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Update notebooks and configutation gallery
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content/en/docs/Examples/Notebooks/General/mask_maker_tutorial.md
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content/en/docs/Examples/Notebooks/General/polar_plotting.md
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| --- | ||
| title: "Polar plotting" | ||
| linkTitle: "Polar plotting" | ||
| weight: 5 | ||
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| description: > | ||
| Polar plotting example. | ||
| --- | ||
| # Polar Plotting Tutorial | ||
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| This demonstration will show how to re-project the NEMO velocities for quiver plotting in polar coordinates. | ||
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| NEMO velocities are usually calculated and saved in along grid i and j directions. This causes an issue when plotting velocities as vectors on a map where it is assumed that i and j velocities point eastwards and northwards but the grid is curvilinear. | ||
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| There are additional isses when plotting quivers over the poles that we will cover. | ||
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| The data we use here comes from a global model that has been cropped to the Arctic region. If you want to see the images, please go to the configuration gallery codes in `example_scripts/configuration_gallery/polar_plotting.py` or in the [documentation](https://british-oceanographic-data-centre.github.io/COAsT/docs/examples/configs_gallery/). | ||
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| **IMPORTANT: you have to install cartopy in order to plot the maps** | ||
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| ```python | ||
| # !pip install cartopy | ||
| ``` | ||
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| ```python | ||
| import matplotlib.pyplot as plt | ||
| import cartopy.crs as ccrs | ||
| import cartopy.feature as cfeature | ||
| import coast | ||
| ``` | ||
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| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pydap/lib.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.responses')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.handlers')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.tests')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
| /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`. | ||
| Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages | ||
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| ### Usage of coast._utils.plot_util.velocity_grid_to_geo() | ||
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| Plotting velocities with curvilinear grid and/or on a polar stereographic projection. | ||
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| ```python | ||
| root = "./" | ||
| # Paths to a single or multiple data files. | ||
| dn_files = root + "example_files/" | ||
| fn_nemo_dat_t = dn_files + "coast_nemo_quiver_thetao.nc" | ||
| fn_nemo_dat_u = dn_files + "coast_nemo_quiver_uo.nc" | ||
| fn_nemo_dat_v = dn_files + "coast_nemo_quiver_vo.nc" | ||
| fn_nemo_config_t = root + "config/gc31_nemo_grid_t.json" | ||
| fn_nemo_config_u = root + "config/gc31_nemo_grid_u.json" | ||
| fn_nemo_config_v = root + "config/gc31_nemo_grid_v.json" | ||
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| # Set path for domain file if required. | ||
| fn_nemo_dom = dn_files + "coast_nemo_quiver_dom.nc" | ||
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| # Define output filepath (optional: None or str) | ||
| fn_out = './quiver_plot.png' | ||
| ``` | ||
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| ```python | ||
| # Read in multiyear data (This example uses NEMO data from a single file.) | ||
| nemo_data_t = coast.Gridded(fn_data=fn_nemo_dat_t, | ||
| fn_domain=fn_nemo_dom, | ||
| config=fn_nemo_config_t, | ||
| ).dataset | ||
| nemo_data_u = coast.Gridded(fn_data=fn_nemo_dat_u, | ||
| fn_domain=fn_nemo_dom, | ||
| config=fn_nemo_config_u, | ||
| ).dataset | ||
| nemo_data_v = coast.Gridded(fn_data=fn_nemo_dat_v, | ||
