Source code for rioxarray.rioxarray

"""
This module is an extension for xarray to provide rasterio capabilities
to xarray datasets/dataarrays.
"""
# pylint: disable=too-many-lines
import math
import warnings
from typing import Any, Dict, Hashable, Iterable, List, Literal, Optional, Tuple, Union

import numpy as np
import pyproj
import rasterio.warp
import rasterio.windows
import xarray
from affine import Affine
from rasterio.control import GroundControlPoint
from rasterio.crs import CRS

from rioxarray._options import EXPORT_GRID_MAPPING, get_option
from rioxarray.crs import crs_from_user_input
from rioxarray.exceptions import (
    DimensionError,
    DimensionMissingCoordinateError,
    InvalidDimensionOrder,
    MissingCRS,
    MissingSpatialDimensionError,
    NoDataInBounds,
    OneDimensionalRaster,
    RioXarrayError,
    TooManyDimensions,
)

DEFAULT_GRID_MAP = "spatial_ref"


def _affine_has_rotation(affine: Affine) -> bool:
    """
    Determine if the affine has rotation.

    Parameters
    ----------
    affine: :obj:`affine.Affine`
        The affine of the grid.

    Returns
    -------
    bool
    """
    return affine.b == affine.d != 0


def _resolution(affine: Affine) -> Tuple[float, float]:
    """
    Determine if the resolution of the affine.
    If it has rotation, the sign of the resolution is lost.

    Based on: https://github.com/mapbox/rasterio/blob/6185a4e4ad72b5669066d2d5004bf46d94a6d298/rasterio/_base.pyx#L943-L951

    Parameters
    ----------
    affine: :obj:`affine.Affine`
        The affine of the grid.


    Returns
    --------
    x_resolution: float
        The X resolution of the affine.
    y_resolution: float
        The Y resolution of the affine.
    """
    if not _affine_has_rotation(affine):
        return affine.a, affine.e
    return (
        math.sqrt(affine.a**2 + affine.d**2),
        math.sqrt(affine.b**2 + affine.e**2),
    )


def affine_to_coords(
    affine: Affine, width: int, height: int, x_dim: str = "x", y_dim: str = "y"
) -> Dict[str, np.ndarray]:
    """Generate 1d pixel centered coordinates from affine.

    Based on code from the xarray rasterio backend.

    Parameters
    ----------
    affine: :obj:`affine.Affine`
        The affine of the grid.
    width: int
        The width of the grid.
    height: int
        The height of the grid.
    x_dim: str, optional
        The name of the X dimension. Default is 'x'.
    y_dim: str, optional
        The name of the Y dimension. Default is 'y'.

    Returns
    -------
    dict: x and y coordinate arrays.

    """
    transform = affine * affine.translation(0.5, 0.5)
    if affine.is_rectilinear and not _affine_has_rotation(affine):
        x_coords, _ = transform * (np.arange(width), np.zeros(width))
        _, y_coords = transform * (np.zeros(height), np.arange(height))
    else:
        x_coords, y_coords = transform * np.meshgrid(
            np.arange(width),
            np.arange(height),
        )
    return {y_dim: y_coords, x_dim: x_coords}


def _generate_spatial_coords(affine: Affine, width: int, height: int) -> Dict[str, Any]:
    """get spatial coords in new transform"""
    new_spatial_coords = affine_to_coords(affine, width, height)
    if new_spatial_coords["x"].ndim == 1:
        return {
            "x": xarray.IndexVariable("x", new_spatial_coords["x"]),
            "y": xarray.IndexVariable("y", new_spatial_coords["y"]),
        }
    return {
        "xc": (("y", "x"), new_spatial_coords["x"]),
        "yc": (("y", "x"), new_spatial_coords["y"]),
    }


def _get_nonspatial_coords(
    src_data_array: Union[xarray.DataArray, xarray.Dataset]
) -> Dict[str, Union[xarray.Variable, xarray.IndexVariable]]:
    coords: Dict[str, Union[xarray.Variable, xarray.IndexVariable]] = {}
    for coord in set(src_data_array.coords) - {
        src_data_array.rio.x_dim,
        src_data_array.rio.y_dim,
        DEFAULT_GRID_MAP,
    }:
        if src_data_array[coord].dims:
            coords[coord] = xarray.IndexVariable(
                src_data_array[coord].dims,
                src_data_array[coord].values,
                src_data_array[coord].attrs,
            )
        else:
            coords[coord] = xarray.Variable(
                src_data_array[coord].dims,
                src_data_array[coord].values,
                src_data_array[coord].attrs,
            )
    return coords


