def test_serialize_deserialize(self):
"""
test create new object from to_dict
"""
gmap = MapFromBNA(testbnamap, 6)
serial = gmap.serialize()
map2 = MapFromBNA.deserialize(serial)
assert gmap == map2
def test_update_from_dict_MapFromBNA(self):
'test update_from_dict for MapFromBNA'
gmap = MapFromBNA(testbnamap, 6)
dict_ = {}
dict_['map_bounds'] = [(-10, 10), (10, 10), (10, -10), (-10, -10)]
dict_['spillable_area'] = [[(-5, 5), (5, 5), (5, -5), (-5, -5)]]
dict_['refloat_halflife'] = 2
assert np.all(gmap.map_bounds != dict_['map_bounds'])
gmap.update_from_dict(dict_)
assert gmap.map_bounds is not dict_['map_bounds']
assert np.all(gmap.map_bounds == dict_['map_bounds'])
def test_in_water_resolution():
'''
Test the limits of the precision, to within an order of magnitude,
defining whether a point is in or out of water.
'''
# Create an 500x500 pixel map, with an LE refloat half-life of 2 hours
# (specified here in seconds).
m = MapFromBNA(filename=testbnamap,
refloat_halflife=2,
raster_size=500 * 500)
# Specify coordinates of the two points that make up the
# southeastern coastline segment of the island in the BNA map.
x1 = -126.78709
y1 = 47.666667
x2 = -126.44218
y2 = 47.833333
# Define a point on the line formed by this coastline segment.
slope = (y2 - y1) / (x2 - x1)
b = y1 - slope * x1
py = 47.7
px = (py - b) / slope
# Find the order of magnitude epsilon change in the latitude that causes
# the given point to "move" from water to land.
# eps == Distance between 1 and the nearest floating point number.
eps = np.spacing(1)
mag = 0.
running = True
while running:
mag = mag + 1.
print 'Order of magnitude: %g' % mag
running = m.in_water((px, py + eps * 10.0**mag, 0.))
# Difference in position within an order of magnitude in
# degrees of latitude necessary to "move" point from water to land.
dlatO0 = eps * 10.0**(mag - 1.)
dlatO1 = eps * 10.0**mag
msg = \
'''A particle positioned on a coastline segment must be moved
something more than {0} meters, but less than {1} meters,
inland before pyGNOME acknowledges it's no longer in water.'''
print msg.format(dlatO0 * 1852.0, dlatO1 * 1852.0)
def test_deserialize(self):
## fixme: this should fail with no spillable area ?!?
jsblob = self.map.serialize()
jsblob['spillable_area'] = None
pprint(jsblob)
# {'approximate_raster_interval': 53.9608870724,
# 'filename': u'/Users/chris.barker/Hazmat/GitLab/pygnome/py_gnome/tests/unit_tests/sample_data/florida_with_lake_small.bna',
# 'id': u'b3590b7d-aab1-11ea-8899-1e00b098d304',
# 'map_bounds': [(-82.8609915978, 24.5472415066),
# (-82.8609915978, 28.1117673335),
# (-80.0313642811, 28.1117673335),
# (-80.0313642811, 24.5472415066)],
# 'name': u'MapFromBNA_8',
# 'obj_type': u'gnome.maps.map.MapFromBNA',
# 'raster_size': 16777216.0,
# 'refloat_halflife': 1.0}
map = MapFromBNA.deserialize(jsblob)
print map.spillable_area
print map.land_polys
assert map.spillable_area is None
assert len(map.map_bounds) == 4
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 9, 15, 12, 0)
mapfile = get_datafile(os.path.join(base_dir, './LongIslandSoundMap.BNA'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours
# # the image output renderer
# global renderer
# one hour timestep
model = Model(start_time=start_time,
duration=timedelta(hours=48),
time_step=3600,
map=gnome_map,
uncertain=True,
cache_enabled=True)
netcdf_file = os.path.join(base_dir, 'script_long_island.nc')
scripting.remove_netcdf(netcdf_file)
print 'adding outputters'
model.outputters += Renderer(mapfile, images_dir, size=(800, 600))
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
spill = point_line_release_spill(num_elements=1000,
start_position=(-72.419992, 41.202120,
0.0),
release_time=start_time)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2)
print 'adding a wind mover:'
series = np.zeros((5, ), dtype=datetime_value_2d)
series[0] = (start_time, (10, 45))
series[1] = (start_time + timedelta(hours=18), (10, 90))
series[2] = (start_time + timedelta(hours=30), (10, 135))
series[3] = (start_time + timedelta(hours=42), (10, 180))
series[4] = (start_time + timedelta(hours=54), (10, 225))
wind = Wind(timeseries=series, units='m/s')
model.movers += WindMover(wind)
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, r"./LI_tidesWAC.CUR"))
tide_file = get_datafile(os.path.join(base_dir, r"./CLISShio.txt"))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
model.movers += c_mover
model.environment += c_mover.tide
print 'viewport is:', [
o.viewport for o in model.outputters if isinstance(o, Renderer)
]
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=6),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-74.15, 40.5, 0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(4, 270, units='m/s')
print 'adding a current mover:'
# url is broken, fix and include the following section
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc')
# cf = GridCurrent.from_netCDF(url)
# renderer.add_grid(cf.grid)
# renderer.delay = 25
# u_mover = PyCurrentMover(cf, default_num_method='Euler')
# model.movers += u_mover
#
return model
def simple_model(output_dir):
start_time = "2018-09-20T12:00"
model = gs.Model(
start_time=start_time,
duration=gs.days(1),
time_step=gs.minutes(30),
name="test model for tideflats",
)
model.map = MapFromBNA(bna_file)
model.movers += gs.constant_wind_mover(10, 300, "m/s")
model.spills += gs.surface_point_line_spill(
num_elements=100,
start_position=(5.4, 53.38, 0),
end_position=(5.8, 53.4, 0),
release_time=start_time,
)
model.outputters += gs.Renderer(
output_timestep=gs.hours(1),
map_filename=bna_file,
output_dir=output_dir,
formats=['gif'], # ['gif', 'png']
image_size=(800, 400),
# viewport=((4.5, 53.0),
# (5.5, 53.5)),
)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 3, 0)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours = 48),
time_step=3600)
