def test_repeated(self):
"""Check that block can be used for interpolation to several sets of positions"""
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
# 100 points within 50x50 pixels over sea (corner of domain)
num_points = 100
np.random.seed(0) # To get the same random numbers each time
x = np.random.uniform(reader.xmin, reader.xmin+800*50, num_points)
y = np.random.uniform(reader.ymax-800*50, reader.ymax, num_points)
z = np.random.uniform(-200, 0, num_points)
variables = ['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
b = ReaderBlock(data, interpolation_horizontal='nearest')
env, prof = b.interpolate(x, y, z, 'sea_water_temperature')
x2 = x[20:30]
y2 = y[20:30]
z2 = z[20:30]
env2, prof2 = b.interpolate(x2, y2, z2, 'sea_water_temperature')
env3, prof3 = b.interpolate(x, y, z, 'sea_water_temperature')
self.assertEqual(env['sea_water_temperature'][0],
env3['sea_water_temperature'][0])
self.assertEqual(env['sea_water_temperature'][20],
env2['sea_water_temperature'][0])
def test_repeated(self):
"""Check that block can be used for interpolation to several sets of positions"""
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
# 100 points within 50x50 pixels over sea (corner of domain)
num_points = 100
np.random.seed(0) # To get the same random numbers each time
x = np.random.uniform(reader.xmin, reader.xmin+800*50, num_points)
y = np.random.uniform(reader.ymax-800*50, reader.ymax, num_points)
z = np.random.uniform(-200, 0, num_points)
variables = ['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
b = ReaderBlock(data, interpolation_horizontal='nearest')
env, prof = b.interpolate(x, y, z, 'sea_water_temperature')
x2 = x[20:30]
y2 = y[20:30]
z2 = z[20:30]
env2, prof2 = b.interpolate(x2, y2, z2, 'sea_water_temperature')
env3, prof3 = b.interpolate(x, y, z, 'sea_water_temperature')
self.assertEqual(env['sea_water_temperature'][0],
env3['sea_water_temperature'][0])
self.assertEqual(env['sea_water_temperature'][20],
env2['sea_water_temperature'][0])
def test_linearNDFast(self):
"""Test interpolation."""
reader = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
reader.buffer = 3
num_points = 50
np.random.seed(0) # To get the same random numbers each time
lons = np.random.uniform(14, 15, num_points)
lats = np.random.uniform(68, 68.4, num_points)
z = np.random.uniform(-20, 0, num_points)
x, y = reader.lonlat2xy(lons, lats)
#z=None
variables = ['x_sea_water_velocity']
# Read a block of data covering the points
data = reader.get_variables(variables,
time=reader.start_time,
x=x,
y=y,
z=z,
block=True)
b = ReaderBlock(data.copy(), interpolation_horizontal='linearNDFast')
x2 = np.random.uniform(x.min(), x.max(), num_points)
y2 = np.random.uniform(y.min(), y.max(), num_points)
z2 = np.random.uniform(-20, 0, num_points)
self.assertTrue(b.covers_positions(x, y, z))
self.assertTrue(b.covers_positions(x2, y2, z2))
# Check that there are holes in the arrays of the ReaderBlock
self.assertEqual(
np.sum(~np.isfinite(b.data_dict['x_sea_water_velocity'])), 1001)
# Check that LinearNDFast interpolation gives a real value
env, prof = b.interpolate(x2,
y2,
z2,
variables,
profiles=variables,
profiles_depth=[-30, 0])
self.assertEqual(np.sum(~np.isfinite(env['x_sea_water_velocity'])), 0)
# Check that the arrays of the ReaderBlock have been filled in
self.assertEqual(
np.sum(~np.isfinite(b.data_dict['x_sea_water_velocity'])), 0)
# Check that nearest interpolation contains some NaN values
b2 = ReaderBlock(data.copy(), interpolation_horizontal='nearest')
env, prof = b2.interpolate(x2,
y2,
z2,
variables,
profiles=variables,
profiles_depth=[-30, 0])
self.assertEqual(np.sum(~np.isfinite(env['x_sea_water_velocity'])), 31)
def test_interpolation_missing(self):
"""Test interpolation."""
