def test_reader_boundary(self):
o = PelagicEggDrift(loglevel=0)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
reader_arctic = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc')
######################################################
# Vertical interpolation is another issue to be fixed:
reader_nordic.zlevels = reader_arctic.z
######################################################
o.add_reader([reader_nordic, reader_arctic])
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 10 # Some wind for mixing
# Seed close to Nordic boundary
o.seed_elements(lon=14.9,
lat=71.1,
radius=2000,
number=100,
time=reader_nordic.start_time,
z=0)
o.set_config('turbulentmixing:timestep', 20)
o.set_config('drift:scheme', 'runge-kutta')
o.run(steps=5, time_step=3600, time_step_output=3600)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertAlmostEqual(o.elements.lat[0], 71.16, 1)
#self.assertAlmostEqual(o.elements.z.min(), -41.92, 1) # With past ROMS-masking
self.assertAlmostEqual(o.elements.z.min(), -40.1, 1)
self.assertAlmostEqual(o.elements.z.max(), -0.01, 1)
#self.assertAlmostEqual(o.elements.lon.max(), 14.949, 2)
self.assertAlmostEqual(o.elements.lon.max(), 14.87, 2)
def test_stranding_roms(self):
o = PelagicEggDrift(loglevel=0)
reader_arctic = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc')
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
o.add_reader(reader_arctic)
o.add_reader(reader_nordic)
o.fallback_values['x_sea_water_velocity'] = 1
o.seed_elements(
lon=13.0,
lat=68.0,
radius=20000,
number=100,
time=[reader_arctic.start_time, reader_nordic.end_time],
z=-30)
o.set_config('general:coastline_action', 'previous')
o.set_config('processes:turbulentmixing', False)
o.max_speed = 1
o.run(end_time=reader_nordic.end_time, time_step=3600 * 36)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), 100)
def test_reader_boundary(self):
o = PelagicEggDrift(loglevel=0)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() + "2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc"
)
reader_arctic = reader_netCDF_CF_generic.Reader(
o.test_data_folder() + "2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc"
)
######################################################
# Vertical interpolation is another issue to be fixed:
reader_nordic.zlevels = reader_arctic.z
######################################################
o.add_reader([reader_nordic, reader_arctic])
o.fallback_values["land_binary_mask"] = 0
o.fallback_values["x_wind"] = 10 # Some wind for mixing
# Seed close to Nordic boundary
o.seed_elements(lon=14.9, lat=71.1, radius=2000, number=100, time=reader_nordic.start_time, z=0)
o.set_config("turbulentmixing:timestep", 20)
o.set_config("turbulentmixing:verticalresolution", 1)
o.set_config("drift:scheme", "runge-kutta")
o.run(steps=5, time_step=3600, time_step_output=3600)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertAlmostEqual(o.elements.lat[0], 71.15, 2)
self.assertAlmostEqual(o.elements.z.min(), -35.0, 3)
self.assertAlmostEqual(o.elements.z.max(), -0.5, 3)
self.assertAlmostEqual(o.elements.lon.max(), 14.87, 2)
def test_stranding_3d(self):
o = PelagicEggDrift(loglevel=30)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
o.add_reader(reader_nordic)
o.fallback_values['y_wind'] = 10 # Some wind for mixing
o.seed_elements(
lon=14.0,
lat=68.15,
radius=2000,
number=100,
time=[reader_nordic.start_time, reader_nordic.end_time],
z=0)
o.set_config('general:coastline_action', 'stranding')
o.set_config('turbulentmixing:timestep', 120)
o.max_speed = .1
o.run(end_time=reader_nordic.end_time, time_step=3600 * 6)
self.assertEqual(o.status_categories[1], 'stranded')
self.assertEqual(o.elements_deactivated.status.min(), 1)
