Merge pull request #638 from MetOffice/637_lfric_extension_to_vertica…

…l_profile

LFRic extension to vertical profile

README.md

@@ -51,3 +51,5 @@ Unless required by applicable law or agreed to in writing, software distributed
 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
 CONDITIONS OF ANY KIND, either express or implied. See the License for the
 specific language governing permissions and limitations under the License.
+
+GitHub Copilot was used in the development of this software.

cset-workflow/extra-meta/colorbar_dict_alphabetical.json

@@ -166,5 +166,10 @@
     "wind_speed_at_10m": {
         "min": 0.0,
         "max": 30.0
+    },
+    "air_potential_temperature": {
+        "min": 230,
+        "max": 340,
+        "cmap": "jet"
     }
 }

cset-workflow/includes/lfric_deterministic_domain_mean_vertical_profile_series.cylc

@@ -1,16 +1,16 @@
 {% if LFRIC_DOMAIN_MEAN_VERTICAL_PROFILE_SERIES %}
 [runtime]
-{% for model_field in LFRIC_PRESSURE_LEVEL_MODEL_FIELDS %}
+{% for model_field in LFRIC_MODEL_LEVEL_MODEL_FIELDS %}
     [[pre_process_lfric_domain_mean_vertical_profile_series_{{model_field}}]]
     inherit = PARALLEL
         [[[environment]]]
         CSET_RECIPE_NAME = "lfric_generic_domain_mean_vertical_profile_series.yaml"
-        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --PLEVEL='{{LFRIC_PRESSURE_LEVELS}}'"
+        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --MLEVEL='{{LFRIC_MODEL_LEVELS}}'"
 
     [[collate_lfric_domain_mean_vertical_profile_series_{{model_field}}]]
     inherit = COLLATE
         [[[environment]]]
         CSET_RECIPE_NAME = "lfric_generic_domain_mean_vertical_profile_series.yaml"
-        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --PLEVEL='{{LFRIC_PRESSURE_LEVELS}}}'"
+        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --MLEVEL='{{LFRIC_MODEL_LEVELS}}'"
 {% endfor %}
 {% endif %}

cset-workflow/includes/lfric_plot_spatial_mlevel_model_field.cylc

@@ -0,0 +1,18 @@
+{% if LFRIC_PLOT_SPATIAL_MODEL_LEVEL_MODEL_FIELD %}
+[runtime]
+{% for model_field in LFRIC_MODEL_LEVEL_MODEL_FIELDS %}
+{% for mlevel in LFRIC_MODEL_LEVELS %}
+    [[process_lfric_generic_mlevel_spatial_plot_sequence_{{model_field}}_{{mlevel}}]]
+    inherit = PARALLEL
+        [[[environment]]]
+        CSET_RECIPE_NAME = "lfric_generic_mlevel_spatial_plot_sequence.yaml"
+        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --MLEVEL='{{mlevel}}'"
+
+    [[collate_lfric_generic_mlevel_spatial_plot_sequence_{{model_field}}_{{mlevel}}]]
+    inherit = COLLATE
+        [[[environment]]]
+        CSET_RECIPE_NAME = "lfric_generic_mlevel_spatial_plot_sequence.yaml"
+        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --MLEVEL='{{mlevel}}'"
+{% endfor %}
+{% endfor %}
+{% endif %}

cset-workflow/includes/lfric_plot_spatial_plevel_model_field.cylc

@@ -0,0 +1,18 @@
+{% if LFRIC_PLOT_SPATIAL_PRESSURE_LEVEL_MODEL_FIELD %}
+[runtime]
+{% for model_field in LFRIC_PRESSURE_LEVEL_MODEL_FIELDS %}
+{% for plevel in LFRIC_PRESSURE_LEVELS %}
+    [[process_lfric_generic_plevel_spatial_plot_sequence_{{model_field}}_{{plevel}}]]
+    inherit = PARALLEL
+        [[[environment]]]
+        CSET_RECIPE_NAME = "lfric_generic_plevel_spatial_plot_sequence.yaml"
+        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --PLEVEL='{{plevel}}'"
+
+    [[collate_lfric_generic_plevel_spatial_plot_sequence_{{model_field}}_{{plevel}}]]
+    inherit = COLLATE
+        [[[environment]]]
+        CSET_RECIPE_NAME = "lfric_generic_plevel_spatial_plot_sequence.yaml"
+        CSET_ADDOPTS = "--VARNAME='{{model_field}}' --PLEVEL='{{plevel}}'"
+{% endfor %}
+{% endfor %}
+{% endif %}

cset-workflow/meta/rose-meta.conf

@@ -472,13 +472,21 @@ trigger=template variables=LFRIC_PRESSURE_LEVEL_MODEL_FIELDS: True;
 compulsory=true
 sort-key=pressure3
 