def _make_coords(
    src_data_array: Union[xarray.DataArray, xarray.Dataset],
    dst_affine: Affine,
    dst_width: int,
    dst_height: int,
    force_generate: bool = False,
):
    """Generate the coordinates of the new projected `xarray.DataArray`"""
    coords = _get_nonspatial_coords(src_data_array)
    if force_generate or (
        src_data_array.rio.x_dim in src_data_array.coords
        and src_data_array.rio.y_dim in src_data_array.coords
    ):
        new_coords = _generate_spatial_coords(dst_affine, dst_width, dst_height)
        new_coords.update(coords)
        return new_coords
    return coords


def _get_data_var_message(obj: Union[xarray.DataArray, xarray.Dataset]) -> str:
    """
    Get message for named data variables.
    """
    try:
        return f" Data variable: {obj.name}" if obj.name else ""
    except AttributeError:
        return ""


def _get_spatial_dims(
    obj: Union[xarray.Dataset, xarray.DataArray], var: Union[Any, Hashable]
) -> Tuple[str, str]:
    """
    Retrieve the spatial dimensions of the dataset
    """
    try:
        return obj[var].rio.x_dim, obj[var].rio.y_dim
    except MissingSpatialDimensionError as err:
        try:
            obj[var].rio.set_spatial_dims(
                x_dim=obj.rio.x_dim, y_dim=obj.rio.x_dim, inplace=True
            )
            return obj.rio.x_dim, obj.rio.y_dim
        except MissingSpatialDimensionError:
            raise err from None


def _has_spatial_dims(
    obj: Union[xarray.Dataset, xarray.DataArray], var: Union[Any, Hashable]
) -> bool:
    """
    Check to see if the variable in the Dataset has spatial dimensions
    """
    try:
        # pylint: disable=pointless-statement
        _get_spatial_dims(obj, var)
    except MissingSpatialDimensionError:
        return False
    return True


