.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/plot_croco_section.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 or to run this example in your browser via Binder. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_plot_croco_section.py: Interpolate a meridional section of CROCO outputs to regular depths =================================================================== In this notebook, we show: * how to compute the depths from s-coordinates, * how to easily find the name of variables and coordinates, * how to interpolate a 3D field with varying depths to regular depths, * how to compute the mixed layer depth from temperature. .. GENERATED FROM PYTHON SOURCE LINES 16-20 Initialisations --------------- Import needed modules. .. GENERATED FROM PYTHON SOURCE LINES 20-32 .. code-block:: Python import numpy as np import xarray as xr import matplotlib.pyplot as plt import cmocean # noqa import xoa from xoa.regrid import regrid1d from xoa.thermdyn import mixed_layer_depth import xoa.meta as xmeta xr.set_options(display_style="text") .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 33-34 Register the :meth:`xarray.Dataset.decode_sigma` callable accessor. .. GENERATED FROM PYTHON SOURCE LINES 34-37 .. code-block:: Python xoa.register_accessors(decode_sigma=True) .. GENERATED FROM PYTHON SOURCE LINES 38-40 The :ref:`xoa ` accessor is also registered by default, and give access to most of the functionalities of the other accessors. .. GENERATED FROM PYTHON SOURCE LINES 42-43 Register the internal CROCO naming specifications .. GENERATED FROM PYTHON SOURCE LINES 43-48 .. code-block:: Python croco_cfg_file = xoa.get_meta_config_file("croco") print(croco_cfg_file) xmeta.register_meta_specs(croco_cfg_file) .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/checkouts/readthedocs.org/user_builds/xoa/conda/develop/lib/python3.14/site-packages/xoa/meta/configs/croco.cfg .. GENERATED FROM PYTHON SOURCE LINES 49-55 You can provide your own configuration file. In this way, the :mod:`xoa.meta` module will recognise the CROCO netcdf names. It would be equivalent to force loading name specs with `xoa.meta.set_meta_specs(xoa.get_meta_config_file("croco"))`. .. GENERATED FROM PYTHON SOURCE LINES 57-60 Read the model -------------- This sample is a meridional extraction of a full 3D CROCO output. .. GENERATED FROM PYTHON SOURCE LINES 60-65 .. code-block:: Python sample_file = xoa.get_data_sample("MODELS/CROCO/SOUTH-AFRICA/croco.south-africa.meridional.nc") print(sample_file) ds = xr.open_dataset(sample_file) print(ds) .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/.cache/xoa/MODELS/CROCO/SOUTH-AFRICA/croco.south-africa.meridional.nc Size: 48kB Dimensions: (time: 1, s_w: 33, eta_rho: 56, xi_rho: 1, s_rho: 32, auxil: 4, xi_u: 1, eta_v: 55) Coordinates: (12/13) * time (time) float64 8B 2.592e+06 * s_w (s_w) float32 132B -1.0 -0.9688 -0.9375 ... -0.0625 -0.03125 0.0 * eta_rho (eta_rho) float32 224B 6.0 7.0 8.0 9.0 ... 58.0 59.0 60.0 61.0 * xi_rho (xi_rho) float32 4B 131.0 lat_rho (eta_rho, xi_rho) float32 224B ... lat_v (eta_v, xi_rho) float32 220B ... ... ... lon_v (eta_v, xi_rho) float32 220B ... * s_rho (s_rho) float32 128B -0.9844 -0.9531 ... -0.04688 -0.01562 * xi_u (xi_u) float32 4B 131.5 lat_u (eta_rho, xi_u) float32 224B ... lon_u (eta_rho, xi_u) float32 224B ... * eta_v (eta_v) float32 220B 6.5 7.5 8.5 9.5 ... 