+[template variables=LFRIC_PLOT_SPATIAL_MODEL_LEVEL_MODEL_FIELD]
+ns=Diagnostics
+description=Create plots for the specified model level fields.
+help=See includes/lfric_plot_spatial_mlevel_model_field.cylc
+type=python_boolean
+compulsory=true
+sort-key=model1
+
 [template variables=LFRIC_DOMAIN_MEAN_VERTICAL_PROFILE_SERIES]
 ns=Diagnostics
 description=Domain averaged vertical profile for each validity time.
-help=See includes/lfric_deterministic_domain_mean_vertical_profile_series.cylc
+help=See includes/lfric_deterministic_domain_mean_vertical_profile_series.cylc. Currently vertical profiles for LFRic only work with LFRIC_MODEL_LEVELS as we currently don't have LFRIC data with a pressure or height coordinate.
 type=python_boolean
 compulsory=true
-sort-key=pressure3
+sort-key=model1
 
 [template variables=LFRIC_PRESSURE_LEVEL_MODEL_FIELDS]
 ns=Diagnostics
@@ -488,6 +496,14 @@ type=python_list
 compulsory=true
 sort-key=pressure3
 
+[template variables=LFRIC_MODEL_LEVEL_MODEL_FIELDS]
+ns=Diagnostics
+description=List of standard names of model fields on model levels to plot.
+help=Include a list of variable names in python list format["var1","var2"].
+type=python_list
+compulsory=true
+sort-key=model1
+
 [template variables=LFRIC_PRESSURE_LEVELS]
 ns=Diagnostics
 description=List of pressure levels to generate plots for.
@@ -496,6 +512,14 @@ type=python_list
 compulsory=true
 sort-key=pressure3
 
+[template variables=LFRIC_MODEL_LEVELS]
+ns=Diagnostics
+description=List of model level numbers to generate plots for.
+help=Include an integer or list of integers of model level numbers in python list format [1,2,3,4,5].
+type=python_list
+compulsory=true
+sort-key=model1
+
 
 [template variables=PLOT_SPATIAL_PRESSURE_LEVEL_MODEL_FIELD]
 ns=Diagnostics

docs/source/changelog.rst

@@ -15,7 +15,13 @@ Unreleased
 .. Highlight any user facing changes. E.g:
 .. "* `@gh-user`_ did foo to bar in :pr:`9999`. This enables baz."
 
-* `@Sylviabohnenstengel`_ documentation: add info on quick pytesting in :pr: `696`
+* `@Sylviabohnenstengel`_ documentation: add info on quick pytesting in :pr:`696`
+* `@Sylviabohnenstengel`_ add constraint operator for lfric full_levels and half_levels
+* `@Sylviabohnenstengel`_ introduced lfric_model_level and lfric_model_level_field to rose meta
+* `@Sylviabohnenstengel`_ expand plot operator add plotting lfric vertical profiles on model levels
+* `@Sylviabohnenstengel`_ expand plot operator add plotting on model levels to spatial plot operator
+* `@Sylviabohnenstengel`_ added new recipe for plotting vertical profiles on model levels for lfric.
+* `@Sylviabohnenstengel`_ added new recipe for plotting spatial lfric data on model levels.
 
 24.6.0 (2024-06-17)
 -------------------

src/CSET/operators/constraints.py

@@ -14,8 +14,8 @@
 
 """Operators to generate constraints to filter with."""
 
+from collections.abc import Iterable
 from datetime import datetime
-from typing import Union
 
 import iris
 import iris.cube
@@ -64,67 +64,45 @@ def generate_var_constraint(varname: str, **kwargs) -> iris.Constraint:
     return varname_constraint
 
 
-def generate_model_level_constraint(
-    model_level_number: Union[int, str], **kwargs
+def generate_level_constraint(
+    coordinate: str, levels: int | list[int], **kwargs
 ) -> iris.Constraint:
-    """Generate constraint for a particular model level number.
+    """Generate constraint for particular levels on the specified coordinate.
 