[docs]class XRasterBase: """This is the base class for the GIS extensions for xarray""" def __init__(self, xarray_obj: Union[xarray.DataArray, xarray.Dataset]): self._obj: Union[xarray.DataArray, xarray.Dataset] = xarray_obj self._x_dim: Optional[Hashable] = None self._y_dim: Optional[Hashable] = None # Determine the spatial dimensions of the `xarray.DataArray` if "x" in self._obj.dims and "y" in self._obj.dims: self._x_dim = "x" self._y_dim = "y" elif "longitude" in self._obj.dims and "latitude" in self._obj.dims: self._x_dim = "longitude" self._y_dim = "latitude" else: # look for coordinates with CF attributes for coord in self._obj.coords: # make sure to only look in 1D coordinates # that has the same dimension name as the coordinate if self._obj.coords[coord].dims != (coord,): continue if (self._obj.coords[coord].attrs.get("axis", "").upper() == "X") or ( self._obj.coords[coord].attrs.get("standard_name", "").lower() in ("longitude", "projection_x_coordinate") ): self._x_dim = coord elif (self._obj.coords[coord].attrs.get("axis", "").upper() == "Y") or ( self._obj.coords[coord].attrs.get("standard_name", "").lower() in ("latitude", "projection_y_coordinate") ): self._y_dim = coord # properties self._count: Optional[int] = None self._height: Optional[int] = None self._width: Optional[int] = None self._crs: Union[rasterio.crs.CRS, None, Literal[False]] = None @property def crs(self) -> Optional[rasterio.crs.CRS]: """:obj:`rasterio.crs.CRS`: Retrieve projection from :obj:`xarray.Dataset` | :obj:`xarray.DataArray` """ if self._crs is not None: return None if self._crs is False else self._crs # look in wkt attributes to avoid using # pyproj CRS if possible for performance for crs_attr in ("spatial_ref", "crs_wkt"): try: self.set_crs( self._obj.coords[self.grid_mapping].attrs[crs_attr], inplace=True, ) return self._crs except KeyError: pass # look in grid_mapping try: self.set_crs( pyproj.CRS.from_cf(self._obj.coords[self.grid_mapping].attrs), inplace=True, ) except (KeyError, pyproj.exceptions.CRSError): try: # look in attrs for 'crs' self.set_crs(self._obj.attrs["crs"], inplace=True) except KeyError: self._crs = False return None return self._crs def _get_obj(self, inplace: bool) -> Union[xarray.Dataset, xarray.DataArray]: """ Get the object to modify. Parameters ---------- inplace: bool If True, returns self. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray` """ if inplace: return self._obj obj_copy = self._obj.copy(deep=True) # preserve attribute information obj_copy.rio._x_dim = self._x_dim obj_copy.rio._y_dim = self._y_dim obj_copy.rio._width = self._width obj_copy.rio._height = self._height obj_copy.rio._crs = self._crs return obj_copy
[docs] def set_crs( self, input_crs: Any, inplace: bool = True ) -> Union[xarray.Dataset, xarray.DataArray]: """ Set the CRS value for the Dataset/DataArray without modifying the dataset/data array. Parameters ---------- input_crs: object Anything accepted by `rasterio.crs.CRS.from_user_input`. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Dataset with crs attribute. """ crs = crs_from_user_input(input_crs) obj = self._get_obj(inplace=inplace) obj.rio._crs = crs return obj
@property def grid_mapping(self) -> str: """ str: The CF grid_mapping attribute. 'spatial_ref' is the default. """ grid_mapping = self._obj.encoding.get( "grid_mapping", self._obj.attrs.get("grid_mapping") ) if grid_mapping is not None: return grid_mapping grid_mapping = DEFAULT_GRID_MAP # search the dataset for the grid mapping name if hasattr(self._obj, "data_vars"): grid_mappings = set() for var in self._obj.data_vars: if not _has_spatial_dims(self._obj, var): continue var_grid_mapping = self._obj[var].encoding.get( "grid_mapping", self._obj[var].attrs.get("grid_mapping") ) if var_grid_mapping is not None: grid_mapping = var_grid_mapping grid_mappings.add(grid_mapping) if len(grid_mappings) > 1: raise RioXarrayError("Multiple grid mappings exist.") return grid_mapping
