Merge branch 'main' into mean_clim_upgrade_lee1043_20240812

CITATION.cff

@@ -45,5 +45,5 @@ keywords:
   - climatology
   - climate variability
 license: BSD-3-Clause
-version: '3.8.1'
-date-released: '2025-01-06'
+version: '3.8.2'
+date-released: '2025-01-09'

README.md

@@ -121,6 +121,7 @@ Release Notes and History
 
 | <div style="width:300%">[Versions]</div> | Update summary   |
 | ------------- | ------------------------------------- |
+| [v3.8.2]      | Technical update
 | [v3.8.1]      | Technical update with new figure (modes of variability multi-panel plot)
 | [v3.8]        | New capability (**figure generation for ENSO**, xCDAT migration completed for **Monsoon Wang** with figure generation), major dependency update (`numpy` >= 2.0)
 | [v3.7.2]      | Technical update
@@ -173,6 +174,7 @@ Release Notes and History
 </details>
 
 [Versions]: https://github.com/PCMDI/pcmdi_metrics/releases
+[v3.8.2]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.8.2
 [v3.8.1]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.8.1
 [v3.8]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.8
 [v3.7.2]: https://github.com/PCMDI/pcmdi_metrics/releases/tag/v3.7.2

conda-env/ci.yml

@@ -19,7 +19,7 @@ dependencies:
     - cdp=1.7.0
     - eofs=2.0.0
     - seaborn=0.12.2
-    - enso_metrics=1.1.4
+    - enso_metrics=1.1.5
     - xcdat=0.7.3
     - xmltodict=0.13.0
     - setuptools=67.7.2

conda-env/dev.yml

@@ -19,7 +19,7 @@ dependencies:
     - cdp=1.7.0
     - eofs=2.0.0
     - seaborn=0.12.2
-    - enso_metrics=1.1.4
+    - enso_metrics=1.1.5
     - xcdat=0.7.3
     - xmltodict=0.13.0
     - setuptools=67.7.2

pcmdi_metrics/_version.py

@@ -1 +1 @@
-__version__ = "3.8.1"
+__version__ = "3.8.2"

pcmdi_metrics/io/xcdat_openxml.py

@@ -114,7 +114,7 @@ def fix_noncompliant_attr(ds: xr.Dataset) -> xr.Dataset:
 
 
 def _xcdat_openxml(
-    xmlfile: str, data_var: str = None, decode_times: bool = True
+    xmlfile: str, data_var: str = None, decode_times: bool = True, chunks=None
 ) -> xr.Dataset:
     """Open input file (xml generated by cdscan)
 
@@ -142,11 +142,11 @@ def _xcdat_openxml(
 
     if len(ncfile_list) > 1:
         ds = xc.open_mfdataset(
-            ncfile_list, data_var=data_var, decode_times=decode_times
+            ncfile_list, data_var=data_var, decode_times=decode_times, chunks=chunks
         )
     else:
         ds = xc.open_dataset(
-            ncfile_list[0], data_var=data_var, decode_times=decode_times
+            ncfile_list[0], data_var=data_var, decode_times=decode_times, chunks=chunks
         )
 
     return ds

pcmdi_metrics/mean_climate/lib/calculate_climatology.py

@@ -14,9 +14,6 @@
 from .plot_clim_maps import plot_climatology
 
 
-# import dask
-
-
 def calculate_climatology(
     var: str,
     infile: str,
@@ -279,20 +276,58 @@ def calculate_climatology(
             # Add annual or seasonal climatology to the dictionary
             ds_clim_dict[s] = ds_clim_s
 
+        if outfilename is not None:
+            out = os.path.join(outdir, outfilename)
+
+        out_season = out.replace(".nc", addf)
 
-        print("output file is", out_season)
         d_clim_dict[s].to_netcdf(
             out_season
         )  # global attributes are automatically saved as well
 
