def test3_run_import(self):
"""Import output file from previous test, and check elements"""
self.o = OceanDrift(loglevel=20)
self.o.io_import_file('unittest.nc')
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 5)
def make_OceanDrift_object(self):
self.o = OceanDrift(loglevel=20)
self.fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
self.o.use_block = False
self.o.config['runge_kutta'] = False
self.reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=-1.5, llcrnrlat=59,
urcrnrlon=7, urcrnrlat=64, resolution='i')
self.o.add_reader([self.fake_eddy, self.reader_basemap])
def import_from_ladim(ladimfile, romsfile):
"""Import Ladim output file as OpenDrift simulation obejct"""
from models.oceandrift import OceanDrift
o = OceanDrift()
from netCDF4 import Dataset, date2num, num2date
if isinstance(romsfile, str):
from opendrift.readers import reader_ROMS_native
romsfile = reader_ROMS_native.Reader(romsfile)
l = Dataset(ladimfile, 'r')
pid = l.variables['pid'][:]
particle_count = l.variables['particle_count'][:]
end_index = np.cumsum(particle_count)
start_index = np.concatenate(([0], end_index[:-1]))
x = l.variables['X'][:]
y = l.variables['Y'][:]
lon, lat = romsfile.xy2lonlat(x, y)
time = num2date(l.variables['time'][:], l.variables['time'].units)
history_dtype_fields = [(name, o.ElementType.variables[name]['dtype'])
for name in o.ElementType.variables]
# Add environment variables
o.history_metadata = o.ElementType.variables.copy()
history_dtype = np.dtype(history_dtype_fields)
num_timesteps = len(time)
num_elements = len(l.dimensions['particle'])
o.history = np.ma.array(np.zeros([num_elements, num_timesteps]),
dtype=history_dtype,
mask=[True])
for n in range(num_timesteps):
start = start_index[n]
active = pid[start:start + particle_count[n]]
o.history['lon'][active, n] = \
lon[start:start+particle_count[n]]
o.history['lat'][active, n] = \
lat[start:start+particle_count[n]]
o.history['status'][active, n] = 0
o.status_categories = ['active', 'missing_data']
firstlast = np.ma.notmasked_edges(o.history['status'], axis=1)
index_of_last = firstlast[1][1]
o.history['status'][np.arange(len(index_of_last)), index_of_last] = 1
kwargs = {}
for var in ['lon', 'lat', 'status']:
kwargs[var] = o.history[var][np.arange(len(index_of_last)),
index_of_last]
kwargs['ID'] = range(num_elements)
o.elements = o.ElementType(**kwargs)
o.elements_deactivated = o.ElementType()
o.remove_deactivated_elements()
# Import time steps from metadata
o.time_step = time[1] - time[0]
o.time_step_output = o.time_step
o.start_time = time[0]
o.time = time[-1]
o.steps_output = num_timesteps
return o
#!/usr/bin/env python
import os
from datetime import datetime, timedelta
import numpy as np
from readers import reader_basemap_landmask
from readers import reader_ROMS_native
from models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Nordic 4km
nordic_native = reader_ROMS_native.Reader(
'test_data/2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=11.0,
llcrnrlat=67.5,
urcrnrlon=16.0,
urcrnrlat=69.0,
resolution='h',
projection='merc')
o.add_reader([reader_basemap, nordic_native])
# Seeding some particles
time = nordic_native.start_time
lon = 12.0
lat = 68.3
#!/usr/bin/env python
# Illustrating the difference between Euler and Runge-Kutta propagation
# schemes, using a "real" current fields from the NorKyst800 model
from datetime import datetime, timedelta
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(
'test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
time = reader_norkyst.start_time
reader_norkyst.interpolation = 'linearND'
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=4,
llcrnrlat=59.9,
urcrnrlon=5.5,
urcrnrlat=61.5,
resolution='h')
o.add_reader([reader_norkyst, reader_basemap])
lon = 4.5
lat = 60.0
# First run, with Euler scheme:
o.config['drift']['scheme'] = 'euler'
o.seed_elements(lon, lat, radius=0, number=1, time=time)
#!/usr/bin/env python
from datetime import datetime, timedelta
import numpy as np
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.openoil import OpenOil
from models.oceandrift import OceanDrift
#o = OpenOil(loglevel=0) # Set loglevel to 0 for debug information
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Arome
#reader_arome = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/arome25/arome_metcoop_default2_5km_latest.nc')
