diff --git a/docs/api.rst b/docs/api.rst index dd89363ba..75150e691 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -565,6 +565,19 @@ Azimuthal aggregations apply an aggregation (i.e. averaging) along circles of co UxDataArray.azimuthal_mean +Neighborhood +~~~~~~~~~~~~ + +Neighborhood filters apply an aggregation (i.e. averaging) to all grid elements within a circular +neighborhood of a specified radius around each grid element. + +.. autosummary:: + :toctree: generated/ + + UxDataArray.neighborhood_filter + UxDataset.neighborhood_filter + + Zonal Average ~~~~~~~~~~~~~ .. autosummary:: diff --git a/test/core/test_dataarray.py b/test/core/test_dataarray.py index b961a5a37..f172539a4 100644 --- a/test/core/test_dataarray.py +++ b/test/core/test_dataarray.py @@ -163,3 +163,96 @@ def test_data_location(): np.ones((3, uxgrid.n_face)), dims=["time", "n_face"], uxgrid=uxgrid ) assert face_time.data_location == "face_centered" + + +class TestNeighborhoodFilter: + """Tests for ``UxDataArray.neighborhood_filter``.""" + + def test_face_centered(self, gridpath, datasetpath): + """A large enough radius should average every face together.""" + uxds = ux.open_dataset( + gridpath("ugrid", "outCSne30", "outCSne30.ug"), + datasetpath("ugrid", "outCSne30", "outCSne30_vortex.nc"), + ) + uxda = uxds["psi"] + + # radius of 0 should select each face's own coordinate, leaving the + # data unchanged + filtered = uxda.neighborhood_filter(func=np.mean, r=0.0) + np.testing.assert_allclose(filtered.values, uxda.values) + + # a large enough radius should include the entire grid in the + # neighborhood of every face, so every filtered value should match + # the global mean of the field + filtered_all = uxda.neighborhood_filter(func=np.mean, r=360.0) + np.testing.assert_allclose(filtered_all.values, uxda.values.mean()) + + assert isinstance(filtered, UxDataArray) + assert filtered.uxgrid == uxda.uxgrid + assert filtered.dims == uxda.dims + assert filtered.shape == uxda.shape + + def test_node_centered(self): + """Neighborhood filter should work for node-centered data.""" + uxgrid = ux.Grid.from_healpix(zoom=1) + data = np.arange(uxgrid.n_node, dtype=float) + uxda = UxDataArray(data, dims=["n_node"], uxgrid=uxgrid, name="node_var") + + filtered = uxda.neighborhood_filter(func=np.mean, r=0.0) + np.testing.assert_allclose(filtered.values, data) + + filtered_all = uxda.neighborhood_filter(func=np.mean, r=360.0) + np.testing.assert_allclose(filtered_all.values, data.mean()) + + def test_edge_centered(self): + """Neighborhood filter should work for edge-centered data.""" + uxgrid = ux.Grid.from_healpix(zoom=1) + data = np.arange(uxgrid.n_edge, dtype=float) + uxda = UxDataArray(data, dims=["n_edge"], uxgrid=uxgrid, name="edge_var") + + filtered = uxda.neighborhood_filter(func=np.mean, r=0.0) + np.testing.assert_allclose(filtered.values, data) + + def test_custom_func_with_partial(self, gridpath, datasetpath): + """A user-defined function (i.e. ``functools.partial``) should work.""" + from functools import partial + + uxds = ux.open_dataset( + gridpath("ugrid", "outCSne30", "outCSne30.ug"), + datasetpath("ugrid", "outCSne30", "outCSne30_vortex.nc"), + ) + uxda = uxds["psi"] + + filtered_max = uxda.neighborhood_filter(func=np.max, r=5.0) + filtered_percentile = uxda.neighborhood_filter( + func=partial(np.percentile, q=100), r=5.0 + ) + + np.testing.assert_allclose(filtered_max.values, filtered_percentile.values) + + def test_extra_dimension_preserved(self, gridpath, datasetpath): + """An extra leading (i.e. time) dimension should be preserved.""" + uxds = ux.open_dataset( + gridpath("ugrid", "outCSne30", "outCSne30.ug"), + datasetpath("ugrid", "outCSne30", "outCSne30_vortex.nc"), + ) + uxda = uxds["psi"] + + data = np.stack([uxda.values, uxda.values * 2.0]) + uxda_time = UxDataArray( + data, dims=["time", "n_face"], uxgrid=uxda.uxgrid, name="psi_time" + ) + + filtered = uxda_time.neighborhood_filter(func=np.mean, r=0.0) + + assert filtered.dims == uxda_time.dims + assert filtered.shape == uxda_time.shape + np.testing.assert_allclose(filtered.values, data) + + def test_invalid_data_location(self): + """Data that is not mapped to a grid element should raise an error.""" + uxgrid = ux.Grid.from_healpix(zoom=1) + uxda = UxDataArray(np.ones(5), dims=["other_dim"], uxgrid=uxgrid) + + with pytest.raises(ValueError): + uxda.neighborhood_filter(func=np.mean, r=1.0) diff --git a/test/core/test_dataset.py b/test/core/test_dataset.py index ace56be19..cc32e1db4 100644 --- a/test/core/test_dataset.py +++ b/test/core/test_dataset.py @@ -170,3 +170,39 @@ def test_uxdataset_to_array(): assert arr1.name is None arr2 = uxds.to_array(dim='custom_dim', name='custom_name') assert arr2.name == 'custom_name' + + +class TestNeighborhoodFilter: + """Tests for ``UxDataset.neighborhood_filter``.""" + + def test_face_centered(self, gridpath, datasetpath): + """Ensures the dataset-level filter matches the per-variable + ``UxDataArray.neighborhood_filter`` results.""" + uxds = ux.open_dataset( + gridpath("ugrid", "outCSne30", "outCSne30.ug"), + datasetpath("ugrid", "outCSne30", "outCSne30_vortex.nc"), + ) + + filtered_ds = uxds.neighborhood_filter(func=np.mean, r=5.0) + filtered_da = uxds["psi"].neighborhood_filter(func=np.mean, r=5.0) + + assert isinstance(filtered_ds, UxDataset) + nt.assert_allclose(filtered_ds["psi"].values, filtered_da.values) + + def test_non_grid_variable_skipped(self): + """Data variables without a grid dimension should be left + untouched.""" + uxgrid = ux.Grid.from_healpix(zoom=1) + + uxds = UxDataset( + data_vars={ + "face_var": ("n_face", np.arange(uxgrid.n_face, dtype=float)), + "scalar_var": ("other_dim", np.array([1.0, 2.0, 3.0])), + }, + uxgrid=uxgrid, + ) + + filtered = uxds.neighborhood_filter(func=np.mean, r=0.0) + + nt.assert_allclose(filtered["face_var"].values, uxds["face_var"].values) + nt.assert_allclose(filtered["scalar_var"].values, uxds["scalar_var"].values) diff --git a/uxarray/core/dataarray.py b/uxarray/core/dataarray.py index a2b55a796..630b4b959 100644 --- a/uxarray/core/dataarray.py +++ b/uxarray/core/dataarray.py @@ -2,7 +2,7 @@ import warnings from html import escape -from typing import TYPE_CHECKING, Any, Hashable, Literal, Mapping, Optional +from typing import TYPE_CHECKING, Any, Callable, Hashable, Literal, Mapping, Optional from warnings import warn import cartopy.crs as ccrs @@ -14,6 +14,7 @@ from xarray.core.utils import UncachedAccessor import uxarray +from uxarray.constants import GRID_DIMS from uxarray.core.aggregation import _uxda_grid_aggregate from uxarray.core.gradient import ( _calculate_edge_face_difference, @@ -30,6 +31,7 @@ from uxarray.formatting_html import array_repr from uxarray.grid import Grid from uxarray.grid.dual import construct_dual +from uxarray.grid.neighbors import _neighborhood_filter from uxarray.grid.validation import _check_duplicate_nodes_indices from uxarray.io._healpix import get_zoom_from_cells from uxarray.plot.accessor import UxDataArrayPlotAccessor @@ -1986,6 +1988,7 @@ def isel( ValueError If more than one grid dimension is selected and `ignore_grid=False`. """ + from uxarray.core.dataarray import UxDataArray from uxarray.core.utils import _validate_indexers indexers, grid_dims = _validate_indexers( @@ -2185,6 +2188,60 @@ def get_dual(self): return uxda + def neighborhood_filter( + self, + func: Callable = np.mean, + r: float = 1.0, + ) -> UxDataArray: + """Apply a neighborhood filter, replacing the value at each grid + element with ``func`` applied to all elements within a circular + neighborhood of radius ``r``. + + Parameters + ---------- + func: Callable, default=np.mean + Apply this function to neighborhood. Must accept an ``axis`` keyword + argument (as ``np.mean``, ``np.median``, and similar NumPy reductions + do). Use ``functools.partial`` to supply additional arguments, e.g. + ``functools.partial(np.percentile, q=90)``. + r : float, default=1. + Radius of neighborhood. For spherical coordinates, the radius is in units of degrees, + and for cartesian coordinates, the radius is in meters. + + Returns + ------- + uxda_filter : UxDataArray + Filtered data. + """ + + if self._face_centered(): + data_mapping = "face centers" + elif self._node_centered(): + data_mapping = "nodes" + elif self._edge_centered(): + data_mapping = "edge centers" + else: + raise ValueError( + "Data_mapping is not face, node, or edge. Could not define data_mapping." + ) + + # Assert last dimension is a GRID dimension. + assert self.dims[-1] in GRID_DIMS, ( + f"expected last dimension of uxDataArray {self.data.dims[-1]} " + f"to be one of {GRID_DIMS}" + ) + + destination_data = _neighborhood_filter( + self.uxgrid, self.data, data_mapping, func=func, r=r + ) + + # Construct UxDataArray for filtered variable. + uxda_filter = self._copy() + + uxda_filter.data = destination_data + + return uxda_filter + def __getattribute__(self, name): """Intercept accessor method calls to return Ux-aware accessors.""" # Lazy import to avoid circular imports diff --git a/uxarray/core/dataset.py b/uxarray/core/dataset.py index 4331dd30d..d02180411 100644 --- a/uxarray/core/dataset.py +++ b/uxarray/core/dataset.py @@ -3,7 +3,7 @@ import os import sys from html import escape -from typing import IO, Any, Hashable, Mapping +from typing import IO, Any, Callable, Hashable, Mapping from warnings import warn import numpy as np @@ -13,6 +13,7 @@ from xarray.core.utils import UncachedAccessor import uxarray +from uxarray.constants import GRID_DIMS from uxarray.core.dataarray import UxDataArray from uxarray.core.utils import _map_dims_to_ugrid, _open_dataset_with_fallback from uxarray.formatting_html import dataset_repr @@ -655,6 +656,52 @@ def to_array( xarr = super().to_array(dim=dim, name=name) return UxDataArray(xarr, uxgrid=self.uxgrid) + def neighborhood_filter( + self, + func: Callable = np.mean, + r: float = 1.0, + ) -> UxDataset: + """Apply a neighborhood filter, replacing the value at each grid + element of every data variable with ``func`` applied to all elements + within a circular neighborhood of radius ``r``. + + Parameters + ---------- + func: Callable, default=np.mean + Apply this function to neighborhood. Must accept an ``axis`` keyword + argument (as ``np.mean``, ``np.median``, and similar NumPy reductions + do). Use ``functools.partial`` to supply additional arguments, e.g. + ``functools.partial(np.percentile, q=90)``. + r : float, default=1. + Radius of neighborhood. For spherical coordinates, the radius is in units of degrees, + and for cartesian coordinates, the radius is in meters. + + Returns + ------- + destination_uxds : UxDataset + Filtered dataset. + """ + + destination_uxds = self._copy() + # Loop through uxDataArrays in uxDataset + for var_name in self.data_vars: + uxda = self[var_name] + + # Skip if uxDataArray has no GRID dimension. + grid_dims = [dim for dim in uxda.dims if dim in GRID_DIMS] + if len(grid_dims) == 0: + continue + + # Put GRID dimension last for UxDataArray.neighborhood_filter. + remember_dim_order = uxda.dims + uxda = uxda.transpose(..., grid_dims[0]) + # Filter uxDataArray. + uxda = uxda.neighborhood_filter(func, r) + # Restore old dimension order. + destination_uxds[var_name] = uxda.transpose(*remember_dim_order) + + return destination_uxds + def to_xarray(self, grid_format: str = "UGRID") -> xr.Dataset: """ Converts a ``ux.UXDataset`` to a ``xr.Dataset``. diff --git a/uxarray/grid/grid.py b/uxarray/grid/grid.py index 2c753f85a..25b5f6b0a 100644 --- a/uxarray/grid/grid.py +++ b/uxarray/grid/grid.py @@ -1772,7 +1772,12 @@ def get_ball_tree( BallTree instance """ - if self._ball_tree is None or reconstruct: + if ( + self._ball_tree is None + or coordinates != self._ball_tree._coordinates + or coordinate_system != self._ball_tree.coordinate_system + or reconstruct + ): self._ball_tree = BallTree( self, coordinates=coordinates, @@ -1780,9 +1785,6 @@ def get_ball_tree( coordinate_system=coordinate_system, reconstruct=reconstruct, ) - else: - if coordinates != self._ball_tree._coordinates: - self._ball_tree.coordinates = coordinates return self._ball_tree @@ -1872,7 +1874,12 @@ def get_kd_tree( KDTree instance """ - if self._kd_tree is None