anemoi-datasets 0.4.5__py3-none-any.whl → 0.5.0__py3-none-any.whl

anemoi/datasets/create/functions/filters/single_level_specific_humidity_to_relative_humidity.py

@@ -0,0 +1,390 @@
+# (C) Copyright 2024 ECMWF.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+#
+
+
+import numpy as np
+from earthkit.data.indexing.fieldlist import FieldArray
+from earthkit.meteo import constants
+from earthkit.meteo import thermo
+
+
+# Alternative proposed by Baudouin Raoult
+class AutoDict(dict):
+    def __missing__(self, key):
+        value = self[key] = type(self)()
+        return value
+
+
+class NewDataField:
+    def __init__(self, field, data, new_name):
+        self.field = field
+        self.data = data
+        self.new_name = new_name
+
+    def to_numpy(self, *args, **kwargs):
+        return self.data
+
+    def metadata(self, key=None, **kwargs):
+        if key is None:
+            return self.field.metadata(**kwargs)
+
+        value = self.field.metadata(key, **kwargs)
+        if key == "param":
+            return self.new_name
+        return value
+
+    def __getattr__(self, name):
+        return getattr(self.field, name)
+
+
+def model_level_pressure(A, B, surface_pressure):
+    """Calculates:
+     - pressure at the model full- and half-levels
+     - delta: depth of log(pressure) at full levels
+     - alpha: alpha term #TODO: more descriptive information
+
+    Parameters
+    ----------
+    A : ndarray
+        A-coefficients defining the model levels
+    B : ndarray
+        B-coefficients defining the model levels
+    surface_pressure: number or ndarray
+        surface pressure (Pa)
+
+    Returns
+    -------
+    ndarray
+        pressure at model full-levels
+    ndarray
+        pressure at model half-levels
+    ndarray
+        delta at full-levels
+    ndarray
+        alpha at full levels
+    """
+
+    # constants
+    PRESSURE_TOA = 0.1  # safety when highest pressure level = 0.0
+
+    # make the calculation agnostic to the number of dimensions
+    ndim = surface_pressure.ndim
+    new_shape_half = (A.shape[0],) + (1,) * ndim
+    A_reshaped = A.reshape(new_shape_half)
+    B_reshaped = B.reshape(new_shape_half)
+
+    # calculate pressure on model half-levels
+    p_half_level = A_reshaped + B_reshaped * surface_pressure[np.newaxis, ...]
+
+    # calculate delta
+    new_shape_full = (A.shape[0] - 1,) + surface_pressure.shape
+    delta = np.zeros(new_shape_full)
+    delta[1:, ...] = np.log(p_half_level[2:, ...] / p_half_level[1:-1, ...])
+
+    # pressure at highest half level<= 0.1
+    if np.any(p_half_level[0, ...] <= PRESSURE_TOA):
+        delta[0, ...] = np.log(p_half_level[1, ...] / PRESSURE_TOA)
+    # pressure at highest half level > 0.1
+    else:
+        delta[0, ...] = np.log(p_half_level[1, ...] / p_half_level[0, ...])
+
+    # calculate alpha
+    alpha = np.zeros(new_shape_full)
+
+    alpha[1:, ...] = 1.0 - p_half_level[1:-1, ...] / (p_half_level[2:, ...] - p_half_level[1:-1, ...]) * delta[1:, ...]
+
+    # pressure at highest half level <= 0.1
+    if np.any(p_half_level[0, ...] <= PRESSURE_TOA):
+        alpha[0, ...] = 1.0  # ARPEGE choice, ECMWF IFS uses log(2)
+    # pressure at highest half level > 0.1
+    else:
+        alpha[0, ...] = 1.0 - p_half_level[0, ...] / (p_half_level[1, ...] - p_half_level[0, ...]) * delta[0, ...]
+
+    # calculate pressure on model full levels
+    # TODO: is there a faster way to calculate the averages?
+    # TODO: introduce option to calculate full levels in more complicated way
+    p_full_level = np.apply_along_axis(lambda m: np.convolve(m, np.ones(2) / 2, mode="valid"), axis=0, arr=p_half_level)
+
+    return p_full_level, p_half_level, delta, alpha
+
+
+def calc_specific_gas_constant(q):
+    """Calculates the specific gas constant of moist air
+    (specific content of cloud particles and hydrometeors are neglected)
+
+    Parameters
+    ----------
+    q : number or ndarray
+        specific humidity
+
+    Returns
+    -------
+    number or ndarray
+        specific gas constant of moist air
+    """
+
+    R = constants.Rd + (constants.Rv - constants.Rd) * q
+    return R
+
+
+def relative_geopotential_thickness(alpha, q, T):
+    """Calculates the geopotential thickness w.r.t the surface on model full-levels
+
+    Parameters
+    ----------
+    alpha : ndarray
+        alpha term of pressure calculations
+    q : ndarray
+        specific humidity (in kg/kg) on model full-levels
+    T : ndarray
+        temperature (in Kelvin) on model full-levels
+
+    Returns
+    -------
+    ndarray
+        geopotential thickness of model full-levels w.r.t. the surface
+    """
+
+    R = calc_specific_gas_constant(q)
+    dphi = np.cumsum(np.flip(alpha * R * T, axis=0), axis=0)
+    dphi = np.flip(dphi, axis=0)
+
+    return dphi
+
+
+def pressure_at_height_level(height, q, T, sp, A, B):
+    """Calculates the pressure at a height level given in meters above surface.
+    This is done by finding the model level above and below the specified height
+    and interpolating the pressure
+
+    Parameters
+    ----------
+    height : number
+        height (in meters) above the surface for which the pressure is wanted
+    q : ndarray
+        specific humidity (kg/kg) at model full-levels
+    T : ndarray
+        temperature (K) at model full-levels
+    sp : ndarray
+        surface pressure (Pa)
+    A : ndarray
+        A-coefficients defining the model levels
+    B : ndarray
+        B-coefficients defining the model levels
+
+    Returns
+    -------
+    number or ndarray
+        pressure (Pa) at the given height level
+    """
+
+    # geopotential thickness of the height level
+    tdphi = height * constants.g
+
+    # pressure(-related) variables
+    p_full, p_half, _, alpha = model_level_pressure(A, B, sp)
+
+    # relative geopot. thickness of full levels
+    dphi = relative_geopotential_thickness(alpha, q, T)
+
+    # find the model full level right above the height level
+    i_phi = (tdphi > dphi).sum(0)
+
+    # initialize the output array
+    p_height = np.zeros_like(i_phi, dtype=np.float64)
+
+    # define mask: requested height is below the lowest model full-level
+    mask = i_phi == 0
+
+    # CASE 1: requested height is below the lowest model full-level
+    # --> interpolation between surface pressure and lowest model full-level
+    p_height[mask] = (p_half[-1, ...] + tdphi / dphi[-1, ...] * (p_full[-1, ...] - p_half[-1, ...]))[mask]
+
+    # CASE 2: requested height is above the lowest model full-level
+    # --> interpolation between between model full-level above and below
+
+    # define some indices for masking and readability
+    i_lev = alpha.shape[0] - i_phi - 1  # convert phi index to model level index
+    indices = np.indices(i_lev.shape)
+    masked_indices = tuple(dim[~mask] for dim in indices)
+    above = (i_lev[~mask],) + masked_indices
+    below = (i_lev[~mask] + 1,) + masked_indices
+
+    dphi_above = dphi[above]
+    dphi_below = dphi[below]
+
+    factor = (tdphi - dphi_above) / (dphi_below - dphi_above)
+    p_height[~mask] = p_full[above] + factor * (p_full[below] - p_full[above])
+
+    return p_height
+
+
+def execute(context, input, height, t, q, sp, new_name="2r", **kwargs):
+    """Convert the single (height) level specific humidity to relative humidity"""
+    result = FieldArray()
+
+    MANDATORY_KEYS = ["A", "B"]
+    OPTIONAL_KEYS = ["t_ml", "q_ml"]
+    MISSING_KEYS = []
+    DEFAULTS = dict(t_ml="t", q_ml="q")
+
+    for key in OPTIONAL_KEYS:
+        if key not in kwargs:
+            print(f"key {key} not found in yaml-file, using default key: {DEFAULTS[key]}")
+            kwargs[key] = DEFAULTS[key]
+
+    for key in MANDATORY_KEYS:
+        if key not in kwargs:
+            MISSING_KEYS.append(key)
+
+    if MISSING_KEYS:
+        raise KeyError(f"Following keys are missing: {', '.join(MISSING_KEYS)}")
+
+    single_level_params = (t, q, sp)
+    model_level_params = (kwargs["t_ml"], kwargs["q_ml"])
+
+    needed_fields = AutoDict()
+
+    # Gather all necessary fields
+    for f in input:
+        key = f.metadata(namespace="mars")
+        param = key.pop("param")
+        # check single level parameters
+        if param in single_level_params:
+            levtype = key.pop("levtype")
+            key = tuple(sorted(key.items()))
+
+            if param in needed_fields[key][levtype]:
+                raise ValueError(f"Duplicate single level field {param} for {key}")
+
+            needed_fields[key][levtype][param] = f
+            if param == q:
+                if kwargs.get("keep_q", False):
