"""
grdfill - Interpolate across holes in a grid.
"""
import warnings
from collections.abc import Sequence
from typing import Literal
import numpy as np
import xarray as xr
from pygmt._typing import PathLike
from pygmt.alias import Alias, AliasSystem
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import build_arg_list, deprecate_parameter, fmt_docstring, use_alias
__doctest_skip__ = ["grdfill"]
def _validate_params(
constantfill=None,
gridfill=None,
neighborfill=None,
splinefill=None,
inquire=False,
mode=None,
):
"""
Validate the fill/inquire parameters.
>>> _validate_params(constantfill=20.0)
>>> _validate_params(inquire=True)
>>> _validate_params(mode="c20.0")
>>> _validate_params(constantfill=20.0, gridfill="bggrid.nc")
Traceback (most recent call last):
...
pygmt.exceptions.GMTInvalidInput: Parameters ... are mutually exclusive.
>>> _validate_params(constantfill=20.0, inquire=True)
Traceback (most recent call last):
...
pygmt.exceptions.GMTInvalidInput: Parameters ... are mutually exclusive.
>>> _validate_params()
Traceback (most recent call last):
...
pygmt.exceptions.GMTInvalidInput: Need to specify parameter ...
"""
_fill_params = "'constantfill'/'gridfill'/'neighborfill'/'splinefill'"
# The deprecated 'mode' parameter is given.
if mode is not None:
msg = (
"The 'mode' parameter is deprecated since v0.15.0 and will be removed in "
f"v0.19.0. Use {_fill_params} instead."
)
warnings.warn(msg, FutureWarning, stacklevel=2)
n_given = sum(
param is not None and param is not False
for param in [constantfill, gridfill, neighborfill, splinefill, inquire, mode]
)
if n_given > 1: # More than one mutually exclusive parameter is given.
msg = f"Parameters {_fill_params}/'inquire'/'mode' are mutually exclusive."
raise GMTInvalidInput(msg)
if n_given == 0: # No parameters are given.
msg = (
f"Need to specify parameter {_fill_params} for filling holes or "
"'inquire' for inquiring the bounds of each hole."
)
raise GMTInvalidInput(msg)
[docs]
@fmt_docstring
# TODO(PyGMT>=0.19.0): Remove the deprecated 'no_data' parameter.
# TODO(PyGMT>=0.19.0): Remove the deprecated 'mode' parameter.
@deprecate_parameter("no_data", "hole", "v0.15.0", remove_version="v0.19.0")
@use_alias(f="coltypes")
def grdfill( # noqa: PLR0913
grid: PathLike | xr.DataArray,
outgrid: PathLike | None = None,
constantfill: float | None = None,
gridfill: PathLike | xr.DataArray | None = None,
neighborfill: float | bool | None = None,
splinefill: float | bool | None = None,
inquire: bool = False,
hole: float | None = None,
mode: str | None = None,
region: Sequence[float | str] | str | None = None,
verbose: Literal["quiet", "error", "warning", "timing", "info", "compat", "debug"]
| bool = False,
**kwargs,
) -> xr.DataArray | np.ndarray | None:
r"""
Interpolate across holes in a grid.
Read a grid that presumably has unfilled holes that the user wants to fill in some
fashion. Holes are identified by NaN values but this criteria can be changed via the
``hole`` parameter. There are several different algorithms that can be used to
replace the hole values. If no holes are found the original unchanged grid is
returned.
Full GMT docs at :gmt-docs:`grdfill.html`.
{aliases}
- Ac = constantfill
- Ag = gridfill
- An = neighborfill
- As = splinefill
- L = inquire
- N = hole
- R = region
- V = verbose
Parameters
----------
{grid}
{outgrid}
constantfill
Fill the holes with a constant value. Specify the constant value to use.
gridfill
Fill the holes with values sampled from another (possibly coarser) grid. Specify
the grid (a file name or an :class:`xarray.DataArray`) to use for the fill.
neighborfill
Fill the holes with the nearest neighbor. Specify the search radius in pixels.