or reconstruct: + if ( + self._kd_tree is None + or coordinates != self._kd_tree._coordinates + or coordinate_system != self._kd_tree.coordinate_system + or reconstruct + ): self._kd_tree = KDTree( self, coordinates=coordinates, @@ -1881,10 +1888,6 @@ def get_kd_tree( reconstruct=reconstruct, ) - else: - if coordinates != self._kd_tree._coordinates: - self._kd_tree.coordinates = coordinates - return self._kd_tree def get_spatial_hash( diff --git a/uxarray/grid/neighbors.py b/uxarray/grid/neighbors.py index 1c4d4f145..a34d15cda 100644 --- a/uxarray/grid/neighbors.py +++ b/uxarray/grid/neighbors.py @@ -1,3 +1,5 @@ +from typing import Callable + import numpy as np import xarray as xr from numba import njit @@ -1129,3 +1131,110 @@ def _construct_edge_face_distances(face_lon, face_lat, edge_faces): ) return edge_face_distances + + +def _get_element_coords(grid, data_mapping: str, coordinate_system: str): + """Gathers the coordinate array used to query a ``BallTree`` for a given + grid element location and coordinate system. + + Parameters + ---------- + grid : Grid + Source grid containing the coordinate arrays. + data_mapping : str + One of "nodes", "edge centers", or "face centers". + coordinate_system : str + Either "spherical" or "cartesian". + + Returns + ------- + coords : np.ndarray + Array of shape (n_elements, 2) for "spherical" (lon, lat) or + (n_elements, 3) for "cartesian" (x, y, z). + """ + prefix_map = { + "nodes": "node", + "edge centers": "edge", + "face centers": "face", + } + + if data_mapping not in prefix_map: + raise ValueError( + f"Invalid data_mapping. Expected 'nodes', 'edge centers', or 'face centers', " + f"but received: {data_mapping}" + ) + + prefix = prefix_map[data_mapping] + + if coordinate_system == "spherical": + lon = getattr(grid, f"{prefix}_lon").values + lat = getattr(grid, f"{prefix}_lat").values + return np.vstack((lon, lat)).T + + elif coordinate_system == "cartesian": + x = getattr(grid, f"{prefix}_x").values + y = getattr(grid, f"{prefix}_y").values + z = getattr(grid, f"{prefix}_z").values + return np.vstack((x, y, z)).T + + else: + raise ValueError( + f"Invalid coordinate_system. Expected either 'spherical' or 'cartesian', " + f"but received {coordinate_system}" + ) + + +def _neighborhood_filter( + grid, + data: np.ndarray, + data_mapping: str, + func: Callable = np.mean, + r: float = 1.0, +): + """Applies ``func`` to the set of grid elements within a circular + neighborhood of radius ``r`` around each element of ``data_mapping``. + + Parameters + ---------- + grid : Grid + Source grid used to construct the ``BallTree`` used for the + neighborhood queries. + data : np.ndarray + Data to filter. The grid dimension (``n_node``, ``n_edge``, or + ``n_face``) is expected to be the last axis. + data_mapping : str + One of "nodes", "edge centers", or "face centers", identifying which + grid element ``data`` is mapped to. + func : Callable, default=np.mean + Function applied to the values found in each neighborhood. Must + accept an ``axis`` keyword argument (as ``np.mean``, ``np.median``, + and similar NumPy reductions do) so that any extra, non-grid + dimensions (e.g. ``time``) are preserved rather than being collapsed. + r : float, default=1. + Radius of the neighborhood. For spherical coordinates, the radius is + in units of degrees, and for cartesian coordinates, the radius is in + meters. + + Returns + ------- + destination_data : np.ndarray + Filtered data, matching the shape of ``data``. + """ + + tree = grid.get_ball_tree(coordinates=data_mapping) + + coordinate_system = tree.coordinate_system + + dest_coords = _get_element_coords(grid, data_mapping, coordinate_system) + + neighbor_indices = tree.query_radius(dest_coords, r=r) + + destination_data = np.empty(data.shape) + + # Apply func along the last (grid) axis only, so any extra leading + # dimensions (e.g. time) are preserved rather than being collapsed. + for i, idx in enumerate(neighbor_indices): + if len(idx): + destination_data[..., i] = func(data[..., idx], axis=-1) + + return destination_data