| fn_domain=fn_nemo_dom, | ||
| config=fn_nemo_config_v, | ||
| ).dataset | ||
| ``` | ||
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| Select surface u and v as an example: | ||
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| ```python | ||
| # Select specific data variables. | ||
| data_u = nemo_data_u[["u_velocity"]] | ||
| data_v = nemo_data_v[["v_velocity"]] | ||
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| # Select one time step and surface currents | ||
| data_u = data_u.isel(t_dim=0, z_dim=0) | ||
| data_v = data_v.isel(t_dim=0, z_dim=0) | ||
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| # Calculate speed | ||
| speed = ((data_u.to_array().values[0, :, :] ** 2 + data_v.to_array().values[0, :, :] ** 2) ** 0.5) | ||
| ``` | ||
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| Calculate adjustment for the curvilinear grid | ||
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| This function may take a while | ||
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| ```python | ||
| uv_velocities = [data_u.to_array().values[0, :, :], data_v.to_array().values[0, :, :]] | ||
| u_new, v_new = coast._utils.plot_util.velocity_grid_to_geo( | ||
| nemo_data_t.longitude.values, nemo_data_t.latitude.values, | ||
| uv_velocities, | ||
| polar_stereo_cartopy_bug_fix=False) | ||
| ``` | ||
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| 100%|██████████| 59/59 [06:59<00:00, 7.11s/it] | ||
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| ```python | ||
| # Apply the CartoPy stereographic polar correction | ||
| # NOTE: This could have been applied automatically with `polar_stereo=True` in | ||
| # coast._utils.plot_util.velocity_grid_to_geo() | ||
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| u_pol, v_pol = coast._utils.plot_util.velocity_polar_bug_fix(u_new, v_new, nemo_data_t.latitude.values) | ||
| ``` | ||
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| ```python | ||
| # Set things up for plotting North Pole stereographic projection | ||
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| # Data projection | ||
| data_crs = ccrs.PlateCarree() | ||
| # Plot projection | ||
| mrc = ccrs.NorthPolarStereo(central_longitude=0.0) | ||
| ``` | ||
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| Below shows the u and v velocities when plotted with and without adjustment. | ||
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| The plot shows three cases: 1:no correction, 2:the NEMO grid correction, and 3:the NEMO grid correction with polar stereographic plot correction. We also plot the final corrected u and v velocities as streamlines. | ||
| - In case 1, the lower latitude velocities aren't too bad but become irregular further north as the grid lines deviate form lat and lon. | ||
| - In case 2, the irregularity still persists even with the grid correction. This is the result of a CartoPy bug which also worsens at high latitudes. | ||
| - In case 3, both corrections have been applied and the velocities quivers now align with the route of strong current speed as would be expected. | ||
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| `!WARNING: UNCOMMENT THE LINES BELOW TO PLOT THE MAPS` | ||
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| ```python | ||
| # Subplot axes settings | ||
| n_r = 2 # Number of subplot rows | ||
| n_c = 2 # Number of subplot columns | ||
| figsize = (10, 10) # Figure size | ||
| subplot_padding = 0.5 # Amount of vertical and horizontal padding between plots | ||
| fig_pad = (0.075, 0.075, 0.1, 0.1) # Figure padding (left, top, right, bottom) | ||
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| # Labels and Titles | ||
| fig_title = "Velocity Plot" # Whole figure title | ||
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| # Create plot and flatten axis array | ||
| fig, ax = plt.subplots(n_r, n_c, subplot_kw={"projection": mrc}, sharey=True, sharex=True, figsize=figsize) | ||
| cax = fig.add_axes([0.3, 0.96, 0.4, 0.01]) | ||
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| ax = ax.flatten() | ||
| for rr in range(n_r * n_c): | ||
| ax[rr].add_feature(cfeature.LAND, zorder=100) | ||
| ax[rr].gridlines() | ||