57.5 58.5 59.5 60.5 Dimensions without coordinates: auxil Data variables: (12/23) AKt (time, s_w, eta_rho, xi_rho) float32 7kB ... Cs_r (s_rho) float32 128B ... Cs_w (s_w) float32 132B ... Vtransform float32 4B ... angle (eta_rho, xi_rho) float32 224B ... el float32 4B ... ... ... time_step (time, auxil) int32 16B ... u (time, s_rho, eta_rho, xi_u) float32 7kB ... v (time, s_rho, eta_v, xi_rho) float32 7kB ... w (time, s_rho, eta_rho, xi_rho) float32 7kB ... xl float32 4B ... zeta (time, eta_rho, xi_rho) float32 224B ... Attributes: (12/57) type: ROMS history file title: BENGUELA TEST MODEL date: rst_file: CROCO_FILES/croco_rst.nc his_file: CROCO_FILES/croco_his.nc avg_file: CROCO_FILES/croco_avg.nc ... ... v_sponge: 0.0 sponge_expl: Sponge parameters : extent (m) & viscosity (m2.s-1) SRCS: main.F step.F read_inp.F timers_roms.F init_scalars.F ini... CPP-options: REGIONAL BENGUELA_VHR MPI OBC_EAST OBC_WEST OBC_NORTH OBC... history: Tue Mar 31 16:26:24 2020: ncks -O -d time,30 -d xi_rho,13... NCO: 4.4.2 .. GENERATED FROM PYTHON SOURCE LINES 66-77 Compute depths from s-coordinates --------------------------------- Decode the dataset according to the CF conventions: 1. Find sigma terms 2. Compute depths 3. Assign depths as coordinates Note that the :meth:`xarray.Dataset.decode_sigma` callable accessor calls the :func:`xoa.sigma.decode_cf_sigma` function. .. GENERATED FROM PYTHON SOURCE LINES 77-81 .. code-block:: Python ds = ds.decode_sigma() print(ds.depth) .. rst-class:: sphx-glr-script-out .. code-block:: none Size: 14kB array([[[[-4.47877110e+03], [-4.45341971e+03], [-4.43332704e+03], ..., [-7.38942221e+01], [-7.34145067e+01], [-7.34091375e+01]], [[-4.10998820e+03], [-4.08677643e+03], [-4.06837911e+03], ..., [-7.04949884e+01], [-7.00423304e+01], [-7.00372638e+01]], [[-3.70399833e+03], [-3.68314549e+03], [-3.66661727e+03], ..., ... ..., [-4.29529272e+00], [-4.27484202e+00], [-4.27461272e+00]], [[-1.00794918e+01], [-1.00480588e+01], [-1.00177861e+01], ..., [-2.57388434e+00], [-2.56165088e+00], [-2.56151371e+00]], [[-3.17876268e+00], [-3.15406668e+00], [-3.12913607e+00], ..., [-8.56901999e-01], [-8.52836074e-01], [-8.52790485e-01]]]], shape=(1, 32, 56, 1)) Coordinates: * time (time) float64 8B 2.592e+06 * s_rho (s_rho) float32 128B -0.9844 -0.9531 -0.9219 ... -0.04688 -0.01562 * eta_rho (eta_rho) float32 224B 6.0 7.0 8.0 9.0 10.0 ... 58.0 59.0 60.0 61.0 * xi_rho (xi_rho) float32 4B 131.0 lat_rho (eta_rho, xi_rho) float32 224B -37.67 -37.61 ... -34.03 -33.96 lon_rho (eta_rho, xi_rho) float32 224B 18.83 18.83 18.83 ... 18.83 18.83 depth (time, s_rho, eta_rho, xi_rho) float64 14kB -4.479e+03 ... -0.8528 Attributes: long_name: Ocean s roms coordinate at rho point Vtransform: 2 standard_name: ocean_layer_depth units: m .. GENERATED FROM PYTHON SOURCE LINES 82-89 Find coordinate names from CF conventions ----------------------------------------- The `depth` was assigned as coordinates at the previous stage. We use the :ref:`xoa ` accessor to easily access the temperature, latitude and depth arrays. The default configuration exposes shortcuts for some variables and coordinates as shown in :metasec:`accessors`. .. GENERATED FROM PYTHON SOURCE LINES 89-94 .. code-block:: Python temp = ds.xoa.temp.squeeze() temp = temp.where(temp != 0) # convert zeros to nans lat_name = temp.xoa.lat.name .. GENERATED FROM PYTHON SOURCE LINES 95-101 Interpolate at regular depths ----------------------------- We interpolate the temperature array from irregular to regular depths. Let's create the output depths. .. GENERATED FROM PYTHON SOURCE LINES 101-106 .. code-block:: Python depth = xr.DataArray( np.linspace(ds.depth.values.min(), ds.depth.values.max(), 1000), name="depth", dims="depth" ) .. GENERATED FROM PYTHON SOURCE LINES 107-108 Let's interpolate the temperature. .. GENERATED FROM PYTHON SOURCE LINES 108-111 .. code-block:: Python tempz = regrid1d(temp, depth, extrap="top") .. GENERATED FROM PYTHON SOURCE LINES 112-118 Compute the mixed layer depths ------------------------------- The mixed layer depths are computed here as the depth at which the temperature is `deltatemp` lower than the surface temperature, thanks to the :func:`xoa.thermdyn.mixed_layer_depth` function. .. GENERATED FROM PYTHON SOURCE LINES 118-123 .. code-block:: Python