.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "gallery/example_trajan.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_gallery_example_trajan.py: 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 .. GENERATED FROM PYTHON SOURCE LINES 12-22 .. code-block:: Python import os from datetime import datetime, timedelta import matplotlib.pyplot as plt import xarray as xr import trajan as ta from opendrift import test_data_folder as tdf from opendrift.readers import reader_netCDF_CF_generic from opendrift.models.openoil import OpenOil .. GENERATED FROM PYTHON SOURCE LINES 23-24 Create test dataset with OpenDrift .. GENERATED FROM PYTHON SOURCE LINES 24-41 .. code-block:: Python o = OpenOil(loglevel=20) # Add forcing reader_arome = reader_netCDF_CF_generic.Reader(tdf + '16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc') reader_norkyst = reader_netCDF_CF_generic.Reader(tdf + '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') .. rst-class:: sphx-glr-script-out .. code-block:: none 13:14:50 INFO opendrift:576: OpenDriftSimulation initialised (version 1.14.8 / v1.14.8-4-g48afd36) 13:14:50 INFO opendrift.readers:63: Opening file with xr.open_dataset 13:14:50 INFO opendrift.readers.reader_netCDF_CF_generic:332: Detected dimensions: {'time': 'time', 'x': 'x', 'y': 'y'} 13:14:50 INFO opendrift.readers:63: Opening file with xr.open_dataset 13:14:50 INFO opendrift.readers.reader_netCDF_CF_generic:332: Detected dimensions: {'x': 'X', 'y': 'Y', 'z': 'depth', 'time': 'time'} 13:14:50 INFO opendrift.models.openoil.openoil:1708: Oil type not specified, using default: GENERIC BUNKER C 13:14:50 INFO opendrift.models.openoil.adios.dirjs:86: Querying ADIOS database for oil: GENERIC BUNKER C 13:14:50 INFO opendrift.models.openoil.openoil:1717: Using density 988.1 and viscosity 0.02169233387797564 of oiltype GENERIC BUNKER C 13:14:50 INFO opendrift.models.basemodel.environment:203: Adding a global landmask from GSHHG 13:14:55 INFO opendrift.models.basemodel.environment:227: Fallback values will be used for the following variables which have no readers: 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_surface_height: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: upward_sea_water_velocity: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_surface_wave_significant_height: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_surface_wave_stokes_drift_x_velocity: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_surface_wave_stokes_drift_y_velocity: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_surface_wave_period_at_variance_spectral_density_maximum: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_ice_area_fraction: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_ice_x_velocity: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_ice_y_velocity: 0.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_water_temperature: 10.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_water_salinity: 34.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: sea_floor_depth_below_sea_level: 10000.000000 13:14:55 INFO opendrift.models.basemodel.environment:230: ocean_vertical_diffusivity: 0.020000 13:14:55 INFO opendrift.models.basemodel.environment:230: ocean_mixed_layer_thickness: 50.000000 13:14:55 INFO opendrift:1810: Skipping environment variable upward_sea_water_velocity because of condition ['drift:vertical_advection', 'is', False] 13:14:55 INFO opendrift:1821: Storing previous values of element property lon because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous'])) 13:14:55 INFO opendrift:1821: Storing previous values of element property lat because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous'])) 13:14:55 INFO opendrift:952: Using existing reader for land_binary_mask to move elements to ocean 13:14:55 INFO opendrift:982: All points are in ocean 13:14:55 INFO opendrift.models.openoil.openoil:692: Oil-water surface tension is 0.035935 Nm 13:14:55 INFO opendrift.models.openoil.openoil:705: Max water fraction not available for GENERIC BUNKER C, using default 13:14:55 INFO opendrift:2118: 2015-11-16 00:00:00 - step 1 of 66 - 1000 active elements (0 deactivated) 13:14:55 INFO opendrift:2118: 2015-11-16 01:00:00 - step 2 of 66 - 1000 active elements (0 deactivated) 13:14:55 INFO opendrift:2118: 2015-11-16 02:00:00 - step 3 of 66 - 1000 active elements (0 deactivated) 13:14:55 INFO opendrift:2118: 2015-11-16 03:00:00 - step 4 of 66 - 1000 active elements (0 deactivated) 13:14:55 INFO opendrift:2118: 2015-11-16 04:00:00 - step 5 of 66 - 1000 active elements (0 deactivated) 13:14:55 INFO opendrift:2118: 2015-11-16 05:00:00 - step 6 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 06:00:00 - step 7 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 07:00:00 - step 8 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 08:00:00 - step 9 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 09:00:00 - step 10 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 10:00:00 - step 11 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 11:00:00 - step 12 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 12:00:00 - step 13 of 66 - 1000 active elements (0 deactivated) 13:14:56 INFO opendrift:2118: 2015-11-16 13:00:00 - step 14 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 14:00:00 - step 15 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 15:00:00 - step 16 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 16:00:00 - step 17 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 17:00:00 - step 18 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 18:00:00 - step 19 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 19:00:00 - step 20 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 20:00:00 - step 21 of 66 - 1000 active elements (0 deactivated) 13:14:57 INFO opendrift:2118: 2015-11-16 21:00:00 - step 22 of 66 - 1000 active elements (0 deactivated) 13:14:58 INFO opendrift:2118: 2015-11-16 22:00:00 - step 23 of 66 - 1000 active elements (0 deactivated) 13:14:58 INFO opendrift:2118: 2015-11-16 23:00:00 - step 24 of 66 - 1000 active elements (0 deactivated) 13:14:58 INFO opendrift:2118: 2015-11-17 00:00:00 - step 25 of 66 - 1000 active elements (0 deactivated) 13:14:58 INFO opendrift:2118: 2015-11-17 01:00:00 - step 26 of 66 - 1000 active elements (0 deactivated) 13:14:58 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`. 