roms-tools 0.0.6__py3-none-any.whl → 0.20__py3-none-any.whl

roms_tools/setup/datasets.py

@@ -0,0 +1,457 @@
+import pooch
+import xarray as xr
+from dataclasses import dataclass, field
+import glob
+from datetime import datetime, timedelta
+import numpy as np
+from typing import Dict, Optional, List
+import dask
+
+# Create a Pooch object to manage the global topography data
+pup_data = pooch.create(
+    # Use the default cache folder for the operating system
+    path=pooch.os_cache("roms-tools"),
+    base_url="https://github.com/CWorthy-ocean/roms-tools-data/raw/main/",
+    # The registry specifies the files that can be fetched
+    registry={
+        "etopo5.nc": "sha256:23600e422d59bbf7c3666090166a0d468c8ee16092f4f14e32c4e928fbcd627b",
+    },
+)
+
+# Create a Pooch object to manage the test data
+pup_test_data = pooch.create(
+    # Use the default cache folder for the operating system
+    path=pooch.os_cache("roms-tools"),
+    base_url="https://github.com/CWorthy-ocean/roms-tools-test-data/raw/main/",
+    # The registry specifies the files that can be fetched
+    registry={
+        "GLORYS_test_data.nc": "648f88ec29c433bcf65f257c1fb9497bd3d5d3880640186336b10ed54f7129d2",
+        "ERA5_regional_test_data.nc": "bd12ce3b562fbea2a80a3b79ba74c724294043c28dc98ae092ad816d74eac794",
+        "ERA5_global_test_data.nc": "8ed177ab64c02caf509b9fb121cf6713f286cc603b1f302f15f3f4eb0c21dc4f",
+        "TPXO_global_test_data.nc": "457bfe87a7b247ec6e04e3c7d3e741ccf223020c41593f8ae33a14f2b5255e60",
+        "TPXO_regional_test_data.nc": "11739245e2286d9c9d342dce5221e6435d2072b50028bef2e86a30287b3b4032",
+    },
+)
+
+
+def fetch_topo(topography_source: str) -> xr.Dataset:
+    """
+    Load the global topography data as an xarray Dataset.
+
+    Parameters
+    ----------
+    topography_source : str
+        The source of the topography data to be loaded. Available options:
+        - "ETOPO5"
+
+    Returns
+    -------
+    xr.Dataset
+        The global topography data as an xarray Dataset.
+    """
+    # Mapping from user-specified topography options to corresponding filenames in the registry
+    topo_dict = {"ETOPO5": "etopo5.nc"}
+
+    # Fetch the file using Pooch, downloading if necessary
+    fname = pup_data.fetch(topo_dict[topography_source])
+
+    # Load the dataset using xarray and return it
+    ds = xr.open_dataset(fname)
+    return ds
+
+
+def download_test_data(filename: str) -> str:
+    """
+    Download the test data file.
+
+    Parameters
+    ----------
+    filename : str
+        The name of the test data file to be downloaded. Available options:
+        - "GLORYS_test_data.nc"
+        - "ERA5_regional_test_data.nc"
+        - "ERA5_global_test_data.nc"
+
+    Returns
+    -------
+    str
+        The path to the downloaded test data file.
+    """
+    # Fetch the file using Pooch, downloading if necessary
+    fname = pup_test_data.fetch(filename)
+
+    return fname
+
+
+@dataclass(frozen=True, kw_only=True)
+class Dataset:
+    """
+    Represents forcing data on original grid.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the data files. Can contain wildcards.
+    start_time : Optional[datetime], optional
+        The start time for selecting relevant data. If not provided, the data is not filtered by start time.
+    end_time : Optional[datetime], optional
+        The end time for selecting relevant data. If not provided, only data at the start_time is selected if start_time is provided,
+        or no filtering is applied if start_time is not provided.
+    var_names : List[str]
+        List of variable names that are required in the dataset.