#reader_arome = reader_netCDF_CF_generic.Reader('test_data/16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
# Norkyst
#reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_norkyst = reader_netCDF_CF_generic.Reader('test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# GlobCurrent
#reader_globcurrent = reader_netCDF_CF_generic.Reader('http://tds0.ifremer.fr/thredds/dodsC/CLS-L4-CUREUL_HS-ALT_SUM-V01.0_FULL_TIME_SERIE') # Total
#reader_globcurrent = reader_netCDF_CF_generic.Reader('http://tds0.ifremer.fr/thredds/dodsC/GC_MOD_TIDE_GLO_010_FES2012_FULL_TIME_SERIE') # FES Tidal
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=3.5, llcrnrlat=59.9,
urcrnrlon=5.5, urcrnrlat=61.2,
resolution='h', projection='merc')
#!/usr/bin/env python
import os
from datetime import datetime, timedelta
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.oceandrift import OceanDrift
ncfile = 'backandforth.nc'
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(
'test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
#reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=3,
llcrnrlat=59,
urcrnrlon=6,
urcrnrlat=62,
resolution='h')
o.add_reader([reader_norkyst, reader_basemap])
################
# Forward run
################
# Seeding some particles
lon = 4.2
lat = 60.1
#!/usr/bin/env python
from datetime import datetime, timedelta
import numpy as np
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(
'test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=4.0, llcrnrlat=59.9,
urcrnrlon=5.5, urcrnrlat=61.2,
resolution='h', projection='merc')
o.add_reader([reader_basemap, reader_norkyst])
# Seeding some particles
lons = np.linspace(4.4, 4.6, 10)
lats = np.linspace(60.0, 60.1, 10)
lons, lats = np.meshgrid(lons, lats)
lons = lons.ravel()
lats = lats.ravel()
# Seed oil elements on a grid at regular time interval
def test_output_time_step(self):
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(script_folder + '/../test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='h', projection='merc')
o1.add_reader([basemap, norkyst])
o1.seed_elements(5.25, 60.2, radius=3000, number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=20)
o2.add_reader([basemap, norkyst])
o2.seed_elements(5.25, 60.2, radius=3000, number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100,25))
self.assertEqual(o2.history.shape, (100,13))
# Check that start and end conditions (longitudes) are idential
self.assertItemsEqual(o1.history['lon'][:,24].compressed(),
o2.history['lon'][:,12].compressed())
self.assertItemsEqual(o1.history['lon'][:,0].compressed(),
o2.history['lon'][:,0].compressed())
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertItemsEqual(o2i.history['lon'][:,12].compressed(),
o2.history['lon'][:,12].compressed())
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
class TestRun(unittest.TestCase):
"""Tests for (non-scalar) LagrangianArray"""
def make_OceanDrift_object(self):
self.o = OceanDrift(loglevel=20)
self.fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
self.o.use_block = False
self.o.config['runge_kutta'] = False
self.reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=-1.5, llcrnrlat=59,
urcrnrlon=7, urcrnrlat=64, resolution='i')
self.o.add_reader([self.fake_eddy, self.reader_basemap])
def test1_seed_single_point_over_time(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements(2.0, 61.0, radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 5)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
def test2_seed_elementss(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements([2.0, 4.5, 3.0], [61.0, 60.0, 62.0],
radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 9)
def test3_run_import(self):
"""Import output file from previous test, and check elements"""
self.o = OceanDrift(loglevel=20)
self.o.io_import_file('unittest.nc')
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 5)
def test4_cleaning(self):
"""Cleaning up"""
os.remove('unittest.nc')
def test_output_time_step(self):
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(script_folder + '/../test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='h', projection='merc')
o1.add_reader([basemap, norkyst])
o1.seed_elements(5.25, 60.2, radius=3000, number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=20)