13:14:58 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`. 13:14:58 INFO opendrift:2118: 2015-11-17 02:00:00 - step 27 of 66 - 1000 active elements (0 deactivated) 13:14:58 INFO opendrift:2118: 2015-11-17 03:00:00 - step 28 of 66 - 1000 active elements (0 deactivated) 13:14:58 INFO opendrift:2118: 2015-11-17 04:00:00 - step 29 of 66 - 1000 active elements (0 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 05:00:00 - step 30 of 66 - 999 active elements (1 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 06:00:00 - step 31 of 66 - 999 active elements (1 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 07:00:00 - step 32 of 66 - 994 active elements (6 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 08:00:00 - step 33 of 66 - 989 active elements (11 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 09:00:00 - step 34 of 66 - 962 active elements (38 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 10:00:00 - step 35 of 66 - 908 active elements (92 deactivated) 13:15:02 INFO opendrift:2118: 2015-11-17 11:00:00 - step 36 of 66 - 853 active elements (147 deactivated) 13:15:03 INFO opendrift:2118: 2015-11-17 12:00:00 - step 37 of 66 - 804 active elements (196 deactivated) 13:15:03 INFO opendrift:2118: 2015-11-17 13:00:00 - step 38 of 66 - 773 active elements (227 deactivated) 13:15:03 INFO opendrift:2118: 2015-11-17 14:00:00 - step 39 of 66 - 737 active elements (263 deactivated) 13:15:03 INFO opendrift:2118: 2015-11-17 15:00:00 - step 40 of 66 - 692 active elements (308 deactivated) 13:15:03 INFO opendrift:2118: 2015-11-17 16:00:00 - step 41 of 66 - 644 active elements (356 deactivated) 13:15:03 INFO opendrift:2118: 2015-11-17 17:00:00 - step 42 of 66 - 590 active elements (410 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-17 18:00:00 - step 43 of 66 - 545 active elements (455 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-17 19:00:00 - step 44 of 66 - 483 active elements (517 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-17 20:00:00 - step 45 of 66 - 401 active elements (599 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-17 21:00:00 - step 46 of 66 - 327 active elements (673 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-17 22:00:00 - step 47 of 66 - 304 active elements (696 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-17 23:00:00 - step 48 of 66 - 286 active elements (714 deactivated) 13:15:04 INFO opendrift:2118: 2015-11-18 00:00:00 - step 49 of 66 - 277 active elements (723 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 01:00:00 - step 50 of 66 - 269 active elements (731 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 02:00:00 - step 51 of 66 - 263 active elements (737 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 03:00:00 - step 52 of 66 - 259 active elements (741 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 04:00:00 - step 53 of 66 - 256 active elements (744 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 05:00:00 - step 54 of 66 - 254 active elements (746 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 06:00:00 - step 55 of 66 - 244 active elements (756 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 07:00:00 - step 56 of 66 - 236 active elements (764 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 08:00:00 - step 57 of 66 - 232 active elements (768 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 09:00:00 - step 58 of 66 - 231 active elements (769 deactivated) 13:15:05 INFO opendrift:2118: 2015-11-18 10:00:00 - step 59 of 66 - 228 active elements (772 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 11:00:00 - step 60 of 66 - 224 active elements (776 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 12:00:00 - step 61 of 66 - 224 active elements (776 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 13:00:00 - step 62 of 66 - 220 active elements (780 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 14:00:00 - step 63 of 66 - 220 active elements (780 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 15:00:00 - step 64 of 66 - 219 active elements (781 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 16:00:00 - step 65 of 66 - 219 active elements (781 deactivated) 13:15:06 INFO opendrift:2118: 2015-11-18 17:00:00 - step 66 of 66 - 218 active elements (782 deactivated) .. raw:: html 
<xarray.Dataset> Size: 12MB
    Dimensions:                                                                              (
                                                                                              trajectory: 1000,
                                                                                              time: 67)
    Coordinates:
      * trajectory                                                                           (trajectory) int32 4kB ...
