Note
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Trajan demo
From OpenDrift 2.0, analysis and plotting of results from OpenDrift simulations will be handled by a new, standalone package: Trajan https://github.com/OpenDrift/trajan
This example creates a test dataset, and demonstrates its anlysis using Trajan
import os
from datetime import datetime, timedelta
import matplotlib.pyplot as plt
import xarray as xr
import trajan as ta
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.openoil import OpenOil
Create test dataset with OpenDrift
o = OpenOil(loglevel=20)
# Add forcing
reader_arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader([reader_norkyst, reader_arome])
# Seeding some particles
o.seed_elements(lon=4.4, lat=60.1, radius=1000, number=1000,
time=reader_arome.start_time)
# Running model
o.run(end_time=reader_norkyst.end_time, outfile='openoil.nc')
14:37:35 INFO opendrift.models.basemodel:533: OpenDriftSimulation initialised (version 1.11.2 / v1.11.2-37-g34f6117)
14:37:35 INFO opendrift.readers.reader_netCDF_CF_generic:102: Opening dataset: /root/project/tests/test_data/16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc
/opt/conda/envs/opendrift/lib/python3.11/site-packages/pyproj/crs/crs.py:1286: UserWarning: You will likely lose important projection information when converting to a PROJ string from another format. See: https://proj.org/faq.html#what-is-the-best-format-for-describing-coordinate-reference-systems
proj = self._crs.to_proj4(version=version)
14:37:36 INFO opendrift.readers.reader_netCDF_CF_generic:314: Detected dimensions: {'time': 'time', 'x': 'x', 'y': 'y'}
14:37:36 INFO opendrift.readers.reader_netCDF_CF_generic:102: Opening dataset: /root/project/tests/test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc
/opt/conda/envs/opendrift/lib/python3.11/site-packages/pyproj/crs/crs.py:1286: UserWarning: You will likely lose important projection information when converting to a PROJ string from another format. See: https://proj.org/faq.html#what-is-the-best-format-for-describing-coordinate-reference-systems
proj = self._crs.to_proj4(version=version)
14:37:36 INFO opendrift.readers.reader_netCDF_CF_generic:314: Detected dimensions: {'x': 'X', 'y': 'Y', 'z': 'depth', 'time': 'time'}
14:37:36 INFO opendrift.models.openoil.openoil:1710: Oil type not specified, using default: GENERIC BUNKER C
14:37:36 INFO opendrift.models.openoil.adios.dirjs:90: Querying ADIOS database for oil: GENERIC BUNKER C
14:37:36 INFO opendrift.models.openoil.openoil:1719: Using density 971.1 and viscosity 0.0005020658058702914 of oiltype GENERIC BUNKER C
14:37:36 INFO opendrift.models.basemodel.environment:218: Adding a dynamical landmask with max. priority based on assumed maximum speed of 1.3 m/s. Adding a customised landmask may be faster...
14:37:41 INFO opendrift.models.basemodel.environment:245: Fallback values will be used for the following variables which have no readers:
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_surface_height: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: upward_sea_water_velocity: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_significant_height: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_stokes_drift_x_velocity: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_stokes_drift_y_velocity: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_period_at_variance_spectral_density_maximum: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_ice_area_fraction: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_ice_x_velocity: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_ice_y_velocity: 0.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_water_temperature: 10.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_water_salinity: 34.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: sea_floor_depth_below_sea_level: 10000.000000
14:37:41 INFO opendrift.models.basemodel.environment:248: ocean_vertical_diffusivity: 0.020000
14:37:41 INFO opendrift.models.basemodel.environment:248: ocean_mixed_layer_thickness: 50.000000
14:37:41 INFO opendrift.models.basemodel:911: Using existing reader for land_binary_mask
14:37:41 INFO opendrift.models.basemodel:922: All points are in ocean
14:37:41 INFO opendrift.models.openoil.openoil:687: Oil-water surface tension is 0.035282 Nm
14:37:41 INFO opendrift.models.openoil.openoil:700: Max water fraction not available for GENERIC BUNKER C, using default
14:37:41 INFO opendrift.models.basemodel:2011: 2015-11-16 00:00:00 - step 1 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 01:00:00 - step 2 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 02:00:00 - step 3 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 03:00:00 - step 4 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 04:00:00 - step 5 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 05:00:00 - step 6 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 06:00:00 - step 7 of 66 - 1000 active elements (0 deactivated)
14:37:42 INFO opendrift.models.basemodel:2011: 2015-11-16 07:00:00 - step 8 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 08:00:00 - step 9 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 09:00:00 - step 10 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 10:00:00 - step 11 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 11:00:00 - step 12 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 12:00:00 - step 13 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 13:00:00 - step 14 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 14:00:00 - step 15 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 15:00:00 - step 16 of 66 - 1000 active elements (0 deactivated)
14:37:43 INFO opendrift.models.basemodel:2011: 2015-11-16 16:00:00 - step 17 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 17:00:00 - step 18 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 18:00:00 - step 19 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 19:00:00 - step 20 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 20:00:00 - step 21 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 21:00:00 - step 22 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 22:00:00 - step 23 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-16 23:00:00 - step 24 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-17 00:00:00 - step 25 of 66 - 1000 active elements (0 deactivated)
14:37:44 INFO opendrift.models.basemodel:2011: 2015-11-17 01:00:00 - step 26 of 66 - 1000 active elements (0 deactivated)
14:37:44 WARNING opendrift.readers.basereader.structured:324: Data block from /root/project/tests/test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc not large enough to cover element positions within timestep. Buffer size (8) must be increased. See `Variables.set_buffer_size`.