| ax[rr].set_extent([-180, 180, 70, 90], crs=data_crs) | ||
| coast._utils.plot_util.set_circle(ax[rr]) | ||
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| cs = ax[0].pcolormesh(nemo_data_t.longitude.values, nemo_data_t.latitude.values, speed, transform=data_crs, vmin=0, vmax=0.3) | ||
| ax[0].quiver(nemo_data_t.longitude.values, nemo_data_t.latitude.values, | ||
| data_u.to_array().values[0, :, :], data_v.to_array().values[0, :, :], | ||
| color='w', transform=data_crs, angles='xy', regrid_shape=40) | ||
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| ax[1].pcolormesh(nemo_data_t.longitude.values, nemo_data_t.latitude.values, speed, transform=data_crs, vmin=0, vmax=0.3) | ||
| ax[1].quiver(nemo_data_t.longitude.values, nemo_data_t.latitude.values, | ||
| u_new, v_new, | ||
| color='w', transform=data_crs, angles='xy', regrid_shape=40) | ||
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| ax[2].pcolormesh(nemo_data_t.longitude.values, nemo_data_t.latitude.values, speed, transform=data_crs, vmin=0, vmax=0.3) | ||
| ax[2].quiver(nemo_data_t.longitude.values, nemo_data_t.latitude.values, | ||
| u_pol, v_pol, | ||
| color='w', transform=data_crs, angles='xy', regrid_shape=40) | ||
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| ax[3].pcolormesh(nemo_data_t.longitude.values, nemo_data_t.latitude.values, speed, transform=data_crs, vmin=0, vmax=0.3) | ||
| ax[3].streamplot(nemo_data_t.longitude.values, nemo_data_t.latitude.values, | ||
| u_pol, v_pol, transform=data_crs, linewidth=1, density=2, color='w', zorder=101) | ||
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| ax[0].set_title('1: No Correction') | ||
| ax[1].set_title('2: NEMO Grid Correction') | ||
| ax[2].set_title('3: Grid Correction and Polar Correction') | ||
| ax[3].set_title('As left but with streamlines') | ||
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| fig.colorbar(cs, cax=cax, orientation='horizontal') | ||
| cax.set_xlabel('U (m s$^{-1}$)') | ||
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| #fig.tight_layout(w_pad=subplot_padding, h_pad=subplot_padding) | ||
| #fig.subplots_adjust(left=(fig_pad[0]), bottom=(fig_pad[1]), right=(1 - fig_pad[2]), top=(1 - fig_pad[3])) | ||
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| plt.show() | ||
| # uncomment this line to save an output image | ||
| # fig.savefig(fn_out) | ||
| ``` | ||
|  | ||
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| Below shows the temperature plots | ||
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| ```python | ||
| # Data to plot | ||
| data_bathy = nemo_data_t.bathymetry.values | ||
| data_temp = nemo_data_t.temperature.isel(t_dim=0, z_dim=0) | ||
| ``` | ||
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| `!WARNING: UNCOMMENT THE LINES BELOW TO PLOT THE MAPS` | ||
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| ```python | ||
| figsize = (5, 5) # Figure size | ||
| fig = plt.figure(figsize=figsize) | ||
| ax1 = fig.add_axes([0.1, 0.1, 0.8, 0.75], projection=mrc) | ||
| cax = fig.add_axes([0.3, 0.96, 0.4, 0.01]) | ||
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| ax1.add_feature(cfeature.LAND, zorder=105) | ||
| ax1.gridlines() | ||
| ax1.set_extent([-180, 180, 70, 90], crs=data_crs) | ||
| coast._utils.plot_util.set_circle(ax1) | ||
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| # We use to a function to re-project the data for plotting contours over the pole. | ||
| cs1 = coast._utils.plot_util.plot_polar_contour( | ||
| nemo_data_t.longitude.values, nemo_data_t.latitude.values, data_bathy, ax1, levels=6, colors="k", zorder=101 | ||
| ) | ||
| cs2 = ax1.pcolormesh( | ||
| nemo_data_t.longitude.values, nemo_data_t.latitude.values, data_temp, transform=data_crs, vmin=-2, vmax=8 | ||
| ) | ||
| cax.set_xlabel(r"SST ($^{\circ}$C)") | ||
| fig.colorbar(cs2, cax=cax, orientation="horizontal") | ||
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| # fig.savefig(fn_out, dpi=120) | ||
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| ``` | ||
|  | ||
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| ```python | ||
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| ``` |
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