"""DEM class and functions."""
from __future__ import annotations
import pathlib
import warnings
from typing import Any, Literal, overload
import geopandas as gpd
import numpy as np
import rasterio as rio
from affine import Affine
from geoutils import SatelliteImage
from geoutils.raster import Mask, RasterType
from pyproj import CRS
from pyproj.crs import CompoundCRS, VerticalCRS
from skgstat import Variogram
from xdem import coreg, terrain
from xdem._typing import MArrayf, NDArrayb, NDArrayf
from xdem.misc import copy_doc
from xdem.spatialstats import (
infer_heteroscedasticity_from_stable,
infer_spatial_correlation_from_stable,
)
from xdem.vcrs import (
_build_ccrs_from_crs_and_vcrs,
_grid_from_user_input,
_parse_vcrs_name_from_product,
_transform_zz,
_vcrs_from_crs,
_vcrs_from_user_input,
)
dem_attrs = ["_vcrs", "_vcrs_name", "_vcrs_grid"]
[docs]
class DEM(SatelliteImage): # type: ignore
"""
The digital elevation model.
The DEM has a single main attribute in addition to that inherited from :class:`geoutils.Raster`:
vcrs: :class:`pyproj.VerticalCRS`
Vertical coordinate reference system of the DEM.
Other derivative attributes are:
vcrs_name: :class:`str`
Name of vertical CRS of the DEM.
vcrs_grid: :class:`str`
Grid path to the vertical CRS of the DEM.
ccrs: :class:`pyproj.CompoundCRS`
Compound vertical and horizontal CRS of the DEM.
The attributes inherited from :class:`geoutils.Raster` are:
data: :class:`np.ndarray`
Data array of the DEM, with dimensions corresponding to (count, height, width).
transform: :class:`affine.Affine`
Geotransform of the DEM.
crs: :class:`pyproj.crs.CRS`
Coordinate reference system of the DEM.
nodata: :class:`int` or :class:`float`
Nodata value of the DEM.
All other attributes are derivatives of those attributes, or read from the file on disk.
See the API for more details.
"""
[docs]
def __init__(
self,
filename_or_dataset: str | RasterType | rio.io.DatasetReader | rio.io.MemoryFile,
vcrs: Literal["Ellipsoid"]
| Literal["EGM08"]
| Literal["EGM96"]
| VerticalCRS
| str
| pathlib.Path
| int
| None = None,
silent: bool = True,
**kwargs: Any,
) -> None:
"""
Instantiate a digital elevation model.
The vertical reference of the DEM can be defined by passing the `vcrs` argument.
Otherwise, a vertical reference is tentatively parsed from the DEM product name.
Inherits all attributes from the :class:`geoutils.Raster` and :class:`geoutils.SatelliteImage` classes.
:param filename_or_dataset: The filename of the dataset.
:param vcrs: Vertical coordinate reference system either as a name ("WGS84", "EGM08", "EGM96"),
an EPSG code or pyproj.crs.VerticalCRS, or a path to a PROJ grid file (https://github.com/OSGeo/PROJ-data).
:param silent: Whether to display vertical reference parsing.
"""
self.data: NDArrayf
self._vcrs: VerticalCRS | Literal["Ellipsoid"] | None = None
self._vcrs_name: str | None = None
self._vcrs_grid: str | None = None
# If DEM is passed, simply point back to DEM
if isinstance(filename_or_dataset, DEM):
for key in filename_or_dataset.__dict__:
setattr(self, key, filename_or_dataset.__dict__[key])
return
# Else rely on parent SatelliteImage class options (including raised errors)
else:
with warnings.catch_warnings():
warnings.filterwarnings("ignore", message="Parse metadata from file not implemented")
super().__init__(filename_or_dataset, silent=silent, **kwargs)
# Ensure DEM has only one band: self.bands can be None when data is not loaded through the Raster class
if self.bands is not None and len(self.bands) > 1:
raise ValueError("DEM rasters should be composed of one band only")
# If the CRS in the raster metadata has a 3rd dimension, could set it as a vertical reference
vcrs_from_crs = _vcrs_from_crs(CRS(self.crs))
if vcrs_from_crs is not None:
# If something was also provided by the user, user takes precedence
# (we leave vcrs as it was for input)
if vcrs is not None:
# Raise a warning if the two are not the same
vcrs_user = _vcrs_from_user_input(vcrs)
if not vcrs_from_crs == vcrs_user:
warnings.warn(
"The CRS in the raster metadata already has a vertical component, "
"the user-input '{}' will override it.".format(vcrs)
)
# Otherwise, use the one from the raster 3D CRS
else:
vcrs = vcrs_from_crs
# If no vertical CRS was provided by the user or defined in the CRS
if vcrs is None:
vcrs = _parse_vcrs_name_from_product(self.product)
# If a vertical reference was parsed or provided by user
if vcrs is not None:
self.set_vcrs(vcrs)
def copy(self, new_array: NDArrayf | None = None) -> DEM:
"""
Copy the DEM, possibly updating the data array.
:param new_array: New data array.
:return: Copied DEM.
"""
new_dem = super().copy(new_array=new_array) # type: ignore
# The rest of attributes are immutable, including pyproj.CRS
for attrs in dem_attrs:
setattr(new_dem, attrs, getattr(self, attrs))
return new_dem # type: ignore
[docs]
@classmethod
def from_array(
cls: type[DEM],
data: NDArrayf | MArrayf,
transform: tuple[float, ...] | Affine,
crs: CRS | int | None,
nodata: int | float | None = None,
area_or_point: Literal["Area", "Point"] | None = None,
tags: dict[str, Any] = None,
cast_nodata: bool = True,
vcrs: Literal["Ellipsoid"]
| Literal["EGM08"]
| Literal["EGM96"]
| str
| pathlib.Path
| VerticalCRS
| int
| None = None,
) -> DEM:
"""Create a DEM from a numpy array and the georeferencing information.
:param data: Input array.
:param transform: Affine 2D transform. Either a tuple(x_res, 0.0, top_left_x,
0.0, y_res, top_left_y) or an affine.Affine object.
:param crs: Coordinate reference system. Either a rasterio CRS, or an EPSG integer.
:param nodata: Nodata value.
:param area_or_point: Pixel interpretation of the raster, will be stored in AREA_OR_POINT metadata.
:param tags: Metadata stored in a dictionary.
:param cast_nodata: Automatically cast nodata value to the default nodata for the new array type if not
compatible. If False, will raise an error when incompatible.
:param vcrs: Vertical coordinate reference system.
:returns: DEM created from the provided array and georeferencing.
"""
# We first apply the from_array of the parent class
rast = SatelliteImage.from_array(
data=data,
transform=transform,
crs=crs,
nodata=nodata,
area_or_point=area_or_point,
tags=tags,
cast_nodata=cast_nodata,
)
# Then add the vcrs to the class call (that builds on top of the parent class)
return cls(filename_or_dataset=rast, vcrs=vcrs)
@property
def vcrs(self) -> VerticalCRS | Literal["Ellipsoid"] | None:
"""Vertical coordinate reference system of the DEM."""
return self._vcrs
@property
def vcrs_grid(self) -> str | None:
"""Grid path of vertical coordinate reference system of the DEM."""
return self._vcrs_grid
@property
def vcrs_name(self) -> str | None:
"""Name of vertical coordinate reference system of the DEM."""
if self.vcrs is not None:
# If it is the ellipsoid
if isinstance(self.vcrs, str):
# Need to call CRS() here to make it work with rasterio.CRS...
vcrs_name = f"Ellipsoid (No vertical CRS). Datum: {CRS(self.crs).ellipsoid.name}."
# Otherwise, return the vertical reference name
else:
vcrs_name = self.vcrs.name
else:
vcrs_name = None
return vcrs_name
[docs]
def set_vcrs(
self,
new_vcrs: Literal["Ellipsoid"] | Literal["EGM08"] | Literal["EGM96"] | str | pathlib.Path | VerticalCRS | int,
) -> None:
"""
Set the vertical coordinate reference system of the DEM.
:param new_vcrs: Vertical coordinate reference system either as a name ("Ellipsoid", "EGM08", "EGM96"),
an EPSG code or pyproj.crs.VerticalCRS, or a path to a PROJ grid file (https://github.com/OSGeo/PROJ-data).
"""
# Get vertical CRS and set it and the grid
self._vcrs = _vcrs_from_user_input(vcrs_input=new_vcrs)
self._vcrs_grid = _grid_from_user_input(vcrs_input=new_vcrs)
@property
def ccrs(self) -> CompoundCRS | CRS | None:
"""Compound horizontal and vertical coordinate reference system of the DEM."""
if self.vcrs is not None:
ccrs = _build_ccrs_from_crs_and_vcrs(crs=self.crs, vcrs=self.vcrs)
return ccrs
else:
return None
@overload
def to_vcrs(
self,
vcrs: Literal["Ellipsoid", "EGM08", "EGM96"] | str | pathlib.Path | VerticalCRS | int,
force_source_vcrs: Literal["Ellipsoid", "EGM08", "EGM96"]
| str
| pathlib.Path
| VerticalCRS
| int
| None = None,
*,
inplace: Literal[False] = False,
) -> DEM:
...
@overload
def to_vcrs(
self,
vcrs: Literal["Ellipsoid", "EGM08", "EGM96"] | str | pathlib.Path | VerticalCRS | int,
force_source_vcrs: Literal["Ellipsoid", "EGM08", "EGM96"]
| str
| pathlib.Path
| VerticalCRS
| int
| None = None,
*,
inplace: Literal[True],
) -> None:
...
@overload
def to_vcrs(
self,
vcrs: Literal["Ellipsoid", "EGM08", "EGM96"] | str | pathlib.Path | VerticalCRS | int,
force_source_vcrs: Literal["Ellipsoid", "EGM08", "EGM96"]
| str
| pathlib.Path
| VerticalCRS
| int
| None = None,
*,
inplace: bool = False,
) -> DEM | None:
...
[docs]
def to_vcrs(
self,
vcrs: Literal["Ellipsoid", "EGM08", "EGM96"] | str | pathlib.Path | VerticalCRS | int,
force_source_vcrs: Literal["Ellipsoid", "EGM08", "EGM96"]
| str
| pathlib.Path
| VerticalCRS
| int
| None = None,
inplace: bool = False,
) -> DEM | None:
"""
Convert the DEM to another vertical coordinate reference system.
:param vcrs: Destination vertical CRS. Either as a name ("WGS84", "EGM08", "EGM96"),
an EPSG code or pyproj.crs.VerticalCRS, or a path to a PROJ grid file (https://github.com/OSGeo/PROJ-data)
:param force_source_vcrs: Force a source vertical CRS (uses metadata by default). Same formats as for `vcrs`.
:param inplace: Whether to return a new DEM (default) or the same DEM updated in-place.
:return: DEM with vertical reference transformed, or None.
"""
if self.vcrs is None and force_source_vcrs is None:
raise ValueError(
"The current DEM has no vertical reference, define one with .set_vref() "
"or by passing `src_vcrs` to perform a conversion."
)
# Initial Compound CRS (only exists if vertical CRS is not None, as checked above)
if force_source_vcrs is not None:
# Warn if a vertical CRS already existed for that DEM
if self.vcrs is not None:
warnings.warn(
category=UserWarning,
message="Overriding the vertical CRS of the DEM with the one provided in `src_vcrs`.",
)
src_ccrs = _build_ccrs_from_crs_and_vcrs(self.crs, vcrs=force_source_vcrs)
else:
src_ccrs = self.ccrs
# New destination Compound CRS
dst_ccrs = _build_ccrs_from_crs_and_vcrs(self.crs, vcrs=_vcrs_from_user_input(vcrs_input=vcrs))
# If both compound CCRS are equal, do not run any transform
if src_ccrs.equals(dst_ccrs):
warnings.warn(
message="Source and destination vertical CRS are the same, skipping vertical transformation.",
category=UserWarning,
)
return None
# Transform elevation with new vertical CRS
zz = self.data
xx, yy = self.coords()
zz_trans = _transform_zz(crs_from=src_ccrs, crs_to=dst_ccrs, xx=xx, yy=yy, zz=zz)
new_data = zz_trans.astype(self.dtype) # type: ignore
# If inplace, update DEM and vcrs
if inplace:
self._data = new_data
self.set_vcrs(new_vcrs=vcrs)
return None
# Otherwise, return new DEM
else:
return DEM.from_array(
data=new_data,
transform=self.transform,
crs=self.crs,
nodata=self.nodata,
area_or_point=self.area_or_point,
tags=self.tags,
vcrs=vcrs,
cast_nodata=False,
)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def slope(
self,
method: str = "Horn",
degrees: bool = True,
use_richdem: bool = False,
) -> RasterType:
return terrain.slope(self, method=method, degrees=degrees, use_richdem=use_richdem)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def aspect(
self,
method: str = "Horn",
degrees: bool = True,
use_richdem: bool = False,
) -> RasterType:
return terrain.aspect(self, method=method, degrees=degrees, use_richdem=use_richdem)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def hillshade(
self,
method: str = "Horn",
azimuth: float = 315.0,
altitude: float = 45.0,
z_factor: float = 1.0,
use_richdem: bool = False,
) -> RasterType:
return terrain.hillshade(
self, method=method, azimuth=azimuth, altitude=altitude, z_factor=z_factor, use_richdem=use_richdem
)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def curvature(
self,
use_richdem: bool = False,
) -> RasterType:
return terrain.curvature(self, use_richdem=use_richdem)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def profile_curvature(
self,
use_richdem: bool = False,
) -> RasterType:
return terrain.profile_curvature(self, use_richdem=use_richdem)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def maximum_curvature(
self,
use_richdem: bool = False,
) -> RasterType:
return terrain.maximum_curvature(self, use_richdem=use_richdem)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def topographic_position_index(self, window_size: int = 3) -> RasterType:
return terrain.topographic_position_index(self, window_size=window_size)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def terrain_ruggedness_index(self, method: str = "Riley", window_size: int = 3) -> RasterType:
return terrain.terrain_ruggedness_index(self, method=method, window_size=window_size)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def roughness(self, window_size: int = 3) -> RasterType:
return terrain.roughness(self, window_size=window_size)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def rugosity(self) -> RasterType:
return terrain.rugosity(self)
[docs]
@copy_doc(terrain, remove_dem_res_params=True)
def fractal_roughness(self, window_size: int = 13) -> RasterType:
return terrain.fractal_roughness(self, window_size=window_size)
@copy_doc(terrain, remove_dem_res_params=True)
def get_terrain_attribute(self, attribute: str | list[str], **kwargs: Any) -> RasterType | list[RasterType]:
return terrain.get_terrain_attribute(self, attribute=attribute, **kwargs)
[docs]
def coregister_3d(
self,
reference_elev: DEM | gpd.GeoDataFrame,
coreg_method: coreg.Coreg = None,
inlier_mask: Mask | NDArrayb = None,
bias_vars: dict[str, NDArrayf | MArrayf | RasterType] = None,
**kwargs: Any,
) -> DEM:
"""
Coregister DEM to a reference DEM in three dimensions.
Any coregistration method or pipeline from xdem.Coreg can be passed. Default is only horizontal and vertical
shifts of Nuth and Kääb (2011).
:param reference_elev: Reference elevation, DEM or elevation point cloud, for the alignment.
:param coreg_method: Coregistration method or pipeline.
:param inlier_mask: Optional. 2D boolean array or mask of areas to include in the analysis (inliers=True).
:param bias_vars: Optional, only for some bias correction methods. 2D array or rasters of bias variables used.
:param kwargs: Keyword arguments passed to Coreg.fit().
:return: Coregistered DEM.
"""
if coreg_method is None:
coreg_method = coreg.NuthKaab()
coreg_method.fit(
reference_elev=reference_elev,
to_be_aligned_elev=self,
inlier_mask=inlier_mask,
bias_vars=bias_vars,
**kwargs,
)
return coreg_method.apply(self)
def estimate_uncertainty(
self,
other_dem: DEM,
stable_terrain: Mask | NDArrayb = None,
precision_of_other: Literal["finer"] | Literal["same"] = "finer",
list_vars: tuple[RasterType | str, ...] = ("slope", "maximum_curvature"),
list_vario_models: str | tuple[str, ...] = ("spherical", "spherical"),
) -> tuple[RasterType, Variogram]:
"""
Estimate uncertainty of DEM.
Derives a map of per-pixel errors (based on slope and curvature by default) and a function describing the
spatial correlation of error (between 0 and 1) with spatial lag (distance between observations).
Uses stable terrain as an error proxy and assumes a higher or similar-precision DEM is used as reference,
see Hugonnet et al. (2022).
:param other_dem: Other DEM to use for estimation, either of finer or similar precision for reliable estimates.
:param stable_terrain: Mask of stable terrain to use as error proxy.
:param precision_of_other: Whether finer precision (3 times more precise = 95% of estimated error will come from
this DEM) or similar precision (for instance another acquisition of the same DEM).
:param list_vars: Variables to use to predict error variability (= elevation heteroscedasticity). Either rasters
or names of a terrain attributes. Defaults to slope and maximum curvature of the DEM.
:param list_vario_models: Variogram forms to model the spatial correlation of error. A list translates into
a sum of models.
:return: Uncertainty raster, Variogram of uncertainty correlation.
"""
# Elevation change
dh = other_dem.reproject(self, silent=True) - self
# If the precision of the other DEM is the same, divide the dh values by sqrt(2)
# See Equation 7 and 8 of Hugonnet et al. (2022)
if precision_of_other == "same":
dh /= np.sqrt(2)
# Derive terrain attributes of DEM if string are passed in the list of variables
list_var_rast = []
for var in list_vars:
if isinstance(var, str):
list_var_rast.append(getattr(terrain, var)(self))
else:
list_var_rast.append(var)
# Estimate per-pixel uncertainty
sig_dh = infer_heteroscedasticity_from_stable(dvalues=dh, list_var=list_var_rast, stable_mask=stable_terrain)[0]
# Estimate spatial correlation
corr_sig = infer_spatial_correlation_from_stable(
dvalues=dh, list_models=list(list_vario_models), stable_mask=stable_terrain, errors=sig_dh
)[2]
return sig_dh, corr_sig
