
action="store_true")
parser.add_argument("--output_png", help="output png filename", type=str)
parser.add_argument("--output_csv", help="output csv filename", type=str)
parser.add_argument("--output_matlab", help="output .m filename", type=str)
parser.add_argument("--plot_result",
help="display the evolved pattern",
action="store_true")
args = parser.parse_args()
print('-' * 45)
print('Starting pattern generator...')
print('-' * 45)
pg = PatternGenerator()
pg.set_rainfall(args.rainfall)
if args.input_config:
pg.load_config(args.input_config)
pg.initial_conditions()
if args.input_csv:
pg.set_starting_pattern_from_file(args.input_csv)
else:
pg.set_random_starting_pattern()
pg.evolve_pattern(steps=args.steps)
if args.make_binary:
pg.plant_biomass = pg.make_binary()
if args.transpose:
pg.plant_biomass = pg.plant_biomass.transpose()
if args.plot_result:
pg.plot_image()
if args.output_csv:
pg.save_as_csv(args.output_csv)
if args.output_png:
pg.save_as_png(args.output_png)
if args.output_matlab:
pg.save_as_matlab(args.output_matlab)
print('Finished generating patterns!\n')