If set to ``True``, the default search radius will be used
(:math:`r^2 = \sqrt{{n^2 + m^2}}`, where (*n,m*) are the node dimensions of the
grid).
splinefill
Fill the holes with a bicubic spline. Specify the tension value to use. If set
to ``True``, no tension will be used.
hole
Set the node value used to identify a point as a member of a hole [Default is
NaN].
inquire
Output the bounds of each hole. The bounds are returned as a 2-D numpy array in
the form of (west, east, south, north). No grid fill takes place and ``outgrid``
is ignored.
mode
Specify the hole-filling algorithm to use. Choose from **c** for constant fill
and append the constant value, **n** for nearest neighbor (and optionally append
a search radius in pixels [default radius is :math:`r^2 = \sqrt{{ X^2 + Y^2 }}`,
where (*X,Y*) are the node dimensions of the grid]), or **s** for bicubic spline
(optionally append a *tension* parameter [Default is no tension]).
.. deprecated:: 0.15.0
Use ``constantfill``, ``gridfill``, ``neighborfill``, or ``splinefill``
instead. The parameter will be removed in v0.19.0.
{region}
{coltypes}
{verbose}
Returns
-------
ret
If ``inquire`` is ``True``, return the bounds of each hole as a 2-D numpy array.
Otherwise, the return type depends on whether the ``outgrid`` parameter is set:
- :class:`xarray.DataArray` if ``outgrid`` is not set
- ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
``outgrid``)
Example
-------
Fill holes in a bathymetric grid with a constant value of 20.
>>> import pygmt
>>> # Load a bathymetric grid with missing data
>>> earth_relief_holes = pygmt.datasets.load_sample_data(name="earth_relief_holes")
>>> # Fill the holes with a constant value of 20
>>> filled_grid = pygmt.grdfill(grid=earth_relief_holes, constantfill=20)
Inquire the bounds of each hole.
>>> pygmt.grdfill(grid=earth_relief_holes, inquire=True)
array([[1.83333333, 6.16666667, 3.83333333, 8.16666667],
[6.16666667, 7.83333333, 0.5 , 2.5 ]])
"""
# Validate the fill/inquire parameters.
_validate_params(constantfill, gridfill, neighborfill, splinefill, inquire, mode)
# _validate_params has already ensured that only one of the parameters is set.
aliasdict = AliasSystem(
A=Alias(mode, name="mode"),
Ac=Alias(constantfill, name="constantfill"),
# For grdfill, append the actual or virtual grid file name later.
Ag=Alias(gridfill is not None, name="gridfill"),
An=Alias(neighborfill, name="neighborfill"),
As=Alias(splinefill, name="splinefill"),
L=Alias(inquire, name="inquire"),
N=Alias(hole, name="hole"),
).add_common(
R=region,
V=verbose,
)
aliasdict.merge(kwargs)
with Session() as lib:
with lib.virtualfile_in(check_kind="raster", data=grid) as vingrd:
if inquire: # Inquire mode.
with lib.virtualfile_out(kind="dataset") as vouttbl:
lib.call_module(
module="grdfill",
args=build_arg_list(aliasdict, infile=vingrd, outfile=vouttbl),
)
return lib.virtualfile_to_dataset(
vfname=vouttbl, output_type="numpy"
)
# Fill mode.
with (
lib.virtualfile_in(
check_kind="raster", data=gridfill, required=False
) as vbggrd,
lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
):
if gridfill is not None:
# Fill by a grid. Append the actual or virtual grid file name.
aliasdict["Ag"] = vbggrd
aliasdict["G"] = voutgrd
lib.call_module(
module="grdfill", args=build_arg_list(aliasdict, infile=vingrd)
)
return lib.virtualfile_to_raster(vfname=voutgrd, outgrid=outgrid)