reader = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
num_points = 50
np.random.seed(0) # To get the same random numbers each time
lons = np.random.uniform(10, 11, num_points)
lats = np.random.uniform(66, 67.0, num_points)
z = np.random.uniform(-200, 0, num_points)
x, y = reader.lonlat2xy(lons, lats)
variables = ['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
# Introduce missing values
data['x_sea_water_velocity'] = np.ma.masked_where(
data['x_sea_water_velocity']>.08,
data['x_sea_water_velocity'])
b = ReaderBlock(data, interpolation_horizontal='linearND')
env, prof = b.interpolate(x, y, z, variables,
profiles=['x_sea_water_velocity'],
profiles_depth=[-30, 0])
self.assertAlmostEqual(env['x_sea_water_velocity'][10],
0.074, 2)
self.assertAlmostEqual(prof['x_sea_water_velocity'][5,48],
-0.090, 2)
def test_interpolation_3dArrays(self):
"""Test interpolation."""
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
# 100000 points within 50x50 pixels over sea (corner of domain)
num_points = 1000
np.random.seed(0) # To get the same random numbers each time
x = np.random.uniform(reader.xmin, reader.xmin+800*50, num_points)
y = np.random.uniform(reader.ymax-800*50, reader.ymax, num_points)
z = np.random.uniform(-200, 0, num_points)
variables = ['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
b = ReaderBlock(data, interpolation_horizontal='nearest')
env, prof = b.interpolate(x, y, z, variables,
profiles=['sea_water_temperature'],
profiles_depth=[-30, 0])
self.assertAlmostEqual(env['x_sea_water_velocity'][100],
0.075019, 3)
self.assertAlmostEqual(prof['sea_water_temperature'][0,11],
7.549999, 3)
self.assertAlmostEqual(prof['sea_water_temperature'][-1,11],
8.389999, 3)
self.assertEqual(prof['z'][-1], b.z[-1])
def test_interpolation_ensemble(self):
data_dict, x, y, z = self.get_synthetic_data_dict()
x = x[0:15]
y = y[0:15]
z = z[0:15]
data_dict['var2d'] = np.ones(data_dict['var2d'].shape)
data_dict['var3d'] = np.ones(data_dict['var3d'].shape)
data_dict['var2de'] = [data_dict['var2d']*1,
data_dict['var2d']*2,
data_dict['var2d']*3]
data_dict['var3de'] = [data_dict['var3d']*31,
data_dict['var3d']*32,
data_dict['var3d']*33]
b = ReaderBlock(data_dict)
interp = b.interpolate(x, y, z)[0] # 1 is profiles
v2 = interp['var2d']
v2e = interp['var2de']
v3 = interp['var3d']
v3e = interp['var3de']
self.assertEqual(v2[0], 1)
self.assertEqual(v2e[0], 1)
self.assertEqual(v2e[1], 2)
self.assertEqual(v2e[3], 1)
self.assertEqual(v3[0], 1)
self.assertEqual(v3e[0], 31)
self.assertEqual(v3e[1], 32)
self.assertAlmostEqual(v3e[3], 31)
def test_interpolation_missing(self):
"""Test interpolation."""
reader = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
num_points = 50
np.random.seed(0) # To get the same random numbers each time
lons = np.random.uniform(10, 11, num_points)
lats = np.random.uniform(66, 67.0, num_points)
z = np.random.uniform(-200, 0, num_points)
x, y = reader.lonlat2xy(lons, lats)
variables = ['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
# Introduce missing values
data['x_sea_water_velocity'].mask[[data['x_sea_water_velocity']>.08]] = True
b = ReaderBlock(data, interpolation_horizontal='linearND')
env, prof = b.interpolate(x, y, z, variables,
profiles=['x_sea_water_velocity'],
profiles_depth=[-30, 0])
self.assertAlmostEqual(env['x_sea_water_velocity'][10],
0.056, 2)
self.assertAlmostEqual(prof['x_sea_water_velocity'][5,48],
-0.090, 2)
def test_interpolation_3dArrays(self):
"""Test interpolation."""