mapfile = get_datafile(os.path.join(base_dir, 'Perfland.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=1, raster_size=1024*1024) # seconds
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(800, 600),
output_timestep=timedelta(hours=1),
timestamp_attrib={'size': 'medium', 'color':'uncert_LE'})
renderer.set_timestamp_attrib(format='%a %c')
renderer.graticule.set_DMS(True)
# renderer.viewport = ((-124.25, 47.5), (-122.0, 48.70))
print 'adding outputters'
model.outputters += renderer
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
spill1 = point_line_release_spill(num_elements=5000,
start_position=(0.0,
0.0,
0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(13, 270, units='m/s')
print 'adding a current mover:'
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
#
# # uncertain_time_delay in hours
# c_mover = GridCurrentMover(curr_file)
# c_mover.uncertain_cross = 0 # default is .25
#
# model.movers += c_mover
return model
def sample_model2_fixture_base():
"""
sample model with no outputter and no spills. Use this as a template for
fixtures to add spills
Uses:
sample_data/MapBounds_Island.bna
Contains: gnome.movers.SimpleMover(velocity=(1.0, -1.0, 0.0))
duration is 1 hour with 15min intervals so 5 timesteps total,
including initial condition,
model is uncertain and cache is not enabled
No spills or outputters defined
To use:
add a spill and run
:returns: It returns a dict -
{'model':model,
'release_start_pos':start_points,
'release_end_pos':end_points}
The release_start_pos and release_end_pos can be used by test to define
the spill's 'start_position' and 'end_position'
"""
release_time = datetime(2012, 9, 15, 12, 0)
# the image output map
mapfile = os.path.join(os.path.dirname(__file__),
'./sample_data/long_island_sound',
'LongIslandSoundMap.BNA')
# the land-water map
map_ = MapFromBNA(mapfile, refloat_halflife=06) # seconds
model = Model(
time_step=timedelta(minutes=10),
start_time=release_time,
duration=timedelta(hours=1),
map=map_,
uncertain=True,
cache_enabled=False,
)
# model.movers += SimpleMover(velocity=(1., -1., 0.0))
# model.uncertain = True
start_points = np.zeros((3, ), dtype=np.float64)
end_points = np.zeros((3, ), dtype=np.float64)
start_points[:] = (-72.83, 41.13, 0)
end_points[:] = (-72.83, 41.13, 0)
return {
'model': model,
'release_start_pos': start_points,
'release_end_pos': end_points
}
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'creating the maps'
mapfile = get_datafile(os.path.join(base_dir, 'LowerMississippiMap.bna'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours
print 'initializing the model'
start_time = datetime(2012, 9, 15, 12, 0)
# default to now, rounded to the nearest hour
model = Model(time_step=600,
start_time=start_time,
duration=timedelta(days=1),
map=gnome_map,
uncertain=True)
print 'adding outputters'
model.outputters += Renderer(mapfile, images_dir, image_size=(800, 600))
netcdf_file = os.path.join(base_dir, 'script_lower_mississippi.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=10000)
print 'adding a wind mover:'
series = np.zeros((5, ), dtype=datetime_value_2d)
series[0] = (start_time, (2, 45))
series[1] = (start_time + timedelta(hours=18), (2, 90))
series[2] = (start_time + timedelta(hours=30), (2, 135))
series[3] = (start_time + timedelta(hours=42), (2, 180))
series[4] = (start_time + timedelta(hours=54), (2, 225))
w_mover = WindMover(Wind(timeseries=series, units='m/s'))
model.movers += w_mover
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, 'LMiss.CUR'))
c_mover = CatsMover(curr_file)
# but do need to scale (based on river stage)
c_mover.scale = True
c_mover.scale_refpoint = (-89.699944, 29.494558)
# based on stage height 10ft (range is 0-18)
c_mover.scale_value = 1.027154
model.movers += c_mover
print 'adding a spill'
spill = point_line_release_spill(num_elements=1000,
start_position=(-89.699944, 29.494558,
0.0),
release_time=start_time)
model.spills += spill
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 1, 1)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=48),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(600, 1200))
renderer.graticule.set_DMS(True)
# renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-122.625, 45.609, 0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# uncertain_time_delay in hours
# vec_field = TriVectorField('COOPSu_CREOFS24.nc')
# u_mover = UGridCurrentMover(vec_field)
c_mover = GridCurrentMover(curr_file)
# c_mover.uncertain_cross = 0 # default is .25
# model.movers += u_mover
model.movers += c_mover
model.save
return model
def test_update_spillable_area_polygons(self):
map = MapFromBNA(bna_with_lake)
map.update_from_dict({
'spillable_area': [
[(-82.86099, 24.54724), (-82.86099, 28.11176),
(-80.03136, 28.11176), (-80.03136, 24.54724)],
[
(-82.86099, 24.54724),
(-82.86099, 28.11176),
(-80.03136, 28.11176),
(-80.03136, 24.54724),
(-80.03136, 28.11176),
(-80.03136, 24.54724),
],
]
})
assert len(map.spillable_area) == 2
assert len(map.spillable_area[1]) == 6
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2006, 3, 31, 20, 0)
model = Model(start_time=start_time,
duration=timedelta(days=3), time_step=30 * 60,
uncertain=True)
print 'adding the map'
mapfile = get_datafile(os.path.join(base_dir, 'coastSF.bna'))
model.map = MapFromBNA(mapfile, refloat_halflife=1) # seconds
renderer = Renderer(mapfile, images_dir, image_size=(800, 600),
draw_ontop='forecast')
renderer.viewport = ((-124.5, 37.), (-120.5, 39))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_sf_bay.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
spill = point_line_release_spill(num_elements=1000,
start_position=(-123.57152, 37.369436,
0.0),
release_time=start_time,
substance=NonWeatheringSubstance(windage_range=(0.01,.04))
#element_type=floating(windage_range=(0.01,
# 0.04)
# )
)
model.spills += spill
# print 'adding a RandomMover:'
# r_mover = gnome.movers.RandomMover(diffusion_coef=50000)
# model.movers += r_mover
print 'adding a grid wind mover:'