[docs] def write_grid_mapping( self, grid_mapping_name: str = DEFAULT_GRID_MAP, inplace: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Write the CF grid_mapping attribute. Parameters ---------- grid_mapping_name: str, optional Name of the grid_mapping coordinate. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with CF compliant CRS information. """ data_obj = self._get_obj(inplace=inplace) if hasattr(data_obj, "data_vars"): for var in data_obj.data_vars: try: x_dim, y_dim = _get_spatial_dims(data_obj, var) except MissingSpatialDimensionError: continue # remove grid_mapping from attributes if it exists # and update the grid_mapping in encoding new_attrs = dict(data_obj[var].attrs) new_attrs.pop("grid_mapping", None) data_obj[var].rio.update_encoding( dict(grid_mapping=grid_mapping_name), inplace=True ).rio.update_attrs(new_attrs, inplace=True).rio.set_spatial_dims( x_dim=x_dim, y_dim=y_dim, inplace=True ) # remove grid_mapping from attributes if it exists # and update the grid_mapping in encoding new_attrs = dict(data_obj.attrs) new_attrs.pop("grid_mapping", None) return data_obj.rio.update_encoding( dict(grid_mapping=grid_mapping_name), inplace=True ).rio.update_attrs(new_attrs, inplace=True)
[docs] def write_crs( self, input_crs: Any = None, grid_mapping_name: str = None, inplace: bool = False, ) -> Union[xarray.Dataset, xarray.DataArray]: """ Write the CRS to the dataset in a CF compliant manner. Parameters ---------- input_crs: Any Anything accepted by `rasterio.crs.CRS.from_user_input`. grid_mapping_name: str, optional Name of the grid_mapping coordinate to store the CRS information in. Default is the grid_mapping name of the dataset. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with CF compliant CRS information. Examples -------- Write the CRS of the current `xarray` object: >>> raster.rio.write_crs("epsg:4326", inplace=True) Write the CRS on a copy: >>> raster = raster.rio.write_crs("epsg:4326") """ if input_crs is not None: data_obj = self.set_crs(input_crs, inplace=inplace) else: data_obj = self._get_obj(inplace=inplace) # get original transform transform = self._cached_transform() # remove old grid maping coordinate if exists grid_mapping_name = ( self.grid_mapping if grid_mapping_name is None else grid_mapping_name ) try: del data_obj.coords[grid_mapping_name] except KeyError: pass if data_obj.rio.crs is None: raise MissingCRS( "CRS not found. Please set the CRS with 'rio.write_crs()'." ) # add grid mapping coordinate data_obj.coords[grid_mapping_name] = xarray.Variable((), 0) if get_option(EXPORT_GRID_MAPPING): grid_map_attrs = pyproj.CRS.from_user_input(data_obj.rio.crs).to_cf() else: grid_map_attrs = {} # spatial_ref is for compatibility with GDAL crs_wkt = data_obj.rio.crs.to_wkt() grid_map_attrs["spatial_ref"] = crs_wkt grid_map_attrs["crs_wkt"] = crs_wkt if transform is not None: grid_map_attrs["GeoTransform"] = " ".join( [str(item) for item in transform.to_gdal()] ) data_obj.coords[grid_mapping_name].rio.set_attrs(grid_map_attrs, inplace=True) # remove old crs if exists data_obj.attrs.pop("crs", None) return data_obj.rio.write_grid_mapping( grid_mapping_name=grid_mapping_name, inplace=True )
[docs] def estimate_utm_crs(self, datum_name: str = "WGS 84") -> rasterio.crs.CRS: """Returns the estimated UTM CRS based on the bounds of the dataset. .. versionadded:: 0.2 .. note:: Requires pyproj 3+ Parameters ---------- datum_name : str, optional The name of the datum to use in the query. Default is WGS 84. Returns ------- rasterio.crs.CRS """ # pylint: disable=import-outside-toplevel try: from pyproj.aoi import AreaOfInterest from pyproj.database import query_utm_crs_info # type: ignore except ImportError: raise RuntimeError("pyproj 3+ required for estimate_utm_crs.") from None if self.crs is None: raise RuntimeError("crs must be set to estimate UTM CRS.") # ensure using geographic coordinates if self.crs.is_geographic: # pylint: disable=no-member minx, miny, maxx, maxy = self.bounds(recalc=True) else: minx, miny, maxx, maxy = self.transform_bounds("EPSG:4326", recalc=True) x_center = np.mean([minx, maxx]) y_center = np.mean([miny, maxy]) utm_crs_list = query_utm_crs_info( datum_name=datum_name, area_of_interest=AreaOfInterest( west_lon_degree=x_center, south_lat_degree=y_center, east_lon_degree=x_center, north_lat_degree=y_center, ), ) try: return CRS.from_epsg(utm_crs_list[0].code) except IndexError: raise RuntimeError("Unable to determine UTM CRS") from None
def _cached_transform(self) -> Optional[Affine]: """ Get the transform from: 1. The GeoTransform metatada property in the grid mapping 2. The transform attribute. """ try: # look in grid_mapping transform = np.fromstring( self._obj.coords[self.grid_mapping].attrs["GeoTransform"], sep=" " ) # Calling .tolist() to assure the arguments are Python float and JSON serializable return Affine.from_gdal(*transform.tolist()) except KeyError: try: return Affine(*self._obj.attrs["transform"][:6]) except KeyError: pass return None