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
# 100000 points within 50x50 pixels over sea (corner of domain)
num_points = 1000
np.random.seed(0) # To get the same random numbers each time
x = np.random.uniform(reader.xmin, reader.xmin+800*50, num_points)
y = np.random.uniform(reader.ymax-800*50, reader.ymax, num_points)
z = np.random.uniform(-200, 0, num_points)
variables = ['x_sea_water_velocity', 'y_sea_water_velocity',
'sea_water_temperature']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
b = ReaderBlock(data, interpolation_horizontal='nearest')
env, prof = b.interpolate(x, y, z, variables,
profiles=['sea_water_temperature'],
profiles_depth=[-30, 0])
self.assertAlmostEqual(env['x_sea_water_velocity'][100],
0.075019, 3)
self.assertAlmostEqual(prof['sea_water_temperature'][0,11],
7.549999, 3)
self.assertAlmostEqual(prof['sea_water_temperature'][-1,11],
8.389999, 3)
self.assertEqual(prof['z'][-1], b.z[-1])
def test_interpolation_ensemble(self):
data_dict, x, y, z = self.get_synthetic_data_dict()
x = x[0:15]
y = y[0:15]
z = z[0:15]
data_dict['var2d'] = np.ones(data_dict['var2d'].shape)
data_dict['var3d'] = np.ones(data_dict['var3d'].shape)
data_dict['var2de'] = [data_dict['var2d']*1,
data_dict['var2d']*2,
data_dict['var2d']*3]
data_dict['var3de'] = [data_dict['var3d']*31,
data_dict['var3d']*32,
data_dict['var3d']*33]
b = ReaderBlock(data_dict)
interp = b.interpolate(x, y, z)[0] # 1 is profiles
v2 = interp['var2d']
v2e = interp['var2de']
v3 = interp['var3d']
v3e = interp['var3de']
self.assertEqual(v2[0], 1)
self.assertEqual(v2e[0], 1)
self.assertEqual(v2e[1], 2)
self.assertEqual(v2e[3], 1)
self.assertEqual(v3[0], 1)
self.assertEqual(v3e[0], 31)
self.assertEqual(v3e[1], 32)
self.assertAlmostEqual(v3e[3], 31)
def test_linearNDFast(self):
"""Test interpolation."""
reader = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
reader.buffer=3
num_points = 50
np.random.seed(0) # To get the same random numbers each time
lons = np.random.uniform(14, 15, num_points)
lats = np.random.uniform(68, 68.4, num_points)
z = np.random.uniform(-20, 0, num_points)
x, y = reader.lonlat2xy(lons, lats)
#z=None
variables = ['x_sea_water_velocity']
# Read a block of data covering the points
data = reader.get_variables(variables, time=reader.start_time,
x=x, y=y, z=z, block=True)
b = ReaderBlock(data.copy(),
interpolation_horizontal='linearNDFast')
x2 = np.random.uniform(x.min(), x.max(), num_points)
y2 = np.random.uniform(y.min(), y.max(), num_points)
z2 = np.random.uniform(-20, 0, num_points)
self.assertTrue(b.covers_positions(x, y, z))
self.assertTrue(b.covers_positions(x2, y2, z2))
# Check that there are holes in the arrays of the ReaderBlock
self.assertEqual(
np.sum(~np.isfinite(b.data_dict['x_sea_water_velocity'])), 1001)
# Check that LinearNDFast interpolation gives a real value
env, prof = b.interpolate(x2, y2, z2,
variables,
profiles=variables,
profiles_depth=[-30, 0])
self.assertEqual(
np.sum(~np.isfinite(env['x_sea_water_velocity'])), 0)
# Check that the arrays of the ReaderBlock have been filled in
self.assertEqual(
np.sum(~np.isfinite(b.data_dict['x_sea_water_velocity'])), 0)
# Check that nearest interpolation contains some NaN values
b2 = ReaderBlock(data.copy(), interpolation_horizontal='nearest')
env, prof = b2.interpolate(x2, y2, z2,