wind_file = get_datafile(os.path.join(base_dir, 'WindSpeedDirSubset.nc'))
topology_file = get_datafile(os.path.join(base_dir,
'WindSpeedDirSubsetTop.dat'))
w_mover = GridWindMover(wind_file, topology_file)
# w_mover.uncertain_time_delay = 6
# w_mover.uncertain_duration = 6
w_mover.uncertain_speed_scale = 1
w_mover.uncertain_angle_scale = 0.2 # default is .4
w_mover.wind_scale = 2
model.movers += w_mover
return model
def make_models():
print 'initializing the model'
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
models = []
start_time = datetime(2012, 10, 27, 0, 30)
duration_hrs = 23
time_step = 450
num_steps = duration_hrs * 3600 / time_step
names = [
'Euler',
'Trapezoid',
'RK4',
]
mapfile = get_datafile(os.path.join(base_dir, 'long_beach.bna'))
print 'gen map'
map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
fn = ('00_dir_roms_display.ncml.nc4')
curr = GridCurrent.from_netCDF(filename=fn)
models = []
for method in names:
mod = Model(start_time=start_time,
duration=timedelta(hours=duration_hrs),
time_step=time_step)
mod.map = map
spill = point_line_release_spill(num_elements=1000,
start_position=(-74.1, 39.7525, 0.0),
release_time=start_time)
mod.spills += spill
mod.movers += RandomMover(diffusion_coef=100)
mod.movers += PyCurrentMover(current=curr, default_num_method=method)
images_dir = method + '-' + str(
time_step / 60) + 'min-' + str(num_steps) + 'steps'
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
renderer.delay = 25
# renderer.add_grid(curr.grid)
mod.outputters += renderer
netCDF_fn = os.path.join(base_dir, images_dir + '.nc')
mod.outputters += NetCDFOutput(netCDF_fn, which_data='all')
models.append(mod)
print 'returning models'
return models
def test_bna_no_map_bounds():
"""
tests that the map bounds will get expanded to include
the bounding box of the land and spillable area.
"""
test_no_bounds_bna = os.path.join(datadir, 'no_map_bounds.bna')
m = MapFromBNA(test_no_bounds_bna)
assert np.array_equal(m.map_bounds, [
(3., 10.),
(3., 11.),
(6., 11.),
(6., 10.),
])
class Test_lake():
"""
tests for handling a BNA with a lake
The code should now return a polygon with a hole for lakes.
And render properly both with the py_gnome renderer and the json output.
"""
map = MapFromBNA(bna_with_lake)
def test_polys(self):
"""
Once loaded, polygons should be there
"""
# There should always be map bounds
assert self.map.map_bounds is not None
# no spillable area in this one
assert self.map.spillable_area is None
# NOTE: current version puts land and lakes in the land_polys set
assert len(self.map.land_polys) == 2
def test_to_geojson(self):
"""
make sure geojson is right
"""
gj = self.map.to_geojson()
# print gj.keys()
# print gj['features'][0].keys()
# print len(gj.features)
# has only the land polys in there.
assert len(gj['features']) == 2
land_polys = gj['features'][0]
assert land_polys['geometry']['type'] == "MultiPolygon"
assert land_polys["properties"]["name"] == "Shoreline Polys"
import json
outfilename = os.path.join(output_dir, "florida_geojson.json")
with open(outfilename, 'w') as outfile:
json.dump(gj, outfile, indent=2)
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2014, 6, 9, 0, 0)
mapfile = get_datafile(os.path.join(base_dir, 'PassamaquoddyMap.bna'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=1) # hours
# # the image output renderer
# global renderer
# one hour timestep
model = Model(start_time=start_time,
duration=timedelta(hours=24),
time_step=360,
map=gnome_map,
uncertain=False,
cache_enabled=True)
print 'adding outputters'
renderer = Renderer(
mapfile,
images_dir,
image_size=(800, 600),
# output_timestep=timedelta(hours=1),
draw_ontop='uncertain')
renderer.viewport = ((-67.15, 45.), (-66.9, 45.2))
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_passamaquoddy.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
spill = point_line_release_spill(num_elements=1000,
start_position=(-66.991344, 45.059316,
0.0),
release_time=start_time)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=30000, uncertain_factor=2)
print 'adding a wind mover:'
series = np.zeros((5, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 90))
series[1] = (start_time + timedelta(hours=18), (5, 180))
series[2] = (start_time + timedelta(hours=30), (5, 135))
series[3] = (start_time + timedelta(hours=42), (5, 180))
series[4] = (start_time + timedelta(hours=54), (5, 225))
wind = Wind(timeseries=series, units='m/s')
model.movers += WindMover(wind)
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(base_dir, 'PQBayCur.nc4'))
topology_file = get_datafile(os.path.join(base_dir,
'PassamaquoddyTOP.dat'))
tide_file = get_datafile(os.path.join(base_dir, 'EstesHead.txt'))
cc_mover = CurrentCycleMover(curr_file,
topology_file,
tide=Tide(tide_file))
model.movers += cc_mover
model.environment += cc_mover.tide
print 'viewport is:', [
o.viewport for o in model.outputters if isinstance(o, Renderer)
]
return model
Tide(testdata['CatsMover']['tide']),
#Wind(filename=testdata['ComponentMover']['wind']),
constant_wind(5., 270, 'knots'),
Wind(timeseries=(sec_to_date(24 * 60 * 60), (0, 0)), units='mps'),
Water(temperature=273),
RandomMover(),
CatsMover(testdata['CatsMover']['curr']),
CatsMover(testdata['CatsMover']['curr'],
tide=Tide(testdata['CatsMover']['tide'])),
ComponentMover(testdata['ComponentMover']['curr']),
ComponentMover(testdata['ComponentMover']['curr'],
wind=constant_wind(5., 270, 'knots')),
#wind=Wind(filename=testdata['ComponentMover']['wind'])),
RandomMover3D(),
SimpleMover(velocity=(10.0, 10.0, 0.0)),
MapFromBNA(testdata['MapFromBNA']['testmap'], 6),
NetCDFOutput(os.path.join(base_dir, u'xtemp.nc')),
Renderer(testdata['Renderer']['bna_sample'],
os.path.join(base_dir, 'output_dir')),
WeatheringOutput(),
spill.PointLineRelease(release_time=datetime.now(),
num_elements=10,
start_position=(0, 0, 0)),
spill.point_line_release_spill(10, (0, 0, 0), datetime.now()),