+    dim_names: Dict[str, str], optional
+        Dictionary specifying the names of dimensions in the dataset.
+
+    Attributes
+    ----------
+    ds : xr.Dataset
+        The xarray Dataset containing the forcing data on its original grid.
+
+    Examples
+    --------
+    >>> dataset = Dataset(
+    ...     filename="data.nc",
+    ...     start_time=datetime(2022, 1, 1),
+    ...     end_time=datetime(2022, 12, 31),
+    ... )
+    >>> dataset.load_data()
+    >>> print(dataset.ds)
+    <xarray.Dataset>
+    Dimensions:  ...
+    """
+
+    filename: str
+    start_time: Optional[datetime] = None
+    end_time: Optional[datetime] = None
+    var_names: List[str]
+    dim_names: Dict[str, str] = field(
+        default_factory=lambda: {
+            "longitude": "longitude",
+            "latitude": "latitude",
+            "time": "time",
+        }
+    )
+
+    ds: xr.Dataset = field(init=False, repr=False)
+
+    def __post_init__(self):
+        ds = self.load_data()
+
+        # Select relevant times
+        if "time" in self.dim_names and self.start_time is not None:
+            ds = self.select_relevant_times(ds)
+
+        # Select relevant fields
+        ds = self.select_relevant_fields(ds)
+
+        # Make sure that latitude is ascending
+        diff = np.diff(ds[self.dim_names["latitude"]])
+        if np.all(diff < 0):
+            ds = ds.isel(**{self.dim_names["latitude"]: slice(None, None, -1)})
+
+        # Check whether the data covers the entire globe
+        is_global = self.check_if_global(ds)
+
+        if is_global:
+            ds = self.concatenate_longitudes(ds)
+
+        object.__setattr__(self, "ds", ds)
+
+    def load_data(self) -> xr.Dataset:
+        """
+        Load dataset from the specified file.
+
+        Returns
+        -------
+        ds : xr.Dataset
+            The loaded xarray Dataset containing the forcing data.
+
+        Raises
+        ------
+        FileNotFoundError
+            If the specified file does not exist.
+        """
+
+        # Check if the file exists
+        matching_files = glob.glob(self.filename)
+        if not matching_files:
+            raise FileNotFoundError(
+                f"No files found matching the pattern '{self.filename}'."
+            )
+
+        # Load the dataset
+        with dask.config.set(**{"array.slicing.split_large_chunks": False}):
+            # Define the chunk sizes
+            chunks = {
+                self.dim_names["latitude"]: -1,
+                self.dim_names["longitude"]: -1,
+            }
+            if "depth" in self.dim_names.keys():
+                chunks[self.dim_names["depth"]] = -1
+            if "time" in self.dim_names.keys():
+                chunks[self.dim_names["time"]] = 1
+
+                ds = xr.open_mfdataset(
+                    self.filename,
+                    combine="nested",
+                    concat_dim=self.dim_names["time"],
+                    coords="minimal",
+                    compat="override",
+                    chunks=chunks,
+                    engine="netcdf4",
+                )
+            else:
+                ds = xr.open_dataset(
+                    self.filename,
+                    chunks=chunks,
+                )
+
+        return ds
+
+    def select_relevant_fields(self, ds) -> xr.Dataset:
+        """
+        Selects and returns a subset of the dataset containing only the variables specified in `self.var_names`.
+
+        Parameters
+        ----------
+        ds : xr.Dataset
+            The input dataset from which variables will be selected.
+
+        Returns
+        -------
+        xr.Dataset
+            A dataset containing only the variables specified in `self.var_names`.
+
+        Raises
+        ------
+        ValueError
+            If `ds` does not contain all variables listed in `self.var_names`.