o2.add_reader([basemap, norkyst])
o2.seed_elements(5.25, 60.2, radius=3000, number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100,25))
self.assertEqual(o2.history.shape, (100,13))
# Check that start and end conditions (longitudes) are idential
self.assertItemsEqual(o1.history['lon'][:,24].compressed(),
o2.history['lon'][:,12].compressed())
self.assertItemsEqual(o1.history['lon'][:,0].compressed(),
o2.history['lon'][:,0].compressed())
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertItemsEqual(o2i.history['lon'][:,12].compressed(),
o2.history['lon'][:,12].compressed())
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
#!/usr/bin/env python
from datetime import datetime, timedelta
import numpy as np
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.oceandrift import OceanDrift
o = OceanDrift() # Basic drift model suitable for passive tracers or drifters
#######################
# Preparing Readers
#######################
reader_current = reader_netCDF_CF_generic.Reader(
'test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
reader_wind = reader_netCDF_CF_generic.Reader(
'test_data/16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=4,
llcrnrlat=59.8,
urcrnrlon=6,
urcrnrlat=61,
resolution='h',
projection='merc')
o.add_reader([reader_basemap, reader_current, reader_wind])
#######################
#!/usr/bin/env python
import os
from datetime import datetime, timedelta
import numpy as np
from readers import reader_basemap_landmask
from readers import reader_ROMS_native
from models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Nordic 4km
nordic_native = reader_ROMS_native.Reader('test_data/2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=11.0, llcrnrlat=67.5,
urcrnrlon=16.0, urcrnrlat=69.0,
resolution='h', projection='merc')
o.add_reader([reader_basemap, nordic_native])
# Seeding some particles
time = nordic_native.start_time
lon = 12.0; lat = 68.3;
# Seed oil elements at defined position and time
o.seed_elements(lon, lat, radius=0, number=10, z=np.linspace(0, -150, 10), time=time)
print o
#!/usr/bin/env python
# Illustrating the difference between Euler and Runge-Kutta propagation
# schemes, using a "real" current fields from the NorKyst800 model
from datetime import datetime, timedelta
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(
'test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
time = reader_norkyst.start_time
reader_norkyst.interpolation = 'linearND'
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=59.9,
urcrnrlon=5.5, urcrnrlat=61.5, resolution='h')
o.add_reader([reader_norkyst, reader_basemap])
lon = 4.5; lat = 60.0;
# First run, with Euler scheme:
o.config['drift']['scheme'] = 'euler'
o.seed_elements(lon, lat, radius=0, number=1, time=time)
o.run(steps=66*2, time_step=1800)
# Second run, with Runge-Kutta scheme:
#!/usr/bin/env python
import os
from datetime import datetime, timedelta
from readers import reader_basemap_landmask
from readers import reader_netCDF_CF_generic
from models.oceandrift import OceanDrift
ncfile = 'backandforth.nc'
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader('test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
#reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=3, llcrnrlat=59,
urcrnrlon=6, urcrnrlat=62, resolution='h')
o.add_reader([reader_norkyst, reader_basemap])
################
# Forward run
################
# Seeding some particles
lon = 4.2; lat = 60.1;
time = reader_norkyst.start_time
o.seed_elements(lon, lat, radius=1000, number=100, time=time)
o.run(steps=50*4, time_step=900, outfile=ncfile)
#!/usr/bin/env python
# Illustrating the difference between Euler and Runge-Kutta propagation
# schemes, using an idealised (analytical) eddy current field.
from datetime import datetime, timedelta
from readers import reader_basemap_landmask
from readers import reader_ArtificialOceanEddy
from models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=-1.5,
llcrnrlat=59,
urcrnrlon=7,
urcrnrlat=64,
resolution='h')
o.add_reader([fake_eddy, reader_basemap])
lon = 2.0
lat = 63.0
# Close to Station M
# First run, with Euler scheme:
o.config['drift']['scheme'] = 'euler'
o.seed_elements(lon, lat, radius=0, number=1, time=datetime(2015, 1, 1))
o.run(steps=300, time_step=3600)