Add Southern Ocean diagnostic and recipe

esmvaltool/config-references.yml

@@ -728,6 +728,10 @@ authors:
     name: Sullivan, Arnold
     institute: CSIRO, Australia
     orcid: https://orcid.org/0000-0002-5712-6195
+  wilder_thomas:
+    name: Wilder, Thomas
+    institute: NCAS, UK
+    orcid:
   wyser_klaus:
     name: Wyser, Klaus
     institute: SMHI, Sweden

esmvaltool/diag_scripts/southern_ocean/diagnostic_acc_sigma_tr.py

@@ -0,0 +1,197 @@
+"""
+Look at this module for guidance how to write your own.
+
+Read the README_PERSONAL_DIAGNOSTIC file associated with this example;
+
+Module for personal diagnostics (example).
+Internal imports from exmvaltool work e.g.:
+
+from esmvalcore.preprocessor import regrid
+from esmvaltool.diag_scripts.shared.supermeans import get_supermean
+
+Pipe output through logger;
+
+Please consult the documentation for help with esmvaltool's functionalities
+and best coding practices.
+"""
+# place your module imports here:
+import gsw
+import xarray as xr
+import numpy as np
+
+# import cmocean
+
+import logging
+
+# operating system manipulations (e.g. path constructions)
+import os
+import sys
+from pathlib import Path
+
+# to manipulate iris cubes
+# import iris
+import matplotlib.pyplot as plt
+from esmvalcore.preprocessor import area_statistics
+
+# import internal esmvaltool modules here
+from esmvaltool.diag_scripts.shared import group_metadata, run_diagnostic, ProvenanceLogger, save_figure
+
+# reuse tools already developed for ocean diagnostics
+from esmvaltool.diag_scripts.ocean import diagnostic_tools as diagtools
+
+# This part sends debug statements to stdout
+# logger = logging.getLogger(os.path.basename(__file__))
+# logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
+
+# This outputs to the run/transect/script1/log.txt file
+logger = logging.getLogger(Path(__file__).stem)
+
+# module checks
+logger.info("GSW version: %s", gsw.__version__)
+
+##### helper functions for the diagnostic go here #####
+
+
+##### key functions for the diagnostic go here #####
+
+def _get_data(cfg):
+
+    '''
+        Get the data from the input files specified in the recipe.
+        Open the files and return a dictionary of xarray datasets.
+    '''
+
+    #TODO needs adjusting for multi dataset recipes
+
+    input_data = cfg["input_data"]
+
+    ds = {}
+    for filename, attributes in input_data.items():
+        logger.info("Loading %s", filename)
+        variable_name = attributes["short_name"]
+        ds[variable_name] = xr.open_dataset(filename)
+
+    return ds
+
+def _compute_sigma(ds):
+    ''' 
+        Compute the sigma2 variable from the input dataset.
+        Uses gsw.density.sigma2 from the gsw toolbox 
+            https://teos-10.github.io/GSW-Python/_modules/gsw/_wrapped_ufuncs.html#sigma2
+    '''
+
+    # logger.info("Numpy so is: %s", ds["so"]["so"].to_numpy())
+    # logger.info("Numpy thetao is: %s", ds["thetao"]["thetao"].to_numpy())
+
+    # pull the data and coords as numpy arrays
+    so = ds["so"]["so"].to_numpy()              # (lev, lat)
+    thetao = ds["thetao"]["thetao"].to_numpy()  # (lev, lat)
+    depth = ds["so"]["lev"].to_numpy()          # (lev,)
+    lat = ds["so"]["lat"].to_numpy()            # (lat,)
+    lon = float(ds["so"]["lon"])                # scalar transect longitude
+
+    # broadcast depth and lat onto the full (lev, lat) transect grid so all
+    # operands match the 2D salinity/temperature fields (gsw broadcasts
+    # every argument together element-wise).
+    depth2d, lat2d = np.meshgrid(depth, lat, indexing="ij")  # both (lev, lat)
+
+    # calculate pressure from depth (latitude-dependent)
+    p = gsw.p_from_z(-depth2d, lat2d)
+    logger.info("Pressure shape: %s", p.shape)
+
+    # TEOS-10 chain: SA (absolute salinity) -> CT (conservative temp) -> sigma2.
+    # calculate absolute salinity from practical salinity
+    SA = gsw.SA_from_SP(so, p, lon, lat2d)
+    logger.info("Absolute salinity shape: %s", SA.shape)
+
+    # calculate conservative temperature from potential temperature
+    CT = gsw.CT_from_pt(SA, thetao)
+    logger.info("Conservative temperature shape: %s", CT.shape)
+
+    # compute sigma2
+    sigma2 = gsw.sigma2(SA, CT)
+
+    # create a new xarray dataset with the same coordinates as the input datasets
+    sigma2_ds = xr.Dataset(
+        {
+            "sigma2": (["lev", "lat"], sigma2)
+        },
+        coords={
+            "time": ds["so"]["time"],
+            "lev": ds["so"]["lev"],
+            "lat": ds["so"]["lat"],
+            "lon": ds["so"]["lon"]
+        },
+        attrs={
+            "short_name": "sigma2",
+            "long_name": "Potential density anomaly referenced to 2000 dbar",
+            "units": "kg/m^3",
+        }
+    )
+
+    return sigma2_ds
+
+def _plot_transect(ds, sigma, cfg):
+    '''
+        Plot the transect of zonal velocity with sigma2 contours overlaid.
+
+        Pass in the ds input like ds["uo"]
+    '''
+
+    # extract data arrays
+    sigma2 = sigma["sigma2"]
+    uo = ds["uo"]
+
+    # create the figure and axis
+    fig, ax = plt.subplots(figsize=(10, 6))
+
+    # produces the grey background for bathymetry
+    ax.set_facecolor("grey")
+
+    uo.plot.contourf(ax=ax, x="lat", y="lev", 
+                     yincrease=False, 
+                     cmap="RdBu_r")
+
+    ct = sigma2.plot.contour(ax=ax, x="lat", y="lev",
+                        yincrease=False,
+                        colors="k",
+                        levels=np.arange(35.5,37.5,0.25))
+
+    plt.clabel(ct, fontsize=10, inline=True)
+
+    ax.set_ylim(4250, -10)
+    ax.set_xlabel("Latitude [degrees_north]")
+    ax.set_ylabel("Depth [m]")
+    ax.set_title("Drake Passage Zonal Velocity Transect with Sigma2 Contours")
+
+    provenance = {
+        "caption": "Zonal velocity transect across Drake Passage with sigma2 contours.",
+        "statistics": ["mean"],
+        "domains": ["drake_passage_transect"],
+        "plot_types": ["contourf", "contour"],
+        "authors": ["wilder_thomas"],
+        "ancestors": list(cfg["input_data"].keys()),
+    }
+
+    # save the figure
+    save_figure("drakepassage_sigma2_transect", provenance, cfg)
+
+
+def main(cfg):
+    # get the data
+    datasets = _get_data(cfg)
+
+    logger.info("Datasets: %s", datasets)
+
+    sigma2_ds = _compute_sigma(datasets)
+
+    logger.info("Sigma2 dataset: %s", sigma2_ds)
+
+
+    _plot_transect(datasets["uo"], sigma2_ds, cfg)
+
+
+
+if __name__ == "__main__":
+    with run_diagnostic() as config:
+        main(config)