self.assertEqual(o.elements_deactivated.status.max(), 1)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 79)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 21)
self.assertEqual(o.num_elements_total(), 100)
def test_stranding_3d(self):
o = PelagicEggDrift(loglevel=30)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
o.add_reader(reader_nordic)
o.set_config('environment:fallback:y_wind', 10) # Some wind for mixing
o.seed_elements(
lon=14.0,
lat=68.15,
radius=2000,
number=100,
time=[reader_nordic.start_time, reader_nordic.end_time],
z=0)
o.set_config('general:coastline_action', 'stranding')
o.set_config('vertical_mixing:timestep', 120)
o.max_speed = .1
o.run(end_time=reader_nordic.end_time, time_step=3600 * 6)
self.assertEqual(o.status_categories[1], 'stranded')
self.assertEqual(o.elements_deactivated.status.min(), 1)
self.assertEqual(o.elements_deactivated.status.max(), 1)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 81)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 19)
self.assertEqual(o.num_elements_total(), 100)
# Check calculated trajectory lengths and speeds
total_length, distances, speeds = o.get_trajectory_lengths()
self.assertAlmostEqual(total_length.max(), 14978.3, 1)
self.assertAlmostEqual(total_length.min(), 1225.2, 1)
self.assertAlmostEqual(speeds.max(), 0.127, 1)
self.assertAlmostEqual(distances.max(), 2859.0, 1)
def test_outside_reader_time_coverage(self):
o = PelagicEggDrift()
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader(reader)
o.fallback_values['x_sea_water_velocity'] = 1
o.fallback_values['land_binary_mask'] = 0
o.set_config('processes:turbulentmixing', False)
o.seed_elements(lon=4.8, lat=60, number=1, time=reader.end_time)
o.run(steps=2)
# Check that fallback value is used when outside time coverage
self.assertEqual(o.history['x_sea_water_velocity'][0][-1], 1.0)
def test_outside_reader_time_coverage(self):
o = PelagicEggDrift()
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader(reader)
o.fallback_values['x_sea_water_velocity'] = 1
o.fallback_values['land_binary_mask'] = 0
o.set_config('processes:turbulentmixing', False)
o.seed_elements(lon=4.8, lat=60, number=1, time=reader.end_time)
o.run(steps=2)
# Check that fallback value is used when outside time coverage
self.assertEqual(o.history['x_sea_water_velocity'][0][-1], 1.0)
def test_stranding_roms(self):
o = PelagicEggDrift(loglevel=0)
reader_arctic = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc')
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader(reader_arctic)
o.add_reader(reader_nordic)
o.fallback_values['x_sea_water_velocity'] = 1
o.seed_elements(lon=13.0, lat=68.0, radius=20000, number=100,
time=[reader_arctic.start_time,
reader_nordic.end_time], z=-30)
o.set_config('general:basemap_resolution', 'c')
o.set_config('general:coastline_action', 'previous')
o.set_config('processes:turbulentmixing', False)
o.max_speed=1
o.run(end_time=reader_nordic.end_time, time_step=3600*36)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), 100)
def test_stranding_3d(self):
o = PelagicEggDrift(loglevel=30)
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader(reader_nordic)
o.fallback_values['y_wind'] = 10 # Some wind for mixing
o.seed_elements(lon=14.0, lat=68.15, radius=2000, number=100,
time=[reader_nordic.start_time,
reader_nordic.end_time], z=0)
o.set_config('general:coastline_action', 'stranding')
o.set_config('turbulentmixing:timestep', 60)
o.set_config('turbulentmixing:verticalresolution', 10)
o.run(end_time=reader_nordic.end_time, time_step=3600*3)
self.assertEqual(o.status_categories[1], 'stranded')
self.assertEqual(o.elements_deactivated.status.min(), 1)
self.assertEqual(o.elements_deactivated.status.max(), 1)
def test_vertical_mixing(self):
# Export to file only at end
o1 = PelagicEggDrift(loglevel=20) # Profiles and vertical mixing