spill.substance.Substance(windage_range=(0.05, 0.07)),
spill.substance.GnomeOil(test_oil, windage_range=(0.05, 0.07)),
spill.substance.NonWeatheringSubstance(windage_range=(0.05, 0.07)),
Skimmer(amount=100,
efficiency=0.3,
active_range=(datetime(2014, 1, 1, 0,
0), datetime(2014, 1, 1, 4, 0)),
def make_model(images_dir=os.path.join(base_dir, 'images')):
# create the maps:
print 'creating the maps'
mapfile = get_datafile(os.path.join(base_dir, 'DelawareRiverMap.bna'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=1) # hours
renderer = Renderer(mapfile,
images_dir,
image_size=(800, 800),
projection_class=GeoProjection)
print 'initializing the model'
start_time = datetime(2012, 8, 20, 13, 0)
# 15 minutes in seconds
# Default to now, rounded to the nearest hour
model = Model(time_step=900,
start_time=start_time,
duration=timedelta(days=1),
map=gnome_map,
uncertain=False)
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_delaware_bay.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=100000)
print 'adding a wind mover:'
# wind_file = get_datafile(os.path.join(base_dir, 'ConstantWind.WND'))
# wind = Wind(filename=wind_file)
series = np.zeros((2, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 270))
series[1] = (start_time + timedelta(hours=25), (5, 270))
wind = Wind(timeseries=series, units='m/s')
# w_mover = WindMover(Wind(timeseries=series, units='knots'))
w_mover = WindMover(wind)
model.movers += w_mover
print 'adding a cats shio mover:'
curr_file = get_datafile(os.path.join(base_dir, 'FloodTides.cur'))
tide_file = get_datafile(os.path.join(base_dir, 'FloodTidesShio.txt'))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
# this is the value in the file (default)
c_mover.scale_refpoint = (-75.081667, 38.7995)
c_mover.scale = True
c_mover.scale_value = 1
model.movers += c_mover
# TODO: cannot add this till environment base class is created
model.environment += c_mover.tide
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, 'Offshore.cur'))
c_mover = CatsMover(curr_file)
# but do need to scale (based on river stage)
c_mover.scale = True
c_mover.scale_refpoint = (-74.7483333, 38.898333)
c_mover.scale_value = .03
model.movers += c_mover
#
# these are from windows they don't match Mac values...
# pat1Angle 315;
# pat1Speed 30; pat1SpeedUnits knots;
# pat1ScaleToValue 0.314426
#
# pat2Angle 225;
# pat2Speed 30; pat2SpeedUnits knots;
# pat2ScaleToValue 0.032882
# scaleBy WindStress
print 'adding a component mover:'
# if only using one current pattern
# comp_mover = ComponentMover(curr_file1, None, wind)
#
# todo: following is not working when model is saved out - fix
# comp_mover = ComponentMover(curr_file1, curr_file2,
# Wind(timeseries=series, units='m/s'))
# comp_mover = ComponentMover(curr_file1, curr_file2,
# wind=Wind(filename=wind_file))
curr_file1 = get_datafile(os.path.join(base_dir, 'NW30ktwinds.cur'))
curr_file2 = get_datafile(os.path.join(base_dir, 'SW30ktwinds.cur'))
comp_mover = ComponentMover(curr_file1, curr_file2, wind)
comp_mover.scale_refpoint = (-75.263166, 39.1428333)
comp_mover.pat1_angle = 315
comp_mover.pat1_speed = 30
comp_mover.pat1_speed_units = 1
# comp_mover.pat1ScaleToValue = .314426
comp_mover.pat1_scale_to_value = .502035
comp_mover.pat2_angle = 225
comp_mover.pat2_speed = 30
comp_mover.pat2_speed_units = 1
# comp_mover.pat2ScaleToValue = .032882
comp_mover.pat2_scale_to_value = .021869
model.movers += comp_mover
print 'adding a spill'
end_time = start_time + timedelta(hours=12)
spill = point_line_release_spill(
num_elements=1000,
release_time=start_time,
# end_release_time=end_time,
start_position=(-75.262319, 39.142987, 0.0),
)
model.spills += spill
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print('get contiguous')
kml_file = os.path.join(base_dir, 'contigua.kml')
with open(kml_file) as f:
contiguous = parser.parse(f).getroot().Document
coordinates = contiguous.Placemark.LineString.coordinates.text.split(' ')
cont_coord = []
for x in coordinates:
x = x.split(',')
if len(x) > 1 and float(x[1]) > -12 and float(x[1]) < -3:
cont_coord.append([float(x[0]), float(x[1])])
print('initializing the model')
start_time = datetime(2022, 1, 22, 12, 0)
mapfile = get_datafile(os.path.join(base_dir, './brazil-coast.BNA'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours
duration = timedelta(days=1)
timestep = timedelta(minutes=5)
end_time = start_time + duration
steps = duration.total_seconds() / timestep.total_seconds()
print("Total step: %.4i " % (steps))
# one hour timestep
model = Model(start_time=start_time,
duration=duration,
time_step=timestep,
map=gnome_map,
uncertain=False,
cache_enabled=False)
oil_name = 'GENERIC MEDIUM CRUDE'
wd = UniformDistribution(low=.0002, high=.0002)
subs = GnomeOil(oil_name, initializers=plume_initializers(distribution=wd))
#model.spills += point_line_release_spill(release_time=start_time, start_position=(-35.153, -8.999, 0.0), num_elements=1000, end_release_time=end_time, substance= subs, units='kg')
#model.spills += point_line_release_spill(release_time=start_time, start_position=(-35.176, -9.135, 0.0), num_elements=1000, end_release_time=end_time, substance= subs, units='kg')
#model.spills += point_line_release_spill(release_time=start_time, start_position=(-35.062, -9.112, 0.0), num_elements=1000, end_release_time=end_time, substance= subs, units='kg')
#model.spills += point_line_release_spill(release_time=start_time, start_position=(-34.994, -9.248, 0.0), num_elements=1000, end_release_time=end_time, substance= subs, units='kg')
for idx in range(0, len(cont_coord)):
model.spills += point_line_release_spill(
num_elements=500,
start_position=(cont_coord[idx][0], cont_coord[idx][1], 0.0),
release_time=start_time,
end_release_time=start_time + timedelta(days=1),
amount=500,
substance=subs,
units='kg')
#shp_file = os.path.join(base_dir, 'surface_concentration')