      * time                                                                                 (time) datetime64[ns] 536B ...
    Data variables: (12/43)
        status                                                                               (trajectory, time) float64 536kB ...
        moving                                                                               (trajectory, time) float64 536kB ...
        age_seconds                                                                          (trajectory, time) float32 268kB ...
        origin_marker                                                                        (trajectory, time) float64 536kB ...
        lon                                                                                  (trajectory, time) float32 268kB ...
        lat                                                                                  (trajectory, time) float32 268kB ...
        ...                                                                                   ...
        sea_water_temperature                                                                (trajectory, time) float32 268kB ...
        sea_water_salinity                                                                   (trajectory, time) float32 268kB ...
        sea_floor_depth_below_sea_level                                                      (trajectory, time) float32 268kB ...
        ocean_vertical_diffusivity                                                           (trajectory, time) float32 268kB ...
        land_binary_mask                                                                     (trajectory, time) float32 268kB ...
        ocean_mixed_layer_thickness                                                          (trajectory, time) float32 268kB ...
    Attributes: (12/165)
        Conventions:                                                             ...
        standard_name_vocabulary:                                                ...
        featureType:                                                             ...
        title:                                                                   ...
        summary:                                                                 ...
        keywords:                                                                ...
        ...                                                                                                               ...
        geospatial_lon_units:                                                    ...
        geospatial_lon_resolution:                                               ...
        runtime:                                                                 ...
        geospatial_vertical_min:                                                 ...
        geospatial_vertical_max:                                                 ...
        geospatial_vertical_positive:                                            ...


.. GENERATED FROM PYTHON SOURCE LINES 42-43 Demonstrating analysis and visualisation of the output dataset, independently of OpenDrift code .. GENERATED FROM PYTHON SOURCE LINES 43-47 .. code-block:: Python if not os.path.exists('openoil.nc'): raise ValueError('Please run create_test_dataset.py first') .. GENERATED FROM PYTHON SOURCE LINES 48-50 Importing a trajectory dataset from a simulation with OpenDrift decode_coords is needed so that lon and lat are not interpreted as coordinate variables .. GENERATED FROM PYTHON SOURCE LINES 50-55 .. code-block:: Python 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 .. GENERATED FROM PYTHON SOURCE LINES 56-57 Displaying a basic plot of trajectories .. GENERATED FROM PYTHON SOURCE LINES 57-62 .. code-block:: Python d.traj.plot(land='mask') ax = plt.gca() ax.set_title('Adding custom title') plt.show() .. image-sg:: /gallery/images/sphx_glr_example_trajan_001.png :alt: Adding custom title :srcset: /gallery/images/sphx_glr_example_trajan_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 63-65 Demonstrating how the Xarray Dataset can be modified, allowing for more flexibility than can be provided through the plotting method of OpenDrift .. GENERATED FROM PYTHON SOURCE LINES 67-68 Extracting only the first 100 elements, and every 4th output time steps: .. GENERATED FROM PYTHON SOURCE LINES 68-72 .. code-block:: Python dsub = d.isel(trajectory=range(0, 100), time=range(0, len(d.time), 4)) dsub.traj.plot(land='h') plt.show() .. image-sg:: /gallery/images/sphx_glr_example_trajan_002.png :alt: example trajan :srcset: /gallery/images/sphx_glr_example_trajan_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 73-74 With several plots on the same figure .. GENERATED FROM PYTHON SOURCE LINES 74-82 .. code-block:: Python 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() .. image-sg:: /gallery/images/sphx_glr_example_trajan_003.png :alt: example trajan :srcset: /gallery/images/sphx_glr_example_trajan_003.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 83-84 Cleaning up .. GENERATED FROM PYTHON SOURCE LINES 84-85 .. code-block:: Python os.remove('openoil.nc') .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 55.065 seconds) .. _sphx_glr_download_gallery_example_trajan.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: example_trajan.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: example_trajan.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: example_trajan.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_