+                    result.append(f)
+            else:
+                result.append(f)
+
+        # check model level parameters
+        elif param in model_level_params:
+            levtype = key.pop("levtype")
+            levelist = key.pop("levelist")
+            key = tuple(sorted(key.items()))
+
+            if param in needed_fields[key][levtype][levelist]:
+                raise ValueError(f"Duplicate model level field {param} for {key} at level {levelist}")
+
+            needed_fields[key][levtype][levelist][param] = f
+
+        # all other parameters
+        else:
+            result.append(f)
+
+    for _, values in needed_fields.items():
+        # some checks
+        if len(values["sfc"]) != 3:
+            raise ValueError("Missing surface fields")
+
+        q_sl = values["sfc"][q].to_numpy(flatten=True)
+        t_sl = values["sfc"][t].to_numpy(flatten=True)
+        sp_sl = values["sfc"][sp].to_numpy(flatten=True)
+
+        nlevels = len(kwargs["A"]) - 1
+        if len(values["ml"]) != nlevels:
+            raise ValueError("Missing model levels")
+
+        for key in values["ml"].keys():
+            if len(values["ml"][key]) != 2:
+                raise ValueError(f"Missing field on level {key}")
+
+        # create 3D arrays for upper air fields
+        levels = list(values["ml"].keys())
+        levels.sort()
+        t_ml = []
+        q_ml = []
+        for level in levels:
+            t_ml.append(values["ml"][level][kwargs["t_ml"]].to_numpy(flatten=True))
+            q_ml.append(values["ml"][level][kwargs["q_ml"]].to_numpy(flatten=True))
+
+        t_ml = np.stack(t_ml)
+        q_ml = np.stack(q_ml)
+
+        # actual conversion from qv --> rh
+        # FIXME:
+        # For now We need to go from qv --> td --> rh to take into account
+        # the mixed / ice phase when T ~ 0C / T < 0C
+        # See https://github.com/ecmwf/earthkit-meteo/issues/15
+        p_sl = pressure_at_height_level(height, q_ml, t_ml, sp_sl, np.array(kwargs["A"]), np.array(kwargs["B"]))
+        td_sl = thermo.dewpoint_from_specific_humidity(q=q_sl, p=p_sl)
+        rh_sl = thermo.relative_humidity_from_dewpoint(t=t_sl, td=td_sl)
+
+        result.append(NewDataField(values["sfc"][q], rh_sl, new_name))
+
+    return result
+
+
+def test():
+    from earthkit.data import from_source
+    from earthkit.data.readers.grib.index import GribFieldList
+
+    # IFS forecasts have both specific humidity and dewpoint
+    sl = from_source(
+        "mars",
+        {
+            "date": "2022-01-01",
+            "class": "od",
+            "expver": "1",
+            "stream": "oper",
+            "levtype": "sfc",
+            "param": "96.174/134.128/167.128/168.128",
+            "time": "00:00:00",
+            "type": "fc",
+            "step": "2",
+            "grid": "O640",
+        },
+    )
+
+    ml = from_source(
+        "mars",
+        {
+            "date": "2022-01-01",
+            "class": "od",
+            "expver": "1",
+            "stream": "oper",
+            "levtype": "ml",
+            "levelist": "130/131/132/133/134/135/136/137",
+            "param": "130/133",
+            "time": "00:00:00",
+            "type": "fc",
+            "step": "2",
+            "grid": "O640",
+        },
+    )
+    source = GribFieldList.merge([sl, ml])
+
+    # IFS A and B coeffients for level 137 - 129
+    kwargs = {
+        "A": [424.414063, 302.476563, 202.484375, 122.101563, 62.781250, 22.835938, 3.757813, 0.0, 0.0],
+        "B": [0.969513, 0.975078, 0.980072, 0.984542, 0.988500, 0.991984, 0.995003, 0.997630, 1.000000],
+    }
+    source = execute(None, source, 2, "2t", "2sh", "sp", "2r", **kwargs)
+
+    temperature = source[2].to_numpy(flatten=True)
+    dewpoint = source[3].to_numpy(flatten=True)
+    relhum = source[4].to_numpy()
+    newdew = thermo.dewpoint_from_relative_humidity(temperature, relhum)
+
+    print(f"Mean difference in dewpoint temperature: {np.abs(newdew - dewpoint).mean():02f} degC")
+    print(f"Median difference in dewpoint temperature: {np.median(np.abs(newdew - dewpoint)):02f} degC")
+    print(f"Maximum difference in dewpoint temperature: {np.abs(newdew - dewpoint).max():02f} degC")
+
+    # source.save("source.grib")
+
+
+if __name__ == "__main__":
+    test()

anemoi/datasets/create/functions/filters/speeddir_to_uv.py

@@ -0,0 +1,77 @@
+# (C) Copyright 2024 ECMWF.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+#
+
+from collections import defaultdict
+
+import numpy as np
+from earthkit.data.indexing.fieldlist import FieldArray
+from earthkit.meteo.wind.array import polar_to_xy
+
+
+class NewDataField:
+    def __init__(self, field, data, new_name):
+        self.field = field
+        self.data = data
+        self.new_name = new_name
+
+    def to_numpy(self, *args, **kwargs):
+        return self.data
+
+    def metadata(self, key=None, **kwargs):
+        if key is None:
+            return self.field.metadata(**kwargs)
+
+        value = self.field.metadata(key, **kwargs)
+        if key == "param":
+            return self.new_name
+        return value
+
+    def __getattr__(self, name):
+        return getattr(self.field, name)
+
+
+def execute(context, input, wind_speed, wind_dir, u_component="u", v_component="v", in_radians=False):
+
+    result = FieldArray()
+
+    wind_params = (wind_speed, wind_dir)
+    wind_pairs = defaultdict(dict)
+
+    for f in input:
+        key = f.metadata(namespace="mars")
+        param = key.pop("param")
+
+        if param not in wind_params:
+            result.append(f)
+            continue
+
+        key = tuple(key.items())
+
+        if param in wind_pairs[key]:
+            raise ValueError(f"Duplicate wind component {param} for {key}")
+
+        wind_pairs[key][param] = f
+
+    for _, pairs in wind_pairs.items():
+        if len(pairs) != 2:
+            raise ValueError("Missing wind component")
+
+        magnitude = pairs[wind_speed]
+        direction = pairs[wind_dir]
+
+        # assert speed.grid_mapping == dir.grid_mapping
+        if in_radians:
+            direction = np.rad2deg(direction)
+
+        u, v = polar_to_xy(magnitude.to_numpy(flatten=True), direction.to_numpy(flatten=True))
+
+        result.append(NewDataField(magnitude, u, u_component))
+        result.append(NewDataField(direction, v, v_component))
+
+    return result

anemoi/datasets/create/functions/filters/uv_to_speeddir.py

@@ -0,0 +1,55 @@
+# (C) Copyright 2024 ECMWF.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+#
+
+from collections import defaultdict
+
+import numpy as np
+from earthkit.data.indexing.fieldlist import FieldArray
+from earthkit.meteo.wind.array import xy_to_polar
+
+from anemoi.datasets.create.functions.filters.speeddir_to_uv import NewDataField
+
+
+def execute(context, input, u_component, v_component, wind_speed, wind_dir, in_radians=False):
+    result = FieldArray()
+
+    wind_params = (u_component, v_component)
+    wind_pairs = defaultdict(dict)
+
+    for f in input:
+        key = f.metadata(namespace="mars")
+        param = key.pop("param")
+
+        if param not in wind_params:
+            result.append(f)
+            continue
+
+        key = tuple(key.items())
+
+        if param in wind_pairs[key]:
+            raise ValueError(f"Duplicate wind component {param} for {key}")
+
+        wind_pairs[key][param] = f
+
+    for _, pairs in wind_pairs.items():
+        if len(pairs) != 2:
+            raise ValueError("Missing wind component")
+
+        u = pairs[u_component]
+        v = pairs[v_component]
+
+        # assert speed.grid_mapping == dir.grid_mapping
+        magnitude, direction = xy_to_polar(u.to_numpy(flatten=True), v.to_numpy(flatten=True))
+        if in_radians:
+            direction = np.deg2rad(direction)
+
+        result.append(NewDataField(u, magnitude, wind_speed))
+        result.append(NewDataField(v, direction, wind_dir))
+
+    return result