variables,
profiles=variables,
profiles_depth=[-30, 0])
self.assertEqual(
np.sum(~np.isfinite(env['x_sea_water_velocity'])), 31)
def test_zNone(self):
d = {}
d['x'] = np.arange(5)
d['y'] = np.arange(7)
d['z'] = 0
d['time'] = None
d['var'] = np.random.rand(5, 6)
rb = ReaderBlock(d)
z = None
i, p = rb.interpolate(np.array([1, 2]), np.array([2, 3]), z, 'var')
self.assertTrue(i['var'][0] > 0)
def test_zNone(self):
d = {}
d['x'] = np.arange(5)
d['y'] = np.arange(7)
d['z'] = 0
d['time'] = None
d['var'] = np.random.rand(5,6)
rb = ReaderBlock(d)
z = None
i,p = rb.interpolate(np.array([1, 2]), np.array([2, 3]), z, 'var')
self.assertTrue(i['var'][0] > 0)
v = reader_arctic.get_variables(variables, time=t, x=x, y=y, z=z, block=True)
time_spent = datetime.now() - start_time
print '%6.2f seconds on this machine' % time_spent.total_seconds()
print '--------------------------------------------------------'
print 'Test 3: Interpolating 3D arrays onto particle positions'
print ' 2.5 seconds on reference machine.'
start_time = datetime.now()
b = ReaderBlock(v, interpolation_horizontal='linearND')
num_points = 10000
x = np.random.uniform(reader_arctic.xmin, reader_arctic.xmax, num_points)
y = np.random.uniform(reader_arctic.ymin, reader_arctic.ymax, num_points)
z = np.random.uniform(-200, 0, num_points)
env, prof = b.interpolate(x, y, z, variables,
profiles=['sea_water_temperature'],
profiles_depth=[-30, 0])
time_spent = datetime.now() - start_time
print '%6.1f seconds on this machine' % time_spent.total_seconds()
print '--------------------------------------------------------'
print 'Test 4: Vertical mixing with 50 elements and 7200 cycles (CPU-heavy)'
print ' 10.0 seconds on reference machine.'
reader_arctic.buffer=10
reader_arctic.verticalbuffer=1
o = OpenOil3D(loglevel=50) # Quiet
o.add_reader(reader_arctic)
o.fallback_values['x_wind'] = 10
o.set_config('turbulentmixing:timestep', 1)
o.seed_elements(lon=15, lat=72, number=50, radius=10000,
v = reader_arctic.get_variables(variables, time=t, x=x, y=y, z=z)
time_spent = datetime.now() - start_time
print('%6.2f seconds on this machine' % time_spent.total_seconds())
print('--------------------------------------------------------')
print('Test 3: Interpolating 3D arrays onto particle positions')
print(' 2.5 seconds on reference machine.')
start_time = datetime.now()
b = ReaderBlock(v, interpolation_horizontal='linearND')
num_points = 10000
x = np.random.uniform(reader_arctic.xmin, reader_arctic.xmax, num_points)
y = np.random.uniform(reader_arctic.ymin, reader_arctic.ymax, num_points)
z = np.random.uniform(-200, 0, num_points)
env, prof = b.interpolate(x,
y,
z,
variables,
profiles=['sea_water_temperature'],
profiles_depth=[-30, 0])
time_spent = datetime.now() - start_time
print('%6.1f seconds on this machine' % time_spent.total_seconds())
print('--------------------------------------------------------')
print('Test 4: Vertical mixing with 50 elements and 7200 cycles (CPU-heavy)')
print(' 10.0 seconds on reference machine.')
reader_arctic.buffer = 10
reader_arctic.verticalbuffer = 1
o = OpenOil(loglevel=50) # Quiet
o.add_reader(reader_arctic)
o.set_config('environment:fallback:x_wind', 10)
o.set_config('environment:fallback:y_wind', 0)
o.set_config('vertical_mixing:timestep', 1)