#scripting.remove_netcdf(shp_file + ".zip")
#model.outputters += ShapeOutput(shp_file,
# zip_output=False,
# surface_conc="kde",
# )
print('adding movers:')
print('adding a RandomMover:')
model.movers += RandomMover(diffusion_coef=10000)
print('adding a current mover:')
# # this is HYCOM currents
curr_file = get_datafile(os.path.join(base_dir, 'currents.nc'))
model.movers += GridCurrentMover(curr_file, num_method='Euler')
print('adding a grid wind mover:')
wind_file = get_datafile(os.path.join(base_dir, 'wind.nc'))
#topology_file = get_datafile(os.path.join(base_dir, 'WindSpeedDirSubsetTop.dat'))
#w_mover = GridWindMover(wind_file, topology_file)
w_mover = GridWindMover(wind_file)
w_mover.uncertain_speed_scale = 1
w_mover.uncertain_angle_scale = 0.2 # default is .4
w_mover.wind_scale = 2
model.movers += w_mover
print('adding outputters')
renderer = Renderer(mapfile,
images_dir,
image_size=(900, 600),
output_timestep=timestep,
draw_ontop='forecast')
#set the viewport to zoom in on the map:
#renderer.viewport = ((-37, -11), (-34, -8)) #alagoas
renderer.viewport = ((-36, -10), (-30, 5))
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'contigua.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='standard',
surface_conc='kde')
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=24),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-74.15, 40.5, 0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = []
for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)),
(25, (5, 90))]:
series.append((start_time + timedelta(hours=i[0]), i[1]))
wind1 = WindTS.constant_wind('wind1', 5, 270, 'knots')
wind2 = WindTS(timeseries=series, units='knots', extrapolate=True)
wind = Wind(timeseries=series, units='knots')
model.movers += PyWindMover(wind=wind2)
# model.movers += WindMover(wind)
# print 'adding a current mover:'
#
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc')
# cf = roms_field(url)
# cf.set_appearance(on=True)
# renderer.grids += [cf]
# renderer.delay = 25
# u_mover = UGridCurrentMover(cf)
# model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 9, 15, 12, 0)
mapfile = get_datafile(os.path.join(base_dir, './LongIslandSoundMap.BNA'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours
# # the image output renderer
# global renderer
# one hour timestep
model = Model(start_time=start_time,
duration=timedelta(hours=48),
time_step=3600,
map=gnome_map,
uncertain=False,
cache_enabled=False)
print 'adding a spill'
et = floating_weathering(substance='FUEL OIL NO.6')
spill = point_line_release_spill(num_elements=1000,
start_position=(-72.419992, 41.202120,
0.0),
release_time=start_time,
amount=1000,
units='kg',
element_type=et)
spill.amount_uncertainty_scale = 1.0
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2)
print 'adding a wind mover:'
series = np.zeros((5, ), dtype=datetime_value_2d)
series[0] = (start_time, (10, 45))
series[1] = (start_time + timedelta(hours=18), (10, 90))
series[2] = (start_time + timedelta(hours=30), (10, 135))
series[3] = (start_time + timedelta(hours=42), (10, 180))
series[4] = (start_time + timedelta(hours=54), (10, 225))
wind = Wind(timeseries=series, units='m/s', speed_uncertainty_scale=0.5)
model.movers += WindMover(wind)
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, r"./LI_tidesWAC.CUR"))
tide_file = get_datafile(os.path.join(base_dir, r"./CLISShio.txt"))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
model.movers += c_mover
model.environment += c_mover.tide
print 'adding Weatherers'
water_env = Water(311.15)
model.environment += water_env
model.weatherers += [
Evaporation(water_env, wind),
Dispersion(),
Burn(), Skimmer()
]
print 'adding outputters'
model.outputters += WeatheringOutput()
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
# create the maps:
print 'creating the maps'
mapfile = get_datafile(os.path.join(base_dir, './MassBayMap.bna'))
gnome_map = MapFromBNA(
mapfile,
refloat_halflife=1, # hours
raster_size=2048 * 2048 # about 4 MB
)
renderer = Renderer(
mapfile,
images_dir,
image_size=(800, 800),
)
print 'initializing the model'
start_time = datetime(2016, 3, 9, 15)
# 1 hour in seconds
# Default to now, rounded to the nearest hour
model = Model(time_step=3600,
start_time=start_time,
duration=timedelta(days=6),
map=gnome_map,
uncertain=True)
print 'adding outputters'
model.outputters += renderer
# netcdf_file = os.path.join(base_dir, 'script_boston.nc')
# scripting.remove_netcdf(netcdf_file)
# model.outputters += NetCDFOutput(netcdf_file, which_data='all')
# model.outputters += KMZOutput(os.path.join(base_dir, 'script_boston.kmz'))
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=100000)
print 'adding a wind mover:'
series = np.zeros((2, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 180))
series[1] = (start_time + timedelta(hours=18), (5, 180))
w = Wind(filename=os.path.join(base_dir, '22NM_WNW_PortAngelesWA.nws'))
w_mover = WindMover(w)
model.movers += w_mover
model.environment += w_mover.wind
# print 'adding a cats shio mover:'
# curr_file = get_datafile(os.path.join(base_dir, r"./EbbTides.cur"))
# tide_file = get_datafile(os.path.join(base_dir, r"./EbbTidesShio.txt"))
# c_mover = CatsMover(curr_file, tide=Tide(tide_file))
# # this is the value in the file (default)
# c_mover.scale_refpoint = (-70.8875, 42.321333)
# c_mover.scale = True
# c_mover.scale_value = -1
# model.movers += c_mover
# # TODO: cannot add this till environment base class is created
# model.environment += c_mover.tide
print 'adding a spill'
end_time = start_time + timedelta(hours=12)
spill = point_line_release_spill(num_elements=100,
start_position=(-70.911432, 42.369142,
0.0),
release_time=start_time,
end_release_time=end_time)
model.spills += spill
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=2),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_ny_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding two spills'
