/
curvature.py
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/
curvature.py
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# std lib
from functools import partial
from typing import Optional, Union
# 3rd-party
try:
import cupy
except ImportError:
class cupy(object):
ndarray = False
import dask.array as da
import numpy as np
import xarray as xr
from numba import cuda
# local modules
from xrspatial.utils import (ArrayTypeFunctionMapping, cuda_args, get_dataarray_resolution, ngjit,
not_implemented_func)
@ngjit
def _cpu(data, cellsize):
out = np.empty(data.shape, np.float32)
out[:] = np.nan
rows, cols = data.shape
for y in range(1, rows - 1):
for x in range(1, cols - 1):
d = (data[y + 1, x] + data[y - 1, x]) / 2 - data[y, x]
e = (data[y, x + 1] + data[y, x - 1]) / 2 - data[y, x]
out[y, x] = -2 * (d + e) * 100 / (cellsize * cellsize)
return out
def _run_numpy(data: np.ndarray,
cellsize: Union[int, float]) -> np.ndarray:
# TODO: handle border edge effect
data = data.astype(np.float32)
out = _cpu(data, cellsize)
return out
def _run_dask_numpy(data: da.Array,
cellsize: Union[int, float]) -> da.Array:
data = data.astype(np.float32)
_func = partial(_cpu, cellsize=cellsize)
out = data.map_overlap(_func,
depth=(1, 1),
boundary=np.nan,
meta=np.array(()))
return out
@cuda.jit(device=True)
def _gpu(arr, cellsize):
d = (arr[1, 0] + arr[1, 2]) / 2 - arr[1, 1]
e = (arr[0, 1] + arr[2, 1]) / 2 - arr[1, 1]
curv = -2 * (d + e) * 100 / (cellsize[0] * cellsize[0])
return curv
@cuda.jit
def _run_gpu(arr, cellsize, out):
i, j = cuda.grid(2)
di = 1
dj = 1
if (i - di >= 0 and i + di <= out.shape[0] - 1 and
j - dj >= 0 and j + dj <= out.shape[1] - 1):
out[i, j] = _gpu(arr[i - di:i + di + 1, j - dj:j + dj + 1], cellsize)
def _run_cupy(data: cupy.ndarray,
cellsize: Union[int, float]) -> cupy.ndarray:
data = data.astype(cupy.float32)
cellsize_arr = cupy.array([float(cellsize)], dtype='f4')
# TODO: add padding
griddim, blockdim = cuda_args(data.shape)
out = cupy.empty(data.shape, dtype='f4')
out[:] = cupy.nan
_run_gpu[griddim, blockdim](data, cellsize_arr, out)
return out
def curvature(agg: xr.DataArray,
name: Optional[str] = 'curvature') -> xr.DataArray:
"""
Calculates, for all cells in the array, the curvature (second
derivative) of each cell based on the elevation of its neighbors
in a 3x3 grid. A positive curvature indicates the surface is
upwardly convex. A negative value indicates it is upwardly
concave. A value of 0 indicates a flat surface.
Units of the curvature output raster are one hundredth (1/100)
of a z-unit.
Parameters
----------
agg : xarray.DataArray
2D NumPy, CuPy, NumPy-backed Dask xarray DataArray of elevation values.
Must contain `res` attribute.
name : str, default='curvature'
Name of output DataArray.
Returns
-------
curvature_agg : xarray.DataArray, of the same type as `agg`
2D aggregate array of curvature values.
All other input attributes are preserved.
References
----------
- arcgis: https://pro.arcgis.com/en/pro-app/latest/tool-reference/spatial-analyst/how-curvature-works.htm # noqa
Examples
--------
Curvature works with NumPy backed xarray DataArray
.. sourcecode:: python
>>> import numpy as np
>>> import dask.array as da
>>> import xarray as xr
>>> from xrspatial import curvature
>>> flat_data = np.zeros((5, 5), dtype=np.float32)
>>> flat_raster = xr.DataArray(flat_data, attrs={'res': (1, 1)})
>>> flat_curv = curvature(flat_raster)
>>> print(flat_curv)
<xarray.DataArray 'curvature' (dim_0: 5, dim_1: 5)>
array([[nan, nan, nan, nan, nan],
[nan, -0., -0., -0., nan],
[nan, -0., -0., -0., nan],
[nan, -0., -0., -0., nan],
[nan, nan, nan, nan, nan]])
Dimensions without coordinates: dim_0, dim_1
Attributes:
res: (1, 1)
Curvature works with Dask with NumPy backed xarray DataArray
.. sourcecode:: python
>>> convex_data = np.array([
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, -1, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=np.float32)
>>> convex_raster = xr.DataArray(
da.from_array(convex_data, chunks=(3, 3)),
attrs={'res': (10, 10)}, name='convex_dask_numpy_raster')
>>> print(convex_raster)
<xarray.DataArray 'convex_dask_numpy_raster' (dim_0: 5, dim_1: 5)>
dask.array<array, shape=(5, 5), dtype=float32, chunksize=(3, 3), chunktype=numpy.ndarray>
Dimensions without coordinates: dim_0, dim_1
Attributes:
res: (10, 10)
>>> convex_curv = curvature(convex_raster, name='convex_curvature')
>>> print(convex_curv) # return a xarray DataArray with Dask-backed array
<xarray.DataArray 'convex_curvature' (dim_0: 5, dim_1: 5)>
dask.array<_trim, shape=(5, 5), dtype=float32, chunksize=(3, 3), chunktype=numpy.ndarray>
Dimensions without coordinates: dim_0, dim_1
Attributes:
res: (10, 10)
>>> print(convex_curv.compute())
<xarray.DataArray 'convex_curvature' (dim_0: 5, dim_1: 5)>
array([[nan, nan, nan, nan, nan],
[nan, -0., 1., -0., nan],
[nan, 1., -4., 1., nan],
[nan, -0., 1., -0., nan],
[nan, nan, nan, nan, nan]])
Dimensions without coordinates: dim_0, dim_1
Attributes:
res: (10, 10)
Curvature works with CuPy backed xarray DataArray.
.. sourcecode:: python
>>> import cupy
>>> concave_data = np.array([
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=np.float32)
>>> concave_raster = xr.DataArray(
cupy.asarray(concave_data),
attrs={'res': (10, 10)}, name='concave_cupy_raster')
>>> concave_curv = curvature(concave_raster)
>>> print(type(concave_curv.data))
<class 'cupy.core.core.ndarray'>
>>> print(concave_curv)
<xarray.DataArray 'curvature' (dim_0: 5, dim_1: 5)>
array([[nan, nan, nan, nan, nan],
[nan, -0., -1., -0., nan],
[nan, -1., 4., -1., nan],
[nan, -0., -1., -0., nan],
[nan, nan, nan, nan, nan]], dtype=float32)
Dimensions without coordinates: dim_0, dim_1
Attributes:
res: (10, 10)
"""
cellsize_x, cellsize_y = get_dataarray_resolution(agg)
cellsize = (cellsize_x + cellsize_y) / 2
mapper = ArrayTypeFunctionMapping(
numpy_func=_run_numpy,
cupy_func=_run_cupy,
dask_func=_run_dask_numpy,
dask_cupy_func=lambda *args: not_implemented_func(
*args, messages='curvature() does not support dask with cupy backed DataArray.'), # noqa
)
out = mapper(agg)(agg.data, cellsize)
return xr.DataArray(out,
name=name,
coords=agg.coords,
dims=agg.dims,
attrs=agg.attrs)