anemoi/datasets/create/functions/sources/grib.py

@@ -11,9 +11,87 @@
 import glob
 
 from earthkit.data import from_source
+from earthkit.data.indexing.fieldlist import FieldArray
 from earthkit.data.utils.patterns import Pattern
 
 
+def _load(context, name, record):
+    ds = None
+
+    param = record["param"]
+
+    if "path" in record:
+        context.info(f"Using {name} from {record['path']} (param={param})")
+        ds = from_source("file", record["path"])
+
+    if "url" in record:
+        context.info(f"Using {name} from {record['url']} (param={param})")
+        ds = from_source("url", record["url"])
+
+    ds = ds.sel(param=param)
+
+    assert len(ds) == 1, f"{name} {param}, expected one field, got {len(ds)}"
+    ds = ds[0]
+
+    return ds.to_numpy(flatten=True), ds.metadata("uuidOfHGrid")
+
+
+class Geography:
+    """This class retrieve the latitudes and longitudes of unstructured grids,
+    and checks if the fields are compatible with the grid.
+    """
+
+    def __init__(self, context, latitudes, longitudes):
+
+        latitudes, uuidOfHGrid_lat = _load(context, "latitudes", latitudes)
+        longitudes, uuidOfHGrid_lon = _load(context, "longitudes", longitudes)
+
+        assert (
+            uuidOfHGrid_lat == uuidOfHGrid_lon
+        ), f"uuidOfHGrid mismatch: lat={uuidOfHGrid_lat} != lon={uuidOfHGrid_lon}"
+
+        context.info(f"Latitudes: {len(latitudes)}, Longitudes: {len(longitudes)}")
+        assert len(latitudes) == len(longitudes)
+
+        self.uuidOfHGrid = uuidOfHGrid_lat
+        self.latitudes = latitudes
+        self.longitudes = longitudes
+        self.first = True
+
+    def check(self, field):
+        if self.first:
+            # We only check the first field, for performance reasons
+            assert (
+                field.metadata("uuidOfHGrid") == self.uuidOfHGrid
+            ), f"uuidOfHGrid mismatch: {field.metadata('uuidOfHGrid')} != {self.uuidOfHGrid}"
+            self.first = False
+
+
+class AddGrid:
+    """An earth-kit.data.Field wrapper that adds grid information."""
+
+    def __init__(self, field, geography):
+        self._field = field
+
+        geography.check(field)
+
+        self._latitudes = geography.latitudes
+        self._longitudes = geography.longitudes
+
+    def __getattr__(self, name):
+        return getattr(self._field, name)
+
+    def __repr__(self) -> str:
+        return repr(self._field)
+
+    def grid_points(self):
+        return self._latitudes, self._longitudes
+
+    @property
+    def resolution(self):
+        return "unknown"
+
+
 def check(ds, paths, **kwargs):
     count = 1
     for k, v in kwargs.items():
@@ -34,9 +112,13 @@ def _expand(paths):
             yield path
 
 
-def execute(context, dates, path, *args, **kwargs):
+def execute(context, dates, path, latitudes=None, longitudes=None, *args, **kwargs):
     given_paths = path if isinstance(path, list) else [path]
 
+    geography = None
+    if latitudes is not None and longitudes is not None:
+        geography = Geography(context, latitudes, longitudes)
+
     ds = from_source("empty")
     dates = [d.isoformat() for d in dates]
 
@@ -56,4 +138,7 @@ def execute(context, dates, path, *args, **kwargs):
     if kwargs:
         check(ds, given_paths, valid_datetime=dates, **kwargs)
 
+    if geography is not None:
+        ds = FieldArray([AddGrid(_, geography) for _ in ds])
+
     return ds