+
+        """
+        missing_vars = [var for var in self.var_names if var not in ds.data_vars]
+        if missing_vars:
+            raise ValueError(
+                f"Dataset does not contain all required variables. The following variables are missing: {missing_vars}"
+            )
+
+        for var in ds.data_vars:
+            if var not in self.var_names:
+                ds = ds.drop_vars(var)
+
+        return ds
+
+    def select_relevant_times(self, ds) -> xr.Dataset:
+
+        """
+        Selects and returns the subset of the dataset corresponding to the specified time range.
+
+        This function filters the dataset to include only the data points within the specified
+        time range, defined by `self.start_time` and `self.end_time`. If `self.end_time` is not
+        provided, it defaults to one day after `self.start_time`.
+
+        Parameters
+        ----------
+        ds : xr.Dataset
+            The input dataset to be filtered.
+
+        Returns
+        -------
+        xr.Dataset
+            A dataset containing only the data points within the specified time range.
+
+        """
+
+        time_dim = self.dim_names["time"]
+
+        if not self.end_time:
+            end_time = self.start_time + timedelta(days=1)
+        else:
+            end_time = self.end_time
+
+        times = (np.datetime64(self.start_time) <= ds[time_dim]) & (
+            ds[time_dim] < np.datetime64(end_time)
+        )
+        ds = ds.where(times, drop=True)
+
+        if not ds.sizes[time_dim]:
+            raise ValueError("No matching times found.")
+
+        if not self.end_time:
+            if ds.sizes[time_dim] != 1:
+                found_times = ds.sizes[time_dim]
+                raise ValueError(
+                    f"There must be exactly one time matching the start_time. Found {found_times} matching times."
+                )
+
+        return ds
+
+    def check_if_global(self, ds) -> bool:
+        """
+        Checks if the dataset covers the entire globe in the longitude dimension.
+
+        This function calculates the mean difference between consecutive longitude values.
+        It then checks if the difference between the first and last longitude values (plus 360 degrees)
+        is close to this mean difference, within a specified tolerance. If it is, the dataset is considered
+        to cover the entire globe in the longitude dimension.
+
+        Returns
+        -------
+        bool
+            True if the dataset covers the entire globe in the longitude dimension, False otherwise.
+
+        """
+        dlon_mean = (
+            ds[self.dim_names["longitude"]].diff(dim=self.dim_names["longitude"]).mean()
+        )
+        dlon = (
+            ds[self.dim_names["longitude"]][0] - ds[self.dim_names["longitude"]][-1]
+        ) % 360.0
+        is_global = np.isclose(dlon, dlon_mean, rtol=0.0, atol=1e-3)
+
+        return is_global
+
+    def concatenate_longitudes(self, ds):
+        """
+        Concatenates the field three times: with longitudes shifted by -360, original longitudes, and shifted by +360.
+
+        Parameters
+        ----------
+        field : xr.DataArray
+            The field to be concatenated.
+
+        Returns
+        -------
+        xr.DataArray
+            The concatenated field, with the longitude dimension extended.
+
+        Notes
+        -----
+        Concatenating three times may be overkill in most situations, but it is safe. Alternatively, we could refactor
+        to figure out whether concatenating on the lower end, upper end, or at all is needed.
+
+        """
+        ds_concatenated = xr.Dataset()
+
+        lon = ds[self.dim_names["longitude"]]
+        lon_minus360 = lon - 360
+        lon_plus360 = lon + 360
+        lon_concatenated = xr.concat(
+            [lon_minus360, lon, lon_plus360], dim=self.dim_names["longitude"]
+        )
+
+        ds_concatenated[self.dim_names["longitude"]] = lon_concatenated
+
+        for var in self.var_names:
+            if self.dim_names["longitude"] in ds[var].dims:
+                field = ds[var]
+                field_concatenated = xr.concat(
+                    [field, field, field], dim=self.dim_names["longitude"]
+                ).chunk({self.dim_names["longitude"]: -1})
+                field_concatenated[self.dim_names["longitude"]] = lon_concatenated
+                ds_concatenated[var] = field_concatenated
+            else:
+                ds_concatenated[var] = ds[var]
+
+        return ds_concatenated
+
+    def choose_subdomain(
+        self, latitude_range, longitude_range, margin, straddle, return_subdomain=False
+    ):
+        """
+        Selects a subdomain from the given xarray Dataset based on latitude and longitude ranges,
+        extending the selection by the specified margin. Handles the conversion of longitude values
+        in the dataset from one range to another.