[docs] def write_transform( self, transform: Optional[Affine] = None, grid_mapping_name: Optional[str] = None, inplace: bool = False, ) -> Union[xarray.Dataset, xarray.DataArray]: """ .. versionadded:: 0.0.30 Write the GeoTransform to the dataset where GDAL can read it in. https://gdal.org/drivers/raster/netcdf.html#georeference Parameters ---------- transform: affine.Affine, optional The transform of the dataset. If not provided, it will be calculated. grid_mapping_name: str, optional Name of the grid_mapping coordinate to store the transform information in. Default is the grid_mapping name of the dataset. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with Geo Transform written. """ transform = transform or self.transform(recalc=True) data_obj = self._get_obj(inplace=inplace) # delete the old attribute to prevent confusion data_obj.attrs.pop("transform", None) grid_mapping_name = ( self.grid_mapping if grid_mapping_name is None else grid_mapping_name ) try: grid_map_attrs = data_obj.coords[grid_mapping_name].attrs.copy() except KeyError: data_obj.coords[grid_mapping_name] = xarray.Variable((), 0) grid_map_attrs = data_obj.coords[grid_mapping_name].attrs.copy() grid_map_attrs["GeoTransform"] = " ".join( [str(item) for item in transform.to_gdal()] ) data_obj.coords[grid_mapping_name].rio.set_attrs(grid_map_attrs, inplace=True) return data_obj.rio.write_grid_mapping( grid_mapping_name=grid_mapping_name, inplace=True )
[docs] def transform(self, recalc: bool = False) -> Affine: """ Parameters ---------- recalc: bool, optional If True, it will re-calculate the transform instead of using the cached transform. Returns ------- :obj:`affine.Afffine`: The affine of the :obj:`xarray.Dataset` | :obj:`xarray.DataArray` """ transform = self._cached_transform() if transform and ( not transform.is_rectilinear or _affine_has_rotation(transform) ): if recalc: warnings.warn( "Transform that is non-rectilinear or with rotation found. " "Unable to recalculate." ) return transform try: src_left, _, _, src_top = self.bounds(recalc=recalc) src_resolution_x, src_resolution_y = self.resolution(recalc=recalc) except (DimensionMissingCoordinateError, DimensionError): return Affine.identity() if transform is None else transform return Affine.translation(src_left, src_top) * Affine.scale( src_resolution_x, src_resolution_y )
[docs] def write_coordinate_system( self, inplace: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Write the coordinate system CF metadata. .. versionadded:: 0.0.30 Parameters ---------- inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: The dataset with the CF coordinate system attributes added. """ data_obj = self._get_obj(inplace=inplace) # add metadata to x,y coordinates is_projected = data_obj.rio.crs and data_obj.rio.crs.is_projected is_geographic = data_obj.rio.crs and data_obj.rio.crs.is_geographic x_coord_attrs = dict(data_obj.coords[self.x_dim].attrs) x_coord_attrs["axis"] = "X" y_coord_attrs = dict(data_obj.coords[self.y_dim].attrs) y_coord_attrs["axis"] = "Y" if is_projected: units = None if hasattr(data_obj.rio.crs, "linear_units_factor"): unit_factor = data_obj.rio.crs.linear_units_factor[-1] if unit_factor != 1: units = f"{unit_factor} metre" else: units = "metre" # X metadata x_coord_attrs["long_name"] = "x coordinate of projection" x_coord_attrs["standard_name"] = "projection_x_coordinate" if units: x_coord_attrs["units"] = units # Y metadata y_coord_attrs["long_name"] = "y coordinate of projection" y_coord_attrs["standard_name"] = "projection_y_coordinate" if units: y_coord_attrs["units"] = units elif is_geographic: # X metadata x_coord_attrs["long_name"] = "longitude" x_coord_attrs["standard_name"] = "longitude" x_coord_attrs["units"] = "degrees_east" # Y metadata y_coord_attrs["long_name"] = "latitude" y_coord_attrs["standard_name"] = "latitude" y_coord_attrs["units"] = "degrees_north" data_obj.coords[self.y_dim].attrs = y_coord_attrs data_obj.coords[self.x_dim].attrs = x_coord_attrs return data_obj
[docs] def set_attrs( self, new_attrs: Dict, inplace: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Set the attributes of the dataset/dataarray and reset rioxarray properties to re-search for them. Parameters ---------- new_attrs: dict A dictionary of new attributes. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with new attributes. """ data_obj = self._get_obj(inplace=inplace) # set the attributes data_obj.attrs = new_attrs # reset rioxarray properties depending # on attributes to be generated data_obj.rio._nodata = None data_obj.rio._crs = None return data_obj