deltatemp = 0.2 mld = -mixed_layer_depth(temp, deltatemp=deltatemp) mldz = -mixed_layer_depth(temp, deltatemp=deltatemp) .. GENERATED FROM PYTHON SOURCE LINES 124-126 Plots ----- .. GENERATED FROM PYTHON SOURCE LINES 128-129 Plot the full section. .. GENERATED FROM PYTHON SOURCE LINES 129-139 .. code-block:: Python fig, axs = plt.subplots(ncols=2, sharex=True, sharey=True, figsize=(10, 4)) kw = dict(levels=np.arange(0, 23)) temp.plot.contourf(lat_name, "depth", cmap="cmo.thermal", ax=axs[0], **kw) temp.plot.contour(lat_name, "depth", colors='k', linewidths=0.3, ax=axs[0], **kw) tempz.plot.contourf(lat_name, "depth", cmap="cmo.thermal", ax=axs[1], **kw) tempz.plot.contour(lat_name, "depth", colors='k', linewidths=0.3, ax=axs[1], **kw) axs[0].set_title("Original") axs[1].set_title("Interpolated") .. image-sg:: /examples/images/sphx_glr_plot_croco_section_001.png :alt: Original, Interpolated :srcset: /examples/images/sphx_glr_plot_croco_section_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/checkouts/readthedocs.org/user_builds/xoa/conda/develop/lib/python3.14/site-packages/xarray/plot/accessor.py:663: FutureWarning: Using positional arguments is deprecated for plot methods, use keyword arguments instead. return dataarray_plot.contourf(self._da, *args, **kwargs) /home/docs/checkouts/readthedocs.org/user_builds/xoa/conda/develop/lib/python3.14/site-packages/xarray/plot/accessor.py:542: FutureWarning: Using positional arguments is deprecated for plot methods, use keyword arguments instead. return dataarray_plot.contour(self._da, *args, **kwargs) /home/docs/checkouts/readthedocs.org/user_builds/xoa/conda/develop/lib/python3.14/site-packages/xarray/plot/accessor.py:663: FutureWarning: Using positional arguments is deprecated for plot methods, use keyword arguments instead. return dataarray_plot.contourf(self._da, *args, **kwargs) /home/docs/checkouts/readthedocs.org/user_builds/xoa/conda/develop/lib/python3.14/site-packages/xarray/plot/accessor.py:542: FutureWarning: Using positional arguments is deprecated for plot methods, use keyword arguments instead. return dataarray_plot.contour(self._da, *args, **kwargs) Text(0.5, 1.0, 'Interpolated') .. GENERATED FROM PYTHON SOURCE LINES 140-141 Plot a zoom near the surface and add the mixed layer depth isoline. .. GENERATED FROM PYTHON SOURCE LINES 141-154 .. code-block:: Python fig, axs = plt.subplots(ncols=2, sharex=True, sharey=True, figsize=(10, 3)) kw = dict(levels=np.arange(0, 23)) temp.plot.contourf(lat_name, "depth", cmap="cmo.thermal", ax=axs[0], **kw) temp.plot.contour(lat_name, "depth", colors='k', linewidths=0.3, ax=axs[0], **kw) mld.plot.line(x=lat_name, color="k", linewidth=2, linestyle="--", ax=axs[0]) tempz.plot.contourf(lat_name, "depth", cmap="cmo.thermal", ax=axs[1], **kw) tempz.plot.contour(lat_name, "depth", colors='k', linewidths=0.3, ax=axs[1], **kw) mldz.plot.line(x=lat_name, color="k", linewidth=2, linestyle="--", ax=axs[1]) axs[0].set_ylim(-300, 0) axs[0].set_title("Original") axs[1].set_title("Interpolated") .. image-sg:: /examples/images/sphx_glr_plot_croco_section_002.png :alt: Original, Interpolated :srcset: /examples/images/sphx_glr_plot_croco_section_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Text(0.5, 1.0, 'Interpolated') .. GENERATED FROM PYTHON SOURCE LINES 155-156 Et voilà! .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 4.672 seconds) .. _sphx_glr_download_examples_plot_croco_section.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/shom-fr/xoa/master?urlpath=lab/tree/notebooks/examples/plot_croco_section.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_croco_section.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_croco_section.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_croco_section.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_