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o1.add_reader([norkyst])
o1.fallback_values['x_wind'] = 8
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.1, 63.3, radius=1000, number=100,
time=norkyst.start_time)
o1.set_config('turbulentmixing:timestep', 20.) # seconds
o1.set_config('turbulentmixing:verticalresolution', 1.) # m
o1.run(steps=20, time_step=300, time_step_output=1800,
export_buffer_length=10, outfile='verticalmixing.nc')
self.assertAlmostEqual(o1.history['z'].min(), -25.0)
self.assertAlmostEqual(o1.history['z'].max(), 0.0)
os.remove('verticalmixing.nc')
def test_vertical_mixing(self):
# Export to file only at end
o1 = PelagicEggDrift(loglevel=20) # Profiles and vertical mixing
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o1.add_reader([norkyst])
o1.fallback_values['x_wind'] = 8
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.1, 63.3, radius=1000, number=100,
time=norkyst.start_time)
o1.set_config('turbulentmixing:timestep', 20.) # seconds
o1.run(steps=20, time_step=300, time_step_output=1800,
export_buffer_length=10, outfile='verticalmixing.nc')
self.assertAlmostEqual(o1.history['z'].min(), -38.1, 1)
self.assertAlmostEqual(o1.history['z'].max(), 0.0, 1)
os.remove('verticalmixing.nc')
def test_get_environment(self):
o = PelagicEggDrift(loglevel=0)
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() + '2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc', name='Nordic')
reader_arctic = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc', name='Arctic')
######################################################
# Vertical interpolation is another issue to be fixed:
reader_nordic.zlevels = reader_arctic.z
######################################################
o.add_reader([reader_nordic, reader_arctic])
# One point covered only by Nordic, two points coverd
# by both readers, and two points covered by none of the readers
testlon = np.array((14.0, 20.0, 20.1, 4, 5))
testlat = np.array((70.1, 76.0, 76.1, 60, 60))
testz = np.random.uniform(0, 0, len(testlon))
self.assertItemsEqual([0], reader_nordic.covers_positions(
testlon, testlat, testz))
self.assertItemsEqual([0, 1, 2], reader_arctic.covers_positions(
testlon, testlat, testz))
o.seed_elements(testlon, testlat, testz, time=reader_nordic.start_time)
o.fallback_values['land_binary_mask'] = 0
env, env_profiles, missing = \
o.get_environment(o.required_variables,
reader_nordic.start_time,
testlon, testlat, testz,
o.required_profiles)
self.assertAlmostEqual(env['sea_water_temperature'][0], 4.338, 2)
self.assertAlmostEqual(env['sea_water_temperature'][1], 0.6282, 3)
self.assertAlmostEqual(env['sea_water_temperature'][4], 10.0)
self.assertItemsEqual(missing, [False,False,False,False,False])
self.assertAlmostEqual(env_profiles['sea_water_temperature'][0,0],
4.338, 2)
self.assertAlmostEqual(env_profiles['sea_water_temperature'][0,4], 10)
self.assertAlmostEqual(env_profiles['sea_water_temperature'][8,2], 10)
self.assertAlmostEqual(env_profiles['sea_water_temperature'][7,2],
2.252265, 3)
# Get separate data
env2, env_profiles2, missing2 = \
o.get_environment(['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature'],
reader_nordic.start_time,
testlon, testlat, testz,
['sea_water_temperature'])
self.assertTrue(env_profiles2 is not None)
self.assertEqual(env_profiles2.keys(), ['z', 'sea_water_temperature'])
# Get separate data, without profile
env3, env_profiles3, missing3 = \
o.get_environment(['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature'],
reader_nordic.start_time,
testlon, testlat, testz,
profiles=None)
self.assertTrue(env_profiles3 is None)
# Get separate data
env4, env_profiles4, missing4 = \
o.get_environment(['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature'],