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 02:00:00 - step 27 of 66 - 1000 active elements (0 deactivated)
14:37:45 WARNING opendrift.readers.basereader.structured:324: Data block from /root/project/tests/test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc not large enough to cover element positions within timestep. Buffer size (8) must be increased. See `Variables.set_buffer_size`.
/root/project/opendrift/readers/interpolation/interpolators.py:17: RuntimeWarning: overflow encountered in cast
data[mask] = np.finfo(np.float64).min
14:37:45 WARNING opendrift.readers.basereader.structured:324: Data block from /root/project/tests/test_data/16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc not large enough to cover element positions within timestep. Buffer size (4) must be increased. See `Variables.set_buffer_size`.
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 03:00:00 - step 28 of 66 - 1000 active elements (0 deactivated)
14:37:45 WARNING opendrift.readers.basereader.structured:324: Data block from /root/project/tests/test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc not large enough to cover element positions within timestep. Buffer size (8) must be increased. See `Variables.set_buffer_size`.
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 04:00:00 - step 29 of 66 - 998 active elements (2 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 05:00:00 - step 30 of 66 - 991 active elements (9 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 06:00:00 - step 31 of 66 - 980 active elements (20 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 07:00:00 - step 32 of 66 - 963 active elements (37 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 08:00:00 - step 33 of 66 - 920 active elements (80 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 09:00:00 - step 34 of 66 - 871 active elements (129 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 10:00:00 - step 35 of 66 - 820 active elements (180 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 11:00:00 - step 36 of 66 - 784 active elements (216 deactivated)
14:37:45 INFO opendrift.models.basemodel:2011: 2015-11-17 12:00:00 - step 37 of 66 - 754 active elements (246 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 13:00:00 - step 38 of 66 - 704 active elements (296 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 14:00:00 - step 39 of 66 - 568 active elements (432 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 15:00:00 - step 40 of 66 - 412 active elements (588 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 16:00:00 - step 41 of 66 - 325 active elements (675 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 17:00:00 - step 42 of 66 - 285 active elements (715 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 18:00:00 - step 43 of 66 - 251 active elements (749 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 19:00:00 - step 44 of 66 - 235 active elements (765 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 20:00:00 - step 45 of 66 - 221 active elements (779 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 21:00:00 - step 46 of 66 - 204 active elements (796 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 22:00:00 - step 47 of 66 - 198 active elements (802 deactivated)
14:37:46 INFO opendrift.models.basemodel:2011: 2015-11-17 23:00:00 - step 48 of 66 - 189 active elements (811 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 00:00:00 - step 49 of 66 - 181 active elements (819 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 01:00:00 - step 50 of 66 - 178 active elements (822 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 02:00:00 - step 51 of 66 - 178 active elements (822 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 03:00:00 - step 52 of 66 - 174 active elements (826 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 04:00:00 - step 53 of 66 - 172 active elements (828 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 05:00:00 - step 54 of 66 - 171 active elements (829 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 06:00:00 - step 55 of 66 - 171 active elements (829 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 07:00:00 - step 56 of 66 - 171 active elements (829 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 08:00:00 - step 57 of 66 - 168 active elements (832 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 09:00:00 - step 58 of 66 - 166 active elements (834 deactivated)
14:37:47 INFO opendrift.models.basemodel:2011: 2015-11-18 10:00:00 - step 59 of 66 - 162 active elements (838 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 11:00:00 - step 60 of 66 - 160 active elements (840 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 12:00:00 - step 61 of 66 - 159 active elements (841 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 13:00:00 - step 62 of 66 - 157 active elements (843 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 14:00:00 - step 63 of 66 - 156 active elements (844 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 15:00:00 - step 64 of 66 - 156 active elements (844 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 16:00:00 - step 65 of 66 - 155 active elements (845 deactivated)
14:37:48 INFO opendrift.models.basemodel:2011: 2015-11-18 17:00:00 - step 66 of 66 - 154 active elements (846 deactivated)
14:37:48 INFO opendrift.export.io_netcdf:116: Wrote 67 steps to file openoil.nc
/opt/conda/envs/opendrift/lib/python3.11/site-packages/numpy/ma/core.py:467: RuntimeWarning: invalid value encountered in cast
fill_value = np.array(fill_value, copy=False, dtype=ndtype)
Demonstrating analysis and visualisation of the output dataset, independently of OpenDrift code
if not os.path.exists('openoil.nc'):
raise ValueError('Please run create_test_dataset.py first')
Importing a trajectory dataset from a simulation with OpenDrift decode_coords is needed so that lon and lat are not interpreted as coordinate variables
d = xr.open_dataset('openoil.nc', decode_coords=False)
# Requirement that status>=0 is needed since non-valid points are not masked in OpenDrift output
d = d.where(d.status>=0) # only active particles
Displaying a basic plot of trajectories
d.traj.plot(land='mask')
ax = plt.gca()
ax.set_title('Adding custom title')
plt.show()
Demonstrating how the Xarray Dataset can be modified, allowing for more flexibility than can be provided through the plotting method of OpenDrift
Extracting only the first 100 elements, and every 4th output time steps:
dsub = d.isel(trajectory=range(0, 100), time=range(0, len(d.time), 4))
dsub.traj.plot(land='h')
plt.show()
With several plots on the same figure
d.traj.plot(color='red', alpha=0.01, land='mask') # Plotting individual trajectories in red
dmean = d.mean('trajectory', skipna=True) # Overlaying a "mean" trajectory in black
dmean.traj.plot(color='k', linewidth=5)
# Showing the a sub-period of the mean trajectory in yellow
dmean.sel(time=slice('2015-11-17', '2015-11-17 12')).traj.plot(color='yellow', linewidth=5)
plt.tight_layout()
plt.show()
Total running time of the script: (0 minutes 48.101 seconds)