# Break the spill into two spills, first with the larger droplets
# and second with the smaller droplets.
# Split the total spill volume (100 m^3) to have most
# in the larger droplet spill.
# Smaller droplets start at a lower depth than larger
end_time = start_time + model.duration
# wd = WeibullDistribution(alpha=1.8,
# lambda_=.00456,
# min_=.0002) # 200 micron min
#
# spill = subsurface_plume_spill(num_elements=10,
# start_position=(-74.15,
# 40.5,
# 7.2),
# release_time=start_time,
# distribution=wd,
# amount=90, # default volume_units=m^3
# units='m^3',
# end_release_time=end_time,
# density=600)
#
# model.spills += spill
# wd = WeibullDistribution(alpha=1.8,
# lambda_=.00456,
# max_=.0002) # 200 micron max
oil_name = 'ALASKA NORTH SLOPE (MIDDLE PIPELINE, 1997)'
wd = UniformDistribution(low=.0002,
high=.0002)
spill = point_line_release_spill(num_elements=10, amount=90,
units='m^3',
start_position=(-74.15,
40.5,
7.2),
release_time=start_time,
substance = GnomeOil(oil_name,initializers=plume_initializers(distribution=wd))
#element_type=plume(distribution=wd,
#substance_name='ALASKA NORTH SLOPE (MIDDLE PIPELINE, 1997)')
)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a RiseVelocityMover:'
model.movers += RiseVelocityMover()
print 'adding a RandomMover3D:'
# model.movers += RandomMover3D(vertical_diffusion_coef_above_ml=5,
# vertical_diffusion_coef_below_ml=.11,
# mixed_layer_depth=10)
# the url is broken, update and include the following four lines
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# gc = GridCurrent.from_netCDF(url)
# u_mover = PyCurrentMover(gc, default_num_method='RK2')
# model.movers += u_mover
# print 'adding a wind mover:'
# series = np.zeros((2, ), dtype=gnome.basic_types.datetime_value_2d)
# series[0] = (start_time, (30, 90))
# series[1] = (start_time + timedelta(hours=23), (30, 90))
# wind = Wind(timeseries=series, units='knot')
#
# default is .4 radians
# w_mover = gnome.movers.WindMover(wind, uncertain_angle_scale=0)
#
# model.movers += w_mover
print 'adding a simple mover:'
# s_mover = SimpleMover(velocity=(0.0, -.3, 0.0))
# model.movers += s_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 5, 18, 0)
model = Model(start_time=start_time, duration=timedelta(days=8),
time_step=4 * 3600, uncertain=False)
mapfile = get_datafile(os.path.join(base_dir, 'mariana_island.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print 'adding renderer'
model.outputters += Renderer(mapfile,
images_dir,
image_size=(800, 600),
)
# draw_back_to_fore=True)
# print "adding netcdf output"
# netcdf_output_file = os.path.join(base_dir,'mariana_output.nc')
# scripting.remove_netcdf(netcdf_output_file)
# model.outputters += NetCDFOutput(netcdf_output_file, which_data='all')
#
# Set up the movers:
#
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=10000)
print 'adding a simple wind mover:'
model.movers += constant_wind_mover(5, 315, units='m/s')
print 'adding a current mover:'
# # this is HYCOM currents
curr_file = get_datafile(os.path.join(base_dir, 'HYCOM.nc'))
model.movers += GridCurrentMover(curr_file,
num_method='Euler');
# #
# # Add some spills (sources of elements)
# #
print 'adding four spill'
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.25, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146.25, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.75, 15.25,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.75, 14.75,
0.0),
release_time=start_time)
return model
def make_model():
print ('initializing the model')
#print (start_date)
start_time = startday
model = Model(start_time=start_time, duration=timedelta(days=30),
#weathering_substeps = 6,
time_step=24 * 3600,
uncertain=False)
mapfile = get_datafile(os.path.join(base_dir,'gulf.bna'))
#mapfile='gulf.bna'
print ('adding the map')
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print ("adding shapefile output")
# with open("Result {}".format(spill_num), "w") as fp:
# fp.write("text")
dir_name = os.path.join (base_dir, season, str(position), "Spillnum {}".format(spill_num))
if not os.path.exists(dir_name):
os.makedirs(dir_name)
#os.makedirs(dir_name, exist_ok =True)
for i in range(1, 31, 1):
model.outputters += ShapeOutput(os.path.join(dir_name, 'gnome_result {id}'.format(id=i)),
zip_output=False,
output_timestep=timedelta(days=i))
images_dir = os.path.join(dir_name, 'image')
# print 'adding renderer'
# model.outputters += Renderer(mapfile,
# images_dir,
# image_size=(800, 600))
# print ('adding renderer')
# dir_image = os.path.join(dir_name)
# model.outputters += Renderer(mapfile,
# dir_image,
# size=(800, 600))
#
# Set up the movers:
#
print ('adding a RandomMover:')
model.movers += RandomMover(diffusion_coef=10000)
print ('adding a simple wind mover:')
wind_file = get_datafile(os.path.join(base_dir, 'ECMWF.nc'))
model.movers += GridWindMover(wind_file)
print ('adding a current mover:')
# # this is NEMO currents
curr_file = get_datafile(os.path.join(base_dir, Currents))
model.movers += GridCurrentMover(curr_file,
num_method='Euler');
# # Add some spills (sources of elements)
print ('adding one spill')
spill = point_line_release_spill(num_elements=1000,
amount= 3200000000 * spilldur , units='grams',
start_position = position,
release_time = start_time,
substance = (sub))
model.spills += spill
####### open excel file
print ('adding Excel file')
workbook = xlsxwriter.Workbook(os.path.join(dir_name, 'Result {}_{}.xlsx'.format(spill_num, position)))
worksheet = workbook.add_worksheet ()
a = ((spilldur*3200)**(-0.3))*0.000069
worksheet.write ('A1', a)
workbook.close()
print ('adding weatherers and cleanup options:')
model.environment += [water,wind,waves]
model.weatherers += Evaporation()
model.weatherers += Emulsification()