esmvaltool/recipes/recipe_so_drakepassage.yml

@@ -0,0 +1,70 @@
+# ESMValTool
+# recipe_so_acc_sigma_tr.yml
+---
+documentation:
+  description:
+    Creates a transect through Drake Passage of zonal velocity with
+    sigma contours overlaid.
+  title:
+    Drake Passage zonal velocity transect with sigma contour
+
+  authors:
+    - wilder_thomas
+
+datasets:
+  - dataset: HadGEM3-GC31-LL
+
+preprocessors:
+  # ------------------------------------------------------------------------
+  # Preprocessor settings for Drake Passage transect
+  # ------------------------------------------------------------------------
+  drakepassage_transect: # does this order matter? No.
+    climate_statistics:
+      operator: 'mean'
+      period: 'full'
+    regrid:
+      target_grid: 1x1
+      scheme: area_weighted
+    extract_transect: # probably needs changing
+      longitude: 293.0
+      latitude: [-65., -54.]
+
+diagnostics:
+  # ------------------------------------------------------------------------
+  # Drake Passage zonal velocity transect with sigma contour
+  # --------------------------------------------------------------------------------
+  transect:
+    description:  Transect of zonal velocity and sigma
+    themes:
+      - phys
+    realms:
+      - ocean
+    variables:
+      thetao: # Temperature ocean
+        ensemble: r1i1p1f3
+        exp: historical
+        grid: gn
+        mip: Omon
+        project: CMIP6
+        timerange: 2000/2001
+        preprocessor: drakepassage_transect
+      so:    # Salinity ocean
+        ensemble: r1i1p1f3
+        exp: historical
+        grid: gn
+        mip: Omon
+        project: CMIP6
+        timerange: 2000/2001
+        preprocessor: drakepassage_transect
+      uo:   # Zonal velocity ocean
+        ensemble: r1i1p1f3
+        exp: historical
+        grid: gn
+        mip: Omon
+        project: CMIP6
+        timerange: 2000/2001
+        preprocessor: drakepassage_transect
+
+    scripts:
+      script1:
+        script: southern_ocean/diagnostic_acc_sigma_tr.py