-    Operator that takes a CF compliant model_level_number string, and uses iris to
-    generate a constraint to be passed into the read operator to minimize the
-    CubeList the read operator loads and speed up loading.
+    Operator that generates a constraint to constrain to specific model or
+    pressure levels. If no levels are specified then any cube with the specified
+    coordinate is rejected.
+
+    Typically ``coordinate`` will be ``"pressure"`` or ``"model_level_number"``
+    for UM, or ``"full_levels"`` or ``"half_levels"`` for LFRic.
 
     Arguments
     ---------
-    model_level_number: str
-        CF compliant model level number.
+    coordinate: str
+        Level coordinate name about which to constraint.
+    levels: int | list[int]
+        CF compliant levels.
 
     Returns
     -------
-    model_level_number_constraint: iris.Constraint
+    constraint: iris.Constraint
     """
-    # Cast to int in case a string is given.
-    model_level_number = int(model_level_number)
-    model_level_number_constraint = iris.Constraint(
-        model_level_number=model_level_number
-    )
-    return model_level_number_constraint
-
-
-def generate_pressure_level_constraint(
-    pressure_levels: Union[int, list[int]], **kwargs
-) -> iris.Constraint:
-    """Generate constraint for the specified pressure_levels.
+    # Ensure is iterable.
+    if not isinstance(levels, Iterable):
+        levels = [levels]
 
-    If no pressure levels are specified then any cube with a pressure coordinate
-    is rejected.
+    # When no levels specified reject cube with level coordinate.
+    if len(levels) == 0:
 
-    Arguments
-    ---------
-    pressure_levels: int|list
-        List of integer pressure levels in hPa either as single integer
-        for a single level or a list of multiple integers.
+        def no_levels(cube):
+            # Reject cubes for which coordinate exists.
+            return not bool(cube.coords(coordinate))
 
-    Returns
-    -------
-    pressure_constraint: iris.Constraint
-    """
-    # If pressure_level is an integer it is converted into a list.
-    if isinstance(pressure_levels, int):
-        pressure_levels = [pressure_levels]
-    if len(pressure_levels) == 0:
-        # If none specified reject cubes with pressure level coordinate.
-        def no_pressure_coordinate(cube):
-            try:
-                cube.coord("pressure")
-            except iris.exceptions.CoordinateNotFoundError:
-                return True
-            return False
-
-        pressure_constraint = iris.Constraint(cube_func=no_pressure_coordinate)
-    else:
-        pressure_constraint = iris.Constraint(pressure=pressure_levels)
+        return iris.Constraint(cube_func=no_levels)
 
-    return pressure_constraint
+    # Filter the coordinate to the desired levels.
+    # Dictionary unpacking is used to provide programmatic keyword arguments.
+    return iris.Constraint(**{coordinate: levels})
 
 
 def generate_cell_methods_constraint(cell_methods: list, **kwargs) -> iris.Constraint:

src/CSET/operators/plot.py

@@ -334,6 +334,7 @@ def _plot_and_save_vertical_line_series(
     cube: iris.cube.Cube,
     coord: iris.coords.Coord,
     filename: str,
+    series_coordinate: str,
     title: str,
     vmin: float,
     vmax: float,
@@ -349,6 +350,8 @@ def _plot_and_save_vertical_line_series(
         Coordinate to plot on y-axis.
     filename: str
         Filename of the plot to write.
+    series_coordinate: str
+        Coordinate to use as vertical axis.
     title: str
         Plot title.
     vmin: float
@@ -360,27 +363,40 @@ def _plot_and_save_vertical_line_series(
     fig = plt.figure(figsize=(8, 8), facecolor="w", edgecolor="k")
     iplt.plot(cube, coord, "o-")
     ax = plt.gca()
-    ax.invert_yaxis()
-    ax.set_yscale("log")
-
-    # Define y-ticks and labels for pressure log axis
-    y_tick_labels = [
-        "1000",
-        "850",
-        "700",
-        "500",
-        "300",
-        "200",
-        "100",
-        "50",
-        "30",
-        "20",
-        "10",
-    ]
-    y_ticks = [1000, 850, 700, 500, 300, 200, 100, 50, 30, 20, 10]
-
-    # Set y-axis limits and ticks
-    ax.set_ylim(1100, 100)
+
+    # Special handling for pressure level data.
+    if series_coordinate == "pressure":
+        # Invert y-axis and set to log scale.
+        ax.invert_yaxis()
+        ax.set_yscale("log")
+
+        # Define y-ticks and labels for pressure log axis.
+        y_tick_labels = [
+            "1000",
+            "850",
+            "700",
+            "500",
+            "300",
+            "200",
+            "100",
+            "50",
+            "30",
+            "20",
+            "10",
+        ]
+        y_ticks = [1000, 850, 700, 500, 300, 200, 100, 50, 30, 20, 10]
+
+        # Set y-axis limits and ticks.
+        ax.set_ylim(1100, 100)
+
+    # test if series_coordinate is model level data. The um data uses model_level_number
+    # and lfric uses full_levels as coordinate.
+    elif series_coordinate in ("model_level_number", "full_levels", "half_levels"):
+        # Define y-ticks and labels for vertical axis.
+        y_ticks = cube.coord(series_coordinate).points
+        y_tick_labels = [str(int(i)) for i in y_ticks]
+        ax.set_ylim(min(y_ticks), max(y_ticks))
+
     ax.set_yticks(y_ticks)
     ax.set_yticklabels(y_tick_labels)
 