model.weatherers += NaturalDispersion()
print ('model full run:')
model.full_run()
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 2, 13, 9, 0)
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
mapfile = get_datafile(os.path.join(base_dir, 'GuamMap.bna'))
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
print 'adding outputters'
renderer = Renderer(mapfile, images_dir, image_size=(800, 600))
renderer.viewport = ((144.6, 13.4), (144.7, 13.5))
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_guam.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
end_time = start_time + timedelta(hours=6)
spill = point_line_release_spill(num_elements=20,
start_position=(144.664166,
13.441944, 0.0),
release_time=start_time,
end_release_time=end_time)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = np.zeros((4, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 135))
series[1] = (start_time + timedelta(hours=23), (5, 135))
series[2] = (start_time + timedelta(hours=25), (5, 0))
series[3] = (start_time + timedelta(hours=48), (5, 0))
wind = Wind(timeseries=series, units='knot')
w_mover = WindMover(wind)
model.movers += w_mover
model.environment += w_mover.wind
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, 'OutsideWAC.cur'))
c_mover = CatsMover(curr_file)
c_mover.scale = True
c_mover.scale_refpoint = (144.601, 13.42)
c_mover.scale_value = .15
model.movers += c_mover
print 'adding a cats shio mover:'
curr_file = get_datafile(os.path.join(base_dir, 'WACFloodTide.cur'))
tide_file = get_datafile(os.path.join(base_dir, 'WACFTideShioHts.txt'))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
# this is different from the value in the file!
c_mover.scale_refpoint = (144.621667, 13.45)
c_mover.scale = True
c_mover.scale_value = 1
# will need the fScaleFactor for heights files
# c_mover.time_dep.scale_factor = 1.1864
c_mover.tide.scale_factor = 1.1864
model.movers += c_mover
model.environment += c_mover.tide
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2016, 4, 5, 18, 0)
model = Model(start_time=start_time,
duration=timedelta(hours=12),
time_step=.25 * 3600)
mapfile = (os.path.join(base_dir, 'coast.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
spill1 = point_line_release_spill(num_elements=500,
start_position=(-82.73888,
27.5475,
0.0),
release_time=start_time,
end_release_time=start_time + timedelta(hours=24))
spill2 = point_line_release_spill(num_elements=500,
start_position=(-82.73888,
27.545,
0.0),
release_time=start_time,
end_release_time=start_time + timedelta(hours=24))
spill3 = point_line_release_spill(num_elements=500,
start_position=(-82.73888,
27.5425,
0.0),
release_time=start_time,
end_release_time=start_time + timedelta(hours=24))
spill4 = point_line_release_spill(num_elements=500,
start_position=(-82.73988,
27.5475,
0.0),
release_time=start_time,
end_release_time=start_time + timedelta(hours=24))
spill5 = point_line_release_spill(num_elements=500,
start_position=(-82.73988,
27.5450,
0.0),
release_time=start_time,
end_release_time=start_time + timedelta(hours=24))
spill6 = point_line_release_spill(num_elements=500,
start_position=(-82.73988,
27.5425,
0.0),
release_time=start_time,
end_release_time=start_time + timedelta(hours=24))
model.spills += spill1
model.spills += spill2
model.spills += spill3
model.spills += spill4
model.spills += spill5
model.spills += spill6
model.spills._spill_container.spills.remove(0)
print 'adding a current mover:'
fn = 'nos.tbofs.fields.n000.20160406.t00z_sgrid.nc'
# fn = 'dbofs_newFormat.nc'
cf = GridCurrent.from_netCDF(filename=fn)
u_mover = PyCurrentMover(cf, extrapolate=True)
# u_mover = GridCurrentMover(fn)
renderer.add_grid(cf.grid)
# renderer.add_vec_prop(cf)
model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(uncertain=False, mode='gnome'):
'''
Create a model from the data in sample_data/boston_data
It contains:
- the GeoProjection
- wind mover
- random mover
- cats shio mover
- cats ossm mover
- plain cats mover
'''
start_time = datetime(2013, 2, 13, 9, 0)
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=timedelta(minutes=30).total_seconds(),
uncertain=uncertain,
map=MapFromBNA(testdata['boston_data']['map'],
refloat_halflife=1),
mode=mode)
print 'adding a spill'
start_position = (144.664166, 13.441944, 0.0)
end_release_time = start_time + timedelta(hours=6)
spill_amount = 1000.0
spill_units = 'kg'
model.spills += point_line_release_spill(num_elements=1000,
start_position=start_position,
release_time=start_time,
end_release_time=end_release_time,
amount=spill_amount,
units=spill_units,
substance=test_oil)
spill = model.spills[-1]
spill_volume = spill.get_mass() / spill.substance.density_at_temp()
# need a scenario for SimpleMover
# model.movers += SimpleMover(velocity=(1.0, -1.0, 0.0))
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=100000)
print 'adding a wind mover:'
series = np.zeros((2, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 180))
series[1] = (start_time + timedelta(hours=18), (5, 180))
w_mover = WindMover(Wind(timeseries=series, units='m/s'))
model.movers += w_mover
model.environment += w_mover.wind
print 'adding a cats shio mover:'
c_mover = CatsMover(testdata['boston_data']['cats_curr2'],
tide=Tide(testdata['boston_data']['cats_shio']))
# c_mover.scale_refpoint should automatically get set from tide object
c_mover.scale = True # default value
c_mover.scale_value = -1
# tide object automatically gets added by model
model.movers += c_mover
print 'adding a cats ossm mover:'
c_mover = CatsMover(testdata['boston_data']['cats_curr2'],
tide=Tide(testdata['boston_data']['cats_ossm']))
c_mover.scale = True # but do need to scale (based on river stage)
c_mover.scale_refpoint = (-70.65, 42.58333, 0.0)
c_mover.scale_value = 1.