reader_nordic.start_time,
testlon, testlat, testz,
['sea_water_temperature'])
self.assertItemsEqual(env['x_sea_water_velocity'],
env2['x_sea_water_velocity'])
#print env_profiles['sea_water_temperature'], '1'*50
#print env_profiles2['sea_water_temperature'], '2'*50
#print env_profiles4['sea_water_temperature'], '4'*50
# Test below should also pass, To be fixed
#self.assertItemsEqual(env_profiles['sea_water_temperature'].ravel(),
# env_profiles2['sea_water_temperature'].ravel())
self.assertItemsEqual(env_profiles2['sea_water_temperature'].ravel(),
env_profiles4['sea_water_temperature'].ravel())
def test_get_environment(self):
o = PelagicEggDrift(loglevel=0)
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() + '2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc', name='Nordic')
reader_arctic = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc', name='Arctic')
######################################################
# Vertical interpolation is another issue to be fixed:
reader_nordic.zlevels = reader_arctic.z
######################################################
o.add_reader([reader_nordic, reader_arctic])
# One point covered only by Nordic, two points coverd
# by both readers, and two points covered by none of the readers
testlon = np.array((14.0, 20.0, 20.1, 4, 5))
testlat = np.array((70.1, 76.0, 76.1, 60, 60))
testz = np.random.uniform(0, 0, len(testlon))
self.assertItemsEqual([0], reader_nordic.covers_positions(
testlon, testlat, testz))
self.assertItemsEqual([0, 1, 2], reader_arctic.covers_positions(
testlon, testlat, testz))
o.seed_elements(testlon, testlat, testz, time=reader_nordic.start_time)
o.fallback_values['land_binary_mask'] = 0
env, env_profiles, missing = \
o.get_environment(o.required_variables,
reader_nordic.start_time,
testlon, testlat, testz,
o.required_profiles)
self.assertAlmostEqual(env['sea_water_temperature'][0], 4.2849, 3)
self.assertAlmostEqual(env['sea_water_temperature'][1], 0.6282, 3)
self.assertAlmostEqual(env['sea_water_temperature'][4], 10.0)
self.assertItemsEqual(missing, [False,False,False,False,False])
self.assertAlmostEqual(env_profiles['sea_water_temperature'][0,0],
4.284938, 3)
self.assertAlmostEqual(env_profiles['sea_water_temperature'][0,4], 10)
self.assertAlmostEqual(env_profiles['sea_water_temperature'][8,2], 10)
self.assertAlmostEqual(env_profiles['sea_water_temperature'][7,2],
2.252265, 3)
# Get separate data
env2, env_profiles2, missing2 = \
o.get_environment(['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature'],
reader_nordic.start_time,
testlon, testlat, testz,
['sea_water_temperature'])
self.assertTrue(env_profiles2 is not None)
self.assertEqual(env_profiles2.keys(), ['z', 'sea_water_temperature'])
# Get separate data, without profile
env3, env_profiles3, missing3 = \
o.get_environment(['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature'],
reader_nordic.start_time,
testlon, testlat, testz,
profiles=None)
self.assertTrue(env_profiles3 is None)
# Get separate data
env4, env_profiles4, missing4 = \
o.get_environment(['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature'],
reader_nordic.start_time,
testlon, testlat, testz,
['sea_water_temperature'])
self.assertItemsEqual(env['x_sea_water_velocity'],
env2['x_sea_water_velocity'])
#print env_profiles['sea_water_temperature'], '1'*50
#print env_profiles2['sea_water_temperature'], '2'*50
#print env_profiles4['sea_water_temperature'], '4'*50
# Test below should also pass, To be fixed
#self.assertItemsEqual(env_profiles['sea_water_temperature'].ravel(),
# env_profiles2['sea_water_temperature'].ravel())
self.assertItemsEqual(env_profiles2['sea_water_temperature'].ravel(),
env_profiles4['sea_water_temperature'].ravel())