[docs] def update_attrs( self, new_attrs: Dict, inplace: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Update the attributes of the dataset/dataarray and reset rioxarray properties to re-search for them. Parameters ---------- new_attrs: dict A dictionary of new attributes to update with. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with updated attributes. """ data_attrs = dict(self._obj.attrs) data_attrs.update(**new_attrs) return self.set_attrs(data_attrs, inplace=inplace)
[docs] def set_encoding( self, new_encoding: Dict, inplace: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Set the encoding of the dataset/dataarray and reset rioxarray properties to re-search for them. .. versionadded:: 0.4 Parameters ---------- new_encoding: dict A dictionary for encoding. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with new attributes. """ data_obj = self._get_obj(inplace=inplace) # set the attributes data_obj.encoding = new_encoding # reset rioxarray properties depending # on attributes to be generated data_obj.rio._nodata = None data_obj.rio._crs = None return data_obj
[docs] def update_encoding( self, new_encoding: Dict, inplace: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Update the encoding of the dataset/dataarray and reset rioxarray properties to re-search for them. .. versionadded:: 0.4 Parameters ---------- new_encoding: dict A dictionary with encoding values to update with. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with updated attributes. """ data_encoding = dict(self._obj.encoding) data_encoding.update(**new_encoding) return self.set_encoding(data_encoding, inplace=inplace)
[docs] def set_spatial_dims( self, x_dim: str, y_dim: str, inplace: bool = True ) -> Union[xarray.Dataset, xarray.DataArray]: """ This sets the spatial dimensions of the dataset. Parameters ---------- x_dim: str The name of the x dimension. y_dim: str The name of the y dimension. inplace: bool, optional If True, it will modify the dataframe in place. Otherwise it will return a modified copy. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Dataset with spatial dimensions set. """ data_obj = self._get_obj(inplace=inplace) if x_dim in data_obj.dims: data_obj.rio._x_dim = x_dim else: raise MissingSpatialDimensionError( f"x dimension ({x_dim}) not found.{_get_data_var_message(data_obj)}" ) if y_dim in data_obj.dims: data_obj.rio._y_dim = y_dim else: raise MissingSpatialDimensionError( f"y dimension ({y_dim}) not found.{_get_data_var_message(data_obj)}" ) return data_obj
@property def x_dim(self) -> Hashable: """Hashable: The dimension for the X-axis.""" if self._x_dim is not None: return self._x_dim raise MissingSpatialDimensionError( "x dimension not found. 'rio.set_spatial_dims()' or " "using 'rename()' to change the dimension name to 'x' can address this." f"{_get_data_var_message(self._obj)}" ) @property def y_dim(self) -> Hashable: """Hashable: The dimension for the Y-axis.""" if self._y_dim is not None: return self._y_dim raise MissingSpatialDimensionError( "y dimension not found. 'rio.set_spatial_dims()' or " "using 'rename()' to change the dimension name to 'y' can address this." f"{_get_data_var_message(self._obj)}" ) @property def width(self) -> int: """int: Returns the width of the dataset (x dimension size)""" if self._width is not None: return self._width self._width = self._obj[self.x_dim].size return self._width @property def height(self) -> int: """int: Returns the height of the dataset (y dimension size)""" if self._height is not None: return self._height self._height = self._obj[self.y_dim].size return self._height @property def shape(self) -> Tuple[int, int]: """tuple(int, int): Returns the shape (height, width)""" return (self.height, self.width) def _check_dimensions(self) -> Optional[str]: """ This function validates that the dimensions 2D/3D and they are are in the proper order. Returns ------- str or None: Name extra dimension. """ extra_dims = tuple(set(list(self._obj.dims)) - set([self.x_dim, self.y_dim])) if len(extra_dims) > 1: raise TooManyDimensions( "Only 2D and 3D data arrays supported." f"{_get_data_var_message(self._obj)}" ) if extra_dims and self._obj.dims != (extra_dims[0], self.y_dim, self.x_dim): dim_info: Tuple = (extra_dims[0], self.y_dim, self.x_dim) raise InvalidDimensionOrder( f"Invalid dimension order. Expected order: {dim_info}. " f"You can use `DataArray.transpose{dim_info}`" " to reorder your dimensions." f"{_get_data_var_message(self._obj)}" ) if not extra_dims and self._obj.dims != (self.y_dim, self.x_dim): dim_info = (self.y_dim, self.x_dim) raise InvalidDimensionOrder( f"Invalid dimension order. Expected order: {dim_info}. " f"You can use `DataArray.transpose{dim_info}`" " to reorder your dimensions." f"{_get_data_var_message(self._obj)}" ) return str(extra_dims[0]) if extra_dims else None @property def count(self) -> int: """int: Returns the band count (z dimension size)""" if self._count is not None: return self._count extra_dim = self._check_dimensions() self._count = 1 if extra_dim is not None: self._count = self._obj[extra_dim].size return self._count def _internal_bounds(self) -> Tuple[float, float, float, float]: """Determine the internal bounds of the `xarray.DataArray`""" if self.x_dim not in self._obj.coords: raise DimensionMissingCoordinateError(f"{self.x_dim} missing coordinates.") if self.y_dim not in self._obj.coords: raise DimensionMissingCoordinateError(f"{self.y_dim} missing coordinates.") try: left = float(self._obj[self.x_dim][0]) right = float(self._obj[self.x_dim][-1]) top = float(self._obj[self.y_dim][0]) bottom = float(self._obj[self.y_dim][-1]) except IndexError: raise NoDataInBounds( "Unable to determine bounds from coordinates." f"{_get_data_var_message(self._obj)}" ) from None return left, bottom, right, top
[docs] def resolution(self, recalc: bool = False) -> Tuple[float, float]: """ Determine if the resolution of the grid. If the transformation has rotation, the sign of the resolution is lost. Parameters ---------- recalc: bool, optional Will force the resolution to be recalculated instead of using the transform attribute. Returns ------- x_resolution, y_resolution: float The resolution of the `xarray.DataArray` | `xarray.Dataset` """ transform = self._cached_transform() if ( not recalc or self.width == 1 or self.height == 1 ) and transform is not None: return _resolution(transform) # if the coordinates of the spatial dimensions are missing # use the cached transform resolution try: left, bottom, right, top = self._internal_bounds() except DimensionMissingCoordinateError: if transform is None: raise return _resolution(transform) if self.width == 1 or self.height == 1: raise OneDimensionalRaster( "Only 1 dimenional array found. Cannot calculate the resolution." f"{_get_data_var_message(self._obj)}" ) resolution_x = (right - left) / (self.width - 1) resolution_y = (bottom - top) / (self.height - 1) return resolution_x, resolution_y
[docs] def bounds(self, recalc: bool = False) -> Tuple[float, float, float, float]: """ Parameters ---------- recalc: bool, optional Will force the bounds to be recalculated instead of using the transform attribute. Returns ------- left, bottom, right, top: float Outermost coordinates of the `xarray.DataArray` | `xarray.Dataset`. """ resolution_x, resolution_y = self.resolution(recalc=recalc) try: # attempt to get bounds from xarray coordinate values left, bottom, right, top = self._internal_bounds() left -= resolution_x / 2.0 right += resolution_x / 2.0 top -= resolution_y / 2.0 bottom += resolution_y / 2.0 except DimensionMissingCoordinateError as error: transform = self._cached_transform() if not transform: raise RioXarrayError("Transform not able to be determined.") from error left = transform.c top = transform.f right = left + resolution_x * self.width bottom = top + resolution_y * self.height return left, bottom, right, top
[docs] def isel_window( self, window: rasterio.windows.Window, pad: bool = False ) -> Union[xarray.Dataset, xarray.DataArray]: """ Use a rasterio.windows.Window to select a subset of the data. .. versionadded:: 0.6.0 pad .. warning:: Float indices are converted to integers. Parameters ---------- window: :class:`rasterio.windows.Window` The window of the dataset to read. pad: bool, default=False Set to True to expand returned DataArray to dimensions of the window Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: The data in the window. """ (row_start, row_stop), (col_start, col_stop) = window.toranges() row_start = 0 if row_start < 0 else math.floor(row_start) row_stop = 0 if row_stop < 0 else math.ceil(row_stop) col_start = 0 if col_start < 0 else math.floor(col_start) col_stop = 0 if col_stop < 0 else math.ceil(col_stop) row_slice = slice(int(row_start), int(row_stop)) col_slice = slice(int(col_start), int(col_stop)) array_subset = ( self._obj.isel({self.y_dim: row_slice, self.x_dim: col_slice}) .copy() # this is to prevent sharing coordinates with the original dataset .rio.set_spatial_dims(x_dim=self.x_dim, y_dim=self.y_dim, inplace=True) .rio.write_transform( transform=rasterio.windows.transform( rasterio.windows.Window.from_slices( rows=row_slice, cols=col_slice, width=self.width, height=self.height, ), self.transform(recalc=True), ), inplace=True, ) ) if pad: return array_subset.rio.pad_box( *rasterio.windows.bounds(window, self.transform(recalc=True)) ) return array_subset