+
+        Parameters
+        ----------
+        latitude_range : tuple
+            A tuple (lat_min, lat_max) specifying the minimum and maximum latitude values of the subdomain.
+        longitude_range : tuple
+            A tuple (lon_min, lon_max) specifying the minimum and maximum longitude values of the subdomain.
+        margin : float
+            Margin in degrees to extend beyond the specified latitude and longitude ranges when selecting the subdomain.
+        straddle : bool
+            If True, target longitudes are expected in the range [-180, 180].
+            If False, target longitudes are expected in the range [0, 360].
+        return_subdomain : bool, optional
+            If True, returns the subset of the original dataset. If False, assigns it to self.ds.
+            Default is False.
+
+        Returns
+        -------
+        xr.Dataset
+            The subset of the original dataset representing the chosen subdomain, including an extended area
+            to cover one extra grid point beyond the specified ranges if return_subdomain is True.
+            Otherwise, returns None.
+
+        Raises
+        ------
+        ValueError
+            If the selected latitude or longitude range does not intersect with the dataset.
+        """
+        lat_min, lat_max = latitude_range
+        lon_min, lon_max = longitude_range
+
+        lon = self.ds[self.dim_names["longitude"]]
+        # Adjust longitude range if needed to match the expected range
+        if not straddle:
+            if lon.min() < -180:
+                if lon_max + margin > 0:
+                    lon_min -= 360
+                    lon_max -= 360
+            elif lon.min() < 0:
+                if lon_max + margin > 180:
+                    lon_min -= 360
+                    lon_max -= 360
+
+        if straddle:
+            if lon.max() > 360:
+                if lon_min - margin < 180:
+                    lon_min += 360
+                    lon_max += 360
+            elif lon.max() > 180:
+                if lon_min - margin < 0:
+                    lon_min += 360
+                    lon_max += 360
+
+        # Select the subdomain
+        subdomain = self.ds.sel(
+            **{
+                self.dim_names["latitude"]: slice(lat_min - margin, lat_max + margin),
+                self.dim_names["longitude"]: slice(lon_min - margin, lon_max + margin),
+            }
+        )
+
+        # Check if the selected subdomain has zero dimensions in latitude or longitude
+        if subdomain[self.dim_names["latitude"]].size == 0:
+            raise ValueError("Selected latitude range does not intersect with dataset.")
+
+        if subdomain[self.dim_names["longitude"]].size == 0:
+            raise ValueError(
+                "Selected longitude range does not intersect with dataset."
+            )
+
+        # Adjust longitudes to expected range if needed
+        lon = subdomain[self.dim_names["longitude"]]
+        if straddle:
+            subdomain[self.dim_names["longitude"]] = xr.where(lon > 180, lon - 360, lon)
+        else:
+            subdomain[self.dim_names["longitude"]] = xr.where(lon < 0, lon + 360, lon)
+
+        if return_subdomain:
+            return subdomain
+        else:
+            object.__setattr__(self, "ds", subdomain)
+
+    def convert_to_negative_depth(self):
+        """
+        Converts the depth values in the dataset to negative if they are non-negative.
+
+        This method checks the values in the depth dimension of the dataset (`self.ds[self.dim_names["depth"]]`).
+        If all values are greater than or equal to zero, it negates them and updates the dataset accordingly.
+
+        """
+        depth = self.ds[self.dim_names["depth"]]
+
+        if (depth >= 0).all():
+            self.ds[self.dim_names["depth"]] = -depth