print 'adding a cats mover:'
c_mover = CatsMover(testdata['boston_data']['cats_curr3'])
c_mover.scale = True # but do need to scale (based on river stage)
c_mover.scale_refpoint = (-70.78333, 42.39333, 0.0)
# the scale factor is 0 if user inputs no sewage outfall effects
c_mover.scale_value = .04
model.movers += c_mover
# TODO: seg faulting for component mover - comment test for now
# print "adding a component mover:"
# comp_mover = ComponentMover(testdata['boston_data']['component_curr1'],
# testdata['boston_data']['component_curr2'],
# w_mover.wind)
# TODO: callback did not work correctly below - fix!
# comp_mover = ComponentMover(component_file1,
# component_file2,
# Wind(timeseries=series, units='m/s'))
# comp_mover.ref_point = (-70.855, 42.275)
# comp_mover.pat1_angle = 315
# comp_mover.pat1_speed = 19.44
# comp_mover.pat1_speed_units = 1
# comp_mover.pat1ScaleToValue = .138855
# comp_mover.pat2_angle = 225
# comp_mover.pat2_speed = 19.44
# comp_mover.pat2_speed_units = 1
# comp_mover.pat2ScaleToValue = .05121
# model.movers += comp_mover
print 'adding a Weatherer'
model.environment += Water(311.15)
skim_start = start_time + timedelta(hours=3)
model.weatherers += [
Evaporation(),
Skimmer(spill_amount * .5,
spill_units,
efficiency=.3,
active_range=(skim_start, skim_start + timedelta(hours=2))),
Burn(0.2 * spill_volume,
1.0, (skim_start, InfDateTime('inf')),
efficiency=0.9)
]
model.outputters += \
CurrentJsonOutput(model.find_by_attr('_ref_as', 'current_movers',
model.movers, allitems=True))
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=4),
time_step=7200)
# mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna'))
mapfile = get_datafile('arctic_coast3.bna')
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
# spill1 = point_line_release_spill(num_elements=10000,
# start_position=(-163.75,
# 69.75,
# 0.0),
# release_time=start_time)
#
spill1 = point_line_release_spill(num_elements=50000,
start_position=(196.25, 69.75, 0.0),
release_time=start_time)
model.spills += spill1
# model.spills += spill2
print 'adding a wind mover:'
# model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
fn = ['arctic_avg2_0001_gnome.nc', 'arctic_avg2_0002_gnome.nc']
# fn = ['C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0001_gnome.nc',
# 'C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0002_gnome.nc']
gt = {'node_lon': 'lon', 'node_lat': 'lat'}
# fn='arctic_avg2_0001_gnome.nc'
wind_method = 'Euler'
method = 'RK2'
print 'adding outputters'
# draw_ontop can be 'uncertain' or 'forecast'
# 'forecast' LEs are in black, and 'uncertain' are in red
# default is 'forecast' LEs draw on top
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
model.outputters += renderer
netcdf_file = os.path.join(base_dir,
str(model.time_step / 60) + method + '.nc')
scripting.remove_netcdf(netcdf_file)
print 'adding movers'
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'loading entire current data'
ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn, grid_topology=gt)
# env1 = get_env_from_netCDF(filename)
# mov = PyCurrentMover.from_netCDF(filename)
ice_aware_curr.ice_velocity.variables[0].dimension_ordering = [
'time', 'x', 'y'
]
ice_aware_wind = IceAwareWind.from_netCDF(
filename=fn,
ice_velocity=ice_aware_curr.ice_velocity,
ice_concentration=ice_aware_curr.ice_concentration,
grid=ice_aware_curr.grid)
curr = GridCurrent.from_netCDF(filename=fn)
# GridCurrent.is_gridded()
# import pprint as pp
# from gnome.utilities.orderedcollection import OrderedCollection
# model.environment = OrderedCollection(dtype=Environment)
# model.environment.add(ice_aware_curr)
# from gnome.environment import WindTS
print 'loading entire wind data'
# i_c_mover = PyCurrentMover(current=ice_aware_curr)
# i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method='Euler')
# i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method=method, extrapolate=True)
i_c_mover = PyCurrentMover(current=ice_aware_curr,
default_num_method=method)
i_w_mover = PyWindMover(wind=ice_aware_wind,
default_num_method=wind_method)
i_c_mover.current.grid.extrapolation_is_allowed = True
# ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360
# ice_aware_curr.grid.build_celltree()
model.movers += i_c_mover
model.movers += i_w_mover
print 'adding an IceAwareRandomMover:'
model.movers += IceAwareRandomMover(
ice_concentration=ice_aware_curr.ice_concentration,
diffusion_coef=1000)
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
# model.environment.add(WindTS.constant(10, 300))
# print('Saving')
# model.environment[0].ice_velocity.variables[0].serialize()
# IceVelocity.deserialize(model.environment[0].ice_velocity.serialize())
# model.save('.')
# from gnome.persist.save_load import load
# print('Loading')
# model2 = load('./Model.zip')
return model