+        print("output file:", out_season)
+
+        # Plot climatology
         if plot and s == "AC":
-            plot_climatology(
-                d_ac,
-                var,
-                season_to_plot="all",
-                output_filename=out_season.replace(".nc", ".png"),
-            )
+            # Check if variable is 4D
+            if is_4d_variable(d_ac, var):
+                # Plot 3 levels (hPa) for 4D variables for quick check
+                levels_to_plot = [200, 500, 850]
+            else:
+                levels_to_plot = [None]
+
+            # Plot climatology for each level
+            for level in levels_to_plot:
+                output_fig_path = out_season.replace(".nc", ".png")
+                if level is not None:
+                    if var in output_fig_path:
+                        output_fig_path = os.path.join(
+                            outdir,
+                            output_fig_path.split("/")[-1].replace(
+                                var, f"{var}-{level}"
+                            ),
+                        )
+                    else:
+                        output_fig_path = output_fig_path.replace(
+                            ".png", f"-{level}.png"
+                        )
+
+                # plot climatology for each level
+                plot_climatology(
+                    d_ac,
+                    var,
+                    level=level,
+                    season_to_plot="all",
+                    output_filename=output_fig_path,
+                    period=f"{start_yr_str}-{end_yr_str}",
+                )
+
+                print("output figure:", output_fig_path)
 
     ds.close()
     return ds_clim_dict  # Return the dictionary of all climatology datasets
-
+
+def is_4d_variable(ds, data_var):
+    da = ds[data_var]
+    print("data_var, da.shape:", data_var, da.shape)
+    return len(da.shape) == 4

pcmdi_metrics/mean_climate/lib/plot_clim_maps.py

@@ -890,6 +890,12 @@ def _load_variable_setting(
                 "colormap": cc.cm.rainbow,
                 "colormap_diff": "jet",
             },
+            500: {
+                "levels": np.linspace(-45, 5, 21),
+                "levels_diff": None,
+                "colormap": cc.cm.rainbow,
+                "colormap_diff": "RdBu_r",
+            },
             850: {
                 "levels": np.arange(-35, 40, 5),
                 "levels_diff": [-15, -10, -5, -2, -1, -0.5, 0, 0.5, 1, 2, 5, 10, 15],
@@ -936,6 +942,12 @@ def _load_variable_setting(
                 "colormap": "PiYG_r",
                 "colormap_diff": "RdBu_r",
             },
+            500: {
+                "levels": np.arange(-40, 45, 5),
+                "levels_diff": np.linspace(-20, 20, 21),
+                "colormap": "PiYG_r",
+                "colormap_diff": "RdBu_r",
+            },
             850: {
                 "levels": [
                     -25,
@@ -967,6 +979,12 @@ def _load_variable_setting(
                 "colormap": "PiYG_r",
                 "colormap_diff": "RdBu_r",
             },
+            500: {
+                "levels": np.linspace(-10, 10, 11),
+                "levels_diff": np.linspace(-5, 5, 6),
+                "colormap": "PiYG_r",
+                "colormap_diff": "RdBu_r",
+            },
             850: {
                 "levels": np.linspace(-10, 10, 11),
                 "levels_diff": np.linspace(-5, 5, 6),
@@ -984,30 +1002,39 @@ def _load_variable_setting(
         },
     }
 
-    # Check if the variable and level exist in the settings
-
-    in_dict = False
+    # Initialize
+    levels = None
+    levels_diff = None
+    cmap = None
+    cmap_diff = None
+    cmap_ext = None
+    cmap_ext_diff = None
 
+    # Check if the variable and level exist in the settings
     if data_var in var_setting_dict:
         if level in var_setting_dict[data_var]:
             settings = var_setting_dict[data_var][level]
-            levels = settings["levels"]
-            levels_diff = settings["levels_diff"]
-            cmap = _get_colormap(settings["colormap"])
-            cmap_diff = _get_colormap(settings["colormap_diff"])
+            levels = settings.get("levels", None)
+            levels_diff = settings.get("levels_diff", None)
+            cmap = _get_colormap(settings.get("colormap", None))
+            cmap_diff = _get_colormap(settings.get("colormap_diff", None))
             cmap_ext = settings.get("colormap_ext", "both")
             cmap_ext_diff = "both"
-            in_dict = True
 
     # Use default settings if not found
-    if not in_dict:
-        vmin = float(ds[data_var].min())
-        vmax = float(ds[data_var].max())
+    vmin = float(ds[data_var].min())
+    vmax = float(ds[data_var].max())
+    if levels is None:
         levels = np.linspace(vmin, vmax, 21)
+    if levels_diff is None:
         levels_diff = np.linspace(vmin / 2.0, vmax / 2.0, 21)
+    if cmap is None:
         cmap = plt.get_cmap("jet")
+    if cmap_diff is None:
         cmap_diff = plt.get_cmap("RdBu_r")
+    if cmap_ext is None:
         cmap_ext = "both"
+    if cmap_ext_diff is None:
         cmap_ext_diff = "both"
 
     if diff: