climate-ref-esmvaltool 0.6.5__py3-none-any.whl → 0.6.6__py3-none-any.whl

climate_ref_esmvaltool/diagnostics/regional_historical_changes.py

@@ -0,0 +1,340 @@
+import copy
+from pathlib import Path
+
+import numpy as np
+import pandas
+import xarray
+
+from climate_ref_core.constraints import (
+    AddSupplementaryDataset,
+    RequireContiguousTimerange,
+    RequireFacets,
+)
+from climate_ref_core.datasets import ExecutionDatasetCollection, FacetFilter, SourceDatasetType
+from climate_ref_core.diagnostics import DataRequirement
+from climate_ref_core.metric_values.typing import SeriesDefinition
+from climate_ref_core.pycmec.metric import CMECMetric, MetricCV
+from climate_ref_core.pycmec.output import CMECOutput
+from climate_ref_esmvaltool.diagnostics.base import ESMValToolDiagnostic
+from climate_ref_esmvaltool.recipe import dataframe_to_recipe
+from climate_ref_esmvaltool.types import MetricBundleArgs, OutputBundleArgs, Recipe
+
+REGIONS = (
+    "Arabian-Peninsula",
+    "Arabian-Sea",
+    "Arctic-Ocean",
+    "Bay-of-Bengal",
+    "C.Australia",
+    "C.North-America",
+    "Caribbean",
+    "Central-Africa",
+    "E.Antarctica",
+    "E.Asia",
+    "E.Australia",
+    "E.C.Asia",
+    "E.Europe",
+    "E.North-America",
+    "E.Siberia",
+    "E.Southern-Africa",
+    "Equatorial.Atlantic-Ocean",
+    "Equatorial.Indic-Ocean",
+    "Equatorial.Pacific-Ocean",
+    "Greenland/Iceland",
+    "Madagascar",
+    "Mediterranean",
+    "N.Atlantic-Ocean",
+    "N.Australia",
+    "N.Central-America",
+    "N.E.North-America",
+    "N.E.South-America",
+    "N.Eastern-Africa",
+    "N.Europe",
+    "N.Pacific-Ocean",
+    "N.South-America",
+    "N.W.North-America",
+    "N.W.South-America",
+    "New-Zealand",
+    "Russian-Arctic",
+    "Russian-Far-East",
+    "S.Asia",
+    "S.Atlantic-Ocean",
+    "S.Australia",
+    "S.Central-America",
+    "S.E.Asia",
+    "S.E.South-America",
+    "S.Eastern-Africa",
+    "S.Indic-Ocean",
+    "S.Pacific-Ocean",
+    "S.South-America",
+    "S.W.South-America",
+    "Sahara",
+    "South-American-Monsoon",
+    "Southern-Ocean",
+    "Tibetan-Plateau",
+    "W.Antarctica",
+    "W.C.Asia",
+    "W.North-America",
+    "W.Siberia",
+    "W.Southern-Africa",
+    "West&Central-Europe",
+    "Western-Africa",
+)
+
+
+def normalize_region(region: str) -> str:
+    """Normalize region name so it can be used in filenames."""
+    return region.replace("&", "-and-").replace("/", "-and-")
+
+
+class RegionalHistoricalAnnualCycle(ESMValToolDiagnostic):
+    """
+    Plot regional historical annual cycle of climate variables.
+    """
+
+    name = "Regional historical annual cycle of climate variables"
+    slug = "regional-historical-annual-cycle"
+    base_recipe = "ref/recipe_ref_annual_cycle_region.yml"
+
+    variables = (
+        "hus",
+        "pr",
+        "psl",
+        "tas",
+        "ua",
+    )
+    series = tuple(
+        SeriesDefinition(
+            file_pattern=f"anncyc-{region}/allplots/*_{var_name}_*.nc",
+            sel={"dim0": 0},  # Select the model and not the observation.
+            dimensions={"region": region},
+            values_name=var_name,
+            index_name="month_number",
+            attributes=[],
+        )
+        for var_name in variables
+        for region in REGIONS
+    )
+
+    data_requirements = (
+        DataRequirement(
+            source_type=SourceDatasetType.CMIP6,
+            filters=(
+                FacetFilter(
+                    facets={
+                        "variable_id": variables,
+                        "experiment_id": "historical",
+                        "frequency": "mon",
+                    },
+                ),
+            ),
+            group_by=("source_id", "member_id", "grid_label"),
+            constraints=(
+                RequireFacets("variable_id", variables),
+                RequireContiguousTimerange(group_by=("instance_id",)),
+                AddSupplementaryDataset.from_defaults("areacella", SourceDatasetType.CMIP6),
+            ),
+        ),
+        DataRequirement(
+            source_type=SourceDatasetType.obs4MIPs,
+            filters=(
+                FacetFilter(
+                    facets={
+                        "variable_id": (
+                            "psl",
+                            "ua",
+                        ),
+                        "source_id": "ERA-5",
+                        "frequency": "mon",
+                    },
+                ),
+            ),
+            group_by=("source_id",),
+            constraints=(RequireContiguousTimerange(group_by=("instance_id",)),),
+            # TODO: Add obs4MIPs datasets once available and working:
+            #
+            # obs4MIPs dataset that cannot be ingested (https://github.com/Climate-REF/climate-ref/issues/260):
+            # - GPCP-V2.3: pr
+            #
+            # Not yet available on obs4MIPs:
+            # - ERA5: hus
+            # - HadCRUT5_ground_5.0.1.0-analysis: tas
+        ),
+    )
+    facets = ()
+
+    @staticmethod
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
+        """Update the recipe."""
+        # Update the dataset.
+        recipe_variables = dataframe_to_recipe(input_files[SourceDatasetType.CMIP6])
+        dataset = recipe_variables["hus"]["additional_datasets"][0]
+        dataset.pop("timerange")
+        dataset["benchmark_dataset"] = True
+        dataset["plot_label"] = "{dataset}.{ensemble}.{grid}".format(**dataset)
+        recipe["datasets"] = [dataset]
+
+        # Generate diagnostics for each region.
+        diagnostics = {}
+        for region in REGIONS:
+            for diagnostic_name, orig_diagnostic in recipe["diagnostics"].items():
+                # Create the diagnostic for the region.
+                diagnostic = copy.deepcopy(orig_diagnostic)
+                normalized_region = normalize_region(region)
+                diagnostics[f"{diagnostic_name}-{normalized_region}"] = diagnostic
+
+                for variable in diagnostic["variables"].values():
+                    # Remove unwanted facets that are part of the dataset.
+                    for facet in ("project", "exp", "ensemble", "grid"):
+                        variable.pop(facet, None)
+                    # Update the preprocessor so it extracts the region.
+                    preprocessor_name = variable["preprocessor"]
+                    preprocessor = copy.deepcopy(recipe["preprocessors"][preprocessor_name])
+                    preprocessor["extract_shape"]["ids"] = {"Name": [region]}
+                    variable["preprocessor"] = f"{preprocessor_name}-{normalized_region}"
+                    recipe["preprocessors"][variable["preprocessor"]] = preprocessor
+
+                # Update plot titles with region name.
+                for script in diagnostic["scripts"].values():
+                    for plot in script["plots"].values():
+                        plot["pyplot_kwargs"] = {"title": f"{{long_name}} {region}"}
+        recipe["diagnostics"] = diagnostics
+
+
+class RegionalHistoricalTimeSeries(RegionalHistoricalAnnualCycle):
+    """
+    Plot regional historical mean and anomaly of climate variables.
+    """
+
+    name = "Regional historical mean and anomaly of climate variables"
+    slug = "regional-historical-timeseries"
+    base_recipe = "ref/recipe_ref_timeseries_region.yml"
+    series = tuple(
+        SeriesDefinition(
+            file_pattern=f"{diagnostic}-{region}/allplots/*_{var_name}_*.nc",
+            sel={"dim0": 0},  # Select the model and not the observation.
+            dimensions={"region": region},
+            values_name=var_name,
+            index_name="time",
+            attributes=[],
+        )
+        for var_name in RegionalHistoricalAnnualCycle.variables
+        for region in REGIONS
+        for diagnostic in ["timeseries_abs", "timeseries"]
+    )
+
+
+class RegionalHistoricalTrend(ESMValToolDiagnostic):
+    """
+    Plot regional historical trend of climate variables.
+    """
+
+    name = "Regional historical trend of climate variables"
+    slug = "regional-historical-trend"
+    base_recipe = "ref/recipe_ref_trend_regions.yml"
+
+    data_requirements = (
+        DataRequirement(
+            source_type=SourceDatasetType.CMIP6,
+            filters=(
+                FacetFilter(
+                    facets={
+                        "variable_id": (
+                            "hus",
+                            "pr",
+                            "psl",
+                            "tas",
+                            "ua",
+                        ),
+                        "experiment_id": "historical",
+                        "frequency": "mon",
+                    },
+                ),
+            ),
+            group_by=("source_id", "member_id", "grid_label"),
+            constraints=(
+                RequireContiguousTimerange(group_by=("instance_id",)),
+                AddSupplementaryDataset.from_defaults("areacella", SourceDatasetType.CMIP6),
+            ),
+        ),
+        DataRequirement(
+            source_type=SourceDatasetType.obs4MIPs,
+            filters=(
+                FacetFilter(
+                    facets={
+                        "variable_id": (
+                            "psl",
+                            "tas",
+                            "ua",
+                        ),
+                        "source_id": "ERA-5",
+                        "frequency": "mon",
+                    },
+                ),
+            ),
+            group_by=("source_id",),
+            constraints=(RequireContiguousTimerange(group_by=("instance_id",)),),
+            # TODO: Add obs4MIPs datasets once available and working:
+            #
+            # obs4MIPs dataset that cannot be ingested (https://github.com/Climate-REF/climate-ref/issues/260):
+            # - GPCP-V2.3: pr
+            #
+            # Not yet available on obs4MIPs:
+            # - ERA5: hus
+            # - HadCRUT5_ground_5.0.1.0-analysis: tas
+        ),
+    )
+    facets = ("grid_label", "member_id", "source_id", "variable_id", "region", "metric")
+
+    @staticmethod
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
+        """Update the recipe."""
+        recipe["datasets"] = []
+        recipe_variables = dataframe_to_recipe(input_files[SourceDatasetType.CMIP6])
+        diagnostics = {}
+        for diagnostic_name, diagnostic in recipe["diagnostics"].items():
+            for variable_name, variable in diagnostic["variables"].items():
+                if variable_name not in recipe_variables:
+                    continue
+                dataset = recipe_variables[variable_name]["additional_datasets"][0]
+                dataset.pop("timerange")
+                variable["additional_datasets"].append(dataset)
+                diagnostics[diagnostic_name] = diagnostic
+        recipe["diagnostics"] = diagnostics
+
+    @classmethod
+    def format_result(
+        cls,
+        result_dir: Path,
+        execution_dataset: ExecutionDatasetCollection,
+        metric_args: MetricBundleArgs,
+        output_args: OutputBundleArgs,
+    ) -> tuple[CMECMetric, CMECOutput]:
+        """Format the result."""
+        metric_args[MetricCV.DIMENSIONS.value] = {
+            "json_structure": ["variable_id", "region", "metric"],
+            "variable_id": {},
+            "region": {},
+            "metric": {"trend": {}},
+        }
+        for file in result_dir.glob("work/*_trends/plot/seaborn_barplot.nc"):
+            ds = xarray.open_dataset(file)
+            source_id = execution_dataset[SourceDatasetType.CMIP6].source_id.iloc[0]
+            select = source_id == np.array([s.strip() for s in ds.dataset.values.astype(str).tolist()])
+            ds.isel(dim0=select)
+            variable_id = next(iter(ds.data_vars.keys()))
+            metric_args[MetricCV.DIMENSIONS.value]["variable_id"][variable_id] = {}
+            metric_args[MetricCV.RESULTS.value][variable_id] = {}
+            for region_value, trend_value in zip(ds.shape_id.astype(str).values, ds[variable_id].values):
+                region = region_value.strip()
+                trend = float(trend_value)
+                if region not in metric_args[MetricCV.DIMENSIONS.value]["region"]:
+                    metric_args[MetricCV.DIMENSIONS.value]["region"][region] = {}
+                metric_args[MetricCV.RESULTS.value][variable_id][region] = {"trend": trend}
+
+        return CMECMetric.model_validate(metric_args), CMECOutput.model_validate(output_args)

climate_ref_esmvaltool/diagnostics/sea_ice_area_basic.py

@@ -42,10 +42,13 @@ class SeaIceAreaBasic(ESMValToolDiagnostic):
     facets = ()
 
     @staticmethod
-    def update_recipe(recipe: Recipe, input_files: pandas.DataFrame) -> None:
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
         """Update the recipe."""
         # Update datasets
-        recipe_variables = dataframe_to_recipe(input_files)
+        recipe_variables = dataframe_to_recipe(input_files[SourceDatasetType.CMIP6])
         recipe["datasets"] = recipe_variables["siconc"]["additional_datasets"]
 
         # Use the timerange from the recipe, as defined in the variable.

climate_ref_esmvaltool/diagnostics/sea_ice_sensitivity.py

@@ -57,9 +57,12 @@ class SeaIceSensitivity(ESMValToolDiagnostic):
     facets = ("experiment_id", "source_id", "region", "metric")
 
     @staticmethod
-    def update_recipe(recipe: Recipe, input_files: pandas.DataFrame) -> None:
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
         """Update the recipe."""
-        recipe_variables = dataframe_to_recipe(input_files)
+        recipe_variables = dataframe_to_recipe(input_files[SourceDatasetType.CMIP6])
         datasets = recipe_variables["tas"]["additional_datasets"]
         for dataset in datasets:
             dataset.pop("mip")

climate_ref_esmvaltool/diagnostics/tcr.py

@@ -54,7 +54,10 @@ class TransientClimateResponse(ESMValToolDiagnostic):
     facets = ("grid_label", "member_id", "source_id", "region", "metric")
 
     @staticmethod
-    def update_recipe(recipe: Recipe, input_files: pandas.DataFrame) -> None:
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
         """Update the recipe."""
         # Only run the diagnostic that computes TCR for a single model.
         recipe["diagnostics"] = {
@@ -77,21 +80,11 @@ class TransientClimateResponse(ESMValToolDiagnostic):
         # Prepare updated datasets section in recipe. It contains two
         # datasets, one for the "1pctCO2" and one for the "piControl"
         # experiment.
-        recipe_variables = dataframe_to_recipe(input_files)
-        recipe_variables = {k: v for k, v in recipe_variables.items() if k != "areacella"}
-
-        # Select a timerange covered by all datasets.
-        start_times, end_times = [], []
-        for variable in recipe_variables.values():
-            for dataset in variable["additional_datasets"]:
-                start, end = dataset["timerange"].split("/")
-                start_times.append(start)
-                end_times.append(end)
-        timerange = f"{max(start_times)}/{min(end_times)}"
-
-        datasets = recipe_variables["tas"]["additional_datasets"]
-        for dataset in datasets:
-            dataset["timerange"] = timerange
+        recipe_variables = dataframe_to_recipe(
+            input_files[SourceDatasetType.CMIP6],
+            equalize_timerange=True,
+        )
+        recipe["datasets"] = recipe_variables["tas"]["additional_datasets"]
 
         # Remove keys from the recipe that are only used for YAML anchors
         keys_to_remove = [
@@ -102,8 +95,6 @@ class TransientClimateResponse(ESMValToolDiagnostic):
         for key in keys_to_remove:
             recipe.pop(key, None)
 
-        recipe["datasets"] = datasets
-
     @staticmethod
     def format_result(
         result_dir: Path,

climate_ref_esmvaltool/diagnostics/tcre.py

@@ -67,12 +67,15 @@ class TransientClimateResponseEmissions(ESMValToolDiagnostic):
     facets = ("grid_label", "member_id", "source_id", "region", "metric")
 
     @staticmethod
-    def update_recipe(recipe: Recipe, input_files: pandas.DataFrame) -> None:
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
         """Update the recipe."""
         # Prepare updated datasets section in recipe. It contains three
         # datasets, "tas" and "fco2antt" for the "esm-1pctCO2" and just "tas"
         # for the "esm-piControl" experiment.
-        recipe_variables = dataframe_to_recipe(input_files)
+        recipe_variables = dataframe_to_recipe(input_files[SourceDatasetType.CMIP6])
         tas_esm_1pctCO2 = next(
             ds for ds in recipe_variables["tas"]["additional_datasets"] if ds["exp"] == "esm-1pctCO2"
         )

climate_ref_esmvaltool/diagnostics/zec.py

@@ -54,12 +54,15 @@ class ZeroEmissionCommitment(ESMValToolDiagnostic):
     facets = ("grid_label", "member_id", "source_id", "region", "metric")
 
     @staticmethod
-    def update_recipe(recipe: Recipe, input_files: pandas.DataFrame) -> None:
+    def update_recipe(
+        recipe: Recipe,
+        input_files: dict[SourceDatasetType, pandas.DataFrame],
+    ) -> None:
         """Update the recipe."""
         # Prepare updated datasets section in recipe. It contains two
         # datasets, one for the "esm-1pct-brch-1000PgC" and one for the "piControl"
         # experiment.
-        datasets = dataframe_to_recipe(input_files)["tas"]["additional_datasets"]
+        datasets = dataframe_to_recipe(input_files[SourceDatasetType.CMIP6])["tas"]["additional_datasets"]
         base_dataset = next(ds for ds in datasets if ds["exp"] == "1pctCO2")
         dataset = next(ds for ds in datasets if ds["exp"] == "esm-1pct-brch-1000PgC")
         start = dataset["timerange"].split("/")[0]

climate_ref_esmvaltool/recipe.py

@@ -12,6 +12,7 @@ from climate_ref_esmvaltool.types import Recipe
 if TYPE_CHECKING:
     import pandas as pd
 
+
 FACETS = {
     "CMIP6": {
         "activity": "activity_id",
@@ -23,6 +24,13 @@ FACETS = {
         "mip": "table_id",
         "short_name": "variable_id",
     },
+    "obs4MIPs": {
+        "dataset": "source_id",
+        "frequency": "frequency",
+        "grid": "grid_label",
+        "institute": "institution_id",
+        "short_name": "variable_id",
+    },
 }
 
 
@@ -90,7 +98,10 @@ def as_facets(
     return facets
 
 
-def dataframe_to_recipe(files: pd.DataFrame) -> dict[str, Any]:
+def dataframe_to_recipe(
+    files: pd.DataFrame,
+    equalize_timerange: bool = False,
+) -> dict[str, Any]:
     """Convert the datasets dataframe to a recipe "variables" section.
 
     Parameters
@@ -110,11 +121,27 @@ def dataframe_to_recipe(files: pd.DataFrame) -> dict[str, Any]:
         if short_name not in variables:
             variables[short_name] = {"additional_datasets": []}
         variables[short_name]["additional_datasets"].append(facets)
+
+    if equalize_timerange:
+        # Select a timerange covered by all datasets.
+        start_times, end_times = [], []
+        for variable in variables.values():
+            for dataset in variable["additional_datasets"]:
+                if "timerange" in dataset:
+                    start, end = dataset["timerange"].split("/")
+                    start_times.append(start)
+                    end_times.append(end)
+        timerange = f"{max(start_times)}/{min(end_times)}"
+        for variable in variables.values():
+            for dataset in variable["additional_datasets"]:
+                if "timerange" in dataset:
+                    dataset["timerange"] = timerange
+
     return variables
 
 
-_ESMVALTOOL_COMMIT = "8f56863a70ba4df76ec501ba0372c571a0af6cf9"
-_ESMVALTOOL_VERSION = f"2.13.0.dev120+g{_ESMVALTOOL_COMMIT[:9]}"
+_ESMVALTOOL_COMMIT = "2c438d0e0cc8904790294c72450eb7f06552c52a"
+_ESMVALTOOL_VERSION = f"2.13.0.dev148+g{_ESMVALTOOL_COMMIT[:9]}"
 
 _RECIPES = pooch.create(
     path=pooch.os_cache("climate_ref_esmvaltool"),
@@ -142,7 +169,16 @@ def load_recipe(recipe: str) -> Recipe:
         The loaded recipe.
     """
     filename = _RECIPES.fetch(recipe)
-    return yaml.safe_load(Path(filename).read_text(encoding="utf-8"))  # type: ignore[no-any-return]
+
+    def normalize(obj: Any) -> Any:
+        # Ensure objects in the recipe are not shared.
+        if isinstance(obj, dict):
+            return {k: normalize(v) for k, v in obj.items()}
+        if isinstance(obj, list):
+            return [normalize(item) for item in obj]
+        return obj
+
+    return normalize(yaml.safe_load(Path(filename).read_text(encoding="utf-8")))  # type: ignore[no-any-return]
 
 
 def prepare_climate_data(datasets: pd.DataFrame, climate_data_dir: Path) -> None:
@@ -165,6 +201,11 @@ def prepare_climate_data(datasets: pd.DataFrame, climate_data_dir: Path) -> None
         if not isinstance(row.path, str):  # pragma: no branch
             msg = f"Invalid path encountered in {row}"
             raise ValueError(msg)
-        tgt = climate_data_dir.joinpath(*row.instance_id.split(".")) / Path(row.path).name
+        if row.instance_id.startswith("obs4MIPs."):
+            version = row.instance_id.split(".")[-1]
+            subdirs: list[str] = ["obs4MIPs", row.source_id, version]  # type: ignore[list-item]
+        else:
+            subdirs = row.instance_id.split(".")
+        tgt = climate_data_dir.joinpath(*subdirs) / Path(row.path).name
         tgt.parent.mkdir(parents=True, exist_ok=True)
         tgt.symlink_to(row.path)

climate_ref_esmvaltool/recipes.txt

@@ -1,11 +1,16 @@
-examples/recipe_python.yml ab3f06d269bb2c1368f4dc39da9bcb232fb2adb1fa556ba769e6c16294ffb4a3
-recipe_calculate_gwl_exceedance_stats.yml 5aa266abc9a8029649b689a2b369a47623b0935d609354332ff4148994642d6b
-recipe_ecs.yml             0cc57034fcb64e32015b4ff949ece5df8cdb8c6f493618b50ceded119fb37918
-recipe_seaice_sensitivity.yml f7247c076e161c582d422947c8155f3ca98549e6f2e4c3b1c76414786d7e50c5
-recipe_tcr.yml             35f9ef035a4e71aff5cac5dd26c49da2162fc00291bf3b0bd16b661b7b2f606b
-recipe_tcre.yml            48fc9e3baf541bbcef7491853ea3a774053771dca33352b41466425faeaa38af
-recipe_zec.yml             b0af7f789b7610ab3f29a6617124aa40c40866ead958204fc199eaf82863de51
-ref/recipe_enso_basicclimatology.yml 9ea7deb7ee668e39ac44618b96496d898bd82285c22dcee4fce4695e0c9fa82b
-ref/recipe_enso_characteristics.yml 34c2518b138068ac96d212910b979d54a8fcedee2c0089b5acd56a42c41dc3e4
-ref/recipe_ref_cre.yml     4375f262479c3b3e1b348b71080a6d758e195bda76516a591182045a3a29aa32
-ref/recipe_ref_sea_ice_area_basic.yml 7d01a8527880663ca28284772f83a8356d9972fb4f022a4000e50a56ce044b09
+examples/recipe_python.yml                  ab3f06d269bb2c1368f4dc39da9bcb232fb2adb1fa556ba769e6c16294ffb4a3
+recipe_calculate_gwl_exceedance_stats.yml   5aa266abc9a8029649b689a2b369a47623b0935d609354332ff4148994642d6b
+recipe_ecs.yml                              0cc57034fcb64e32015b4ff949ece5df8cdb8c6f493618b50ceded119fb37918
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+ref/recipe_enso_basicclimatology.yml        9ea7deb7ee668e39ac44618b96496d898bd82285c22dcee4fce4695e0c9fa82b
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+ref/recipe_ref_trend_regions.yml            18fe246a51474bd12172ab1ba141efac999a247de7774822f77ae6ef144645fe