@@ -566,7 +582,7 @@ def plot_line_series(
 def plot_vertical_line_series(
     cube: iris.cube.Cube,
     filename: str = None,
-    series_coordinate: str = "pressure",
+    series_coordinate: str = "model_level_number",
     sequence_coordinate: str = "time",
     # line_coordinate: str = "realization",
     **kwargs,
@@ -586,7 +602,9 @@ def plot_vertical_line_series(
         Name of the plot to write, used as a prefix for plot sequences. Defaults
         to the recipe name.
     series_coordinate: str, optional
-        Coordinate to plot on the y-axis. Defaults to ``pressure``.
+        Coordinate to plot on the y-axis. Can be ``pressure`` or
+        ``model_level_number`` for UM, or ``full_levels`` or ``half_levels``
+        for LFRic. Defaults to ``model_level_number``.
         This coordinate must exist in the cube.
     sequence_coordinate: str, optional
         Coordinate about which to make a plot sequence. Defaults to ``"time"``.
@@ -650,6 +668,7 @@ def plot_vertical_line_series(
             cube_slice,
             coord,
             plot_filename,
+            series_coordinate,
             title=title,
             vmin=vmin,
             vmax=vmax,

src/CSET/operators/read.py

@@ -75,6 +75,7 @@ def read_cube(
         If the constraint doesn't produce a single cube.
     """
     cubes = read_cubes(loadpath, constraint, filename_pattern)
+    # TODO: Fix coordinate name to enable full level and half level merging.
     # Check filtered cubes is a CubeList containing one cube.
     if len(cubes) == 1:
         return cubes[0]

src/CSET/recipes/generic_domain_mean_vertical_profile_series.yaml

@@ -11,8 +11,9 @@ parallel:
         operator: constraints.generate_var_constraint
         varname: $VARNAME
       pressure_level_constraint:
-        operator: constraints.generate_pressure_level_constraint
-        pressure_levels: $PLEVEL
+        operator: constraints.generate_level_constraint
+        coordinate: "pressure"
+        levels: $PLEVEL
       validity_time_constraint:
         operator: constraints.generate_time_constraint
         time_start: $VALIDITY_TIME

src/CSET/recipes/generic_plevel_spatial_plot_sequence.yaml

@@ -14,8 +14,9 @@ parallel:
         operator: constraints.generate_time_constraint
         time_start: $VALIDITY_TIME
       pressure_level_constraint:
-        operator: constraints.generate_pressure_level_constraint
-        pressure_levels: $PLEVEL
+        operator: constraints.generate_level_constraint
+        coordinate: "pressure"
+        levels: $PLEVEL
 
   - operator: write.write_cube_to_nc
 

src/CSET/recipes/generic_surface_domain_mean_time_series.yaml

@@ -14,8 +14,9 @@ parallel:
         operator: constraints.generate_cell_methods_constraint
         cell_methods: []
       pressure_level_constraint:
-        operator: constraints.generate_pressure_level_constraint
-        pressure_levels: []
+        operator: constraints.generate_level_constraint
+        coordinate: "pressure"
+        levels: []
       validity_time_constraint:
         operator: constraints.generate_time_constraint
         time_start: $VALIDITY_TIME