[docs] def slice_xy( self, minx: float, miny: float, maxx: float, maxy: float, ) -> Union[xarray.Dataset, xarray.DataArray]: """Slice the array by x,y bounds. Parameters ---------- minx: float Minimum bound for x coordinate. miny: float Minimum bound for y coordinate. maxx: float Maximum bound for x coordinate. maxy: float Maximum bound for y coordinate. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: The data in the slice. """ left, bottom, right, top = self._internal_bounds() if top > bottom: y_slice = slice(maxy, miny) else: y_slice = slice(miny, maxy) if left > right: x_slice = slice(maxx, minx) else: x_slice = slice(minx, maxx) subset = ( self._obj.sel({self.x_dim: x_slice, self.y_dim: y_slice}) .copy() # this is to prevent sharing coordinates with the original dataset .rio.set_spatial_dims(x_dim=self.x_dim, y_dim=self.y_dim, inplace=True) .rio.write_transform(inplace=True) ) return subset
[docs] def transform_bounds( self, dst_crs: Any, densify_pts: int = 21, recalc: bool = False ) -> Tuple[float, float, float, float]: """Transform bounds from src_crs to dst_crs. Optionally densifying the edges (to account for nonlinear transformations along these edges) and extracting the outermost bounds. Note: this does not account for the antimeridian. Parameters ---------- dst_crs: str, :obj:`rasterio.crs.CRS`, or dict Target coordinate reference system. densify_pts: uint, optional Number of points to add to each edge to account for nonlinear edges produced by the transform process. Large numbers will produce worse performance. Default: 21 (gdal default). recalc: bool, optional Will force the bounds to be recalculated instead of using the transform attribute. Returns ------- left, bottom, right, top: float Outermost coordinates in target coordinate reference system. """ return rasterio.warp.transform_bounds( self.crs, dst_crs, *self.bounds(recalc=recalc), densify_pts=densify_pts )
[docs] def write_gcps( self, gcps: Iterable[GroundControlPoint], gcp_crs: Any, grid_mapping_name: str = None, inplace: bool = False, ) -> Union[xarray.Dataset, xarray.DataArray]: """ Write the GroundControlPoints to the dataset. https://rasterio.readthedocs.io/en/latest/topics/georeferencing.html#ground-control-points Parameters ---------- gcp: list of :obj:`rasterio.control.GroundControlPoint` The Ground Control Points to integrate to the dataset. gcp_crs: str, :obj:`rasterio.crs.CRS`, or dict Coordinate reference system for the GCPs. grid_mapping_name: str, optional Name of the grid_mapping coordinate to store the GCPs information in. Default is the grid_mapping name of the dataset. inplace: bool, optional If True, it will write to the existing dataset. Default is False. Returns ------- :obj:`xarray.Dataset` | :obj:`xarray.DataArray`: Modified dataset with Ground Control Points written. """ grid_mapping_name = ( self.grid_mapping if grid_mapping_name is None else grid_mapping_name ) data_obj = self._get_obj(inplace=True) data_obj = data_obj.rio.write_crs( gcp_crs, grid_mapping_name=grid_mapping_name, inplace=inplace ) geojson_gcps = _convert_gcps_to_geojson(gcps) data_obj.coords[grid_mapping_name].attrs["gcps"] = geojson_gcps return data_obj
[docs] def get_gcps(self) -> Optional[List[GroundControlPoint]]: """ Get the GroundControlPoints from the dataset. https://rasterio.readthedocs.io/en/latest/topics/georeferencing.html#ground-control-points Returns ------- list of :obj:`rasterio.control.GroundControlPoint` or None The Ground Control Points from the dataset or None if not applicable """ try: geojson_gcps = self._obj.coords[self.grid_mapping].attrs["gcps"] except (KeyError, AttributeError): return None gcps = [ GroundControlPoint( x=gcp["geometry"]["coordinates"][0], y=gcp["geometry"]["coordinates"][1], z=gcp["geometry"]["coordinates"][2], row=gcp["properties"]["row"], col=gcp["properties"]["col"], id=gcp["properties"]["id"], info=gcp["properties"]["info"], ) for gcp in geojson_gcps["features"] ] return gcps
def _convert_gcps_to_geojson( gcps: Iterable[GroundControlPoint], ) -> Dict: """ Convert GCPs to geojson. Parameters ---------- gcps: The list of GroundControlPoint instances. Returns ------- A FeatureCollection dict. """ features = [ dict( type="Feature", properties=dict(id=gcp.id, info=gcp.info, row=gcp.row, col=gcp.col), geometry=dict(type="Point", coordinates=[gcp.x, gcp.y, gcp.z]), ) for gcp in gcps ] return dict(type="FeatureCollection", features=features)