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pygmt.triangulate: Refactor to use codes consistent with other wrappers #3073

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Feb 28, 2024
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pygmt.triangulate: Refactor to use codes consistent with other wrappers #3073

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7dc2ae5
Refactor the triangulate wrapper to make it easier to maintain
seisman Feb 27, 2024
c61efc0
Merge branch 'main' into refactor/triangulate
seisman Feb 28, 2024
400d57d
Show aliases in docs
seisman Feb 28, 2024
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227 changes: 57 additions & 170 deletions pygmt/src/triangulate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@

import pandas as pd
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
GMTTempFile,
build_arg_string,
Expand Down Expand Up @@ -64,109 +63,7 @@ class triangulate: # noqa: N801
w="wrap",
)
@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma")
def _triangulate(
data=None, x=None, y=None, z=None, *, output_type, outfile=None, **kwargs
):
"""
Delaunay triangulation or Voronoi partitioning and gridding of Cartesian data.

Must provide ``outfile`` or ``outgrid``.

Full option list at :gmt-docs:`triangulate.html`

{aliases}

Parameters
----------
x/y/z : np.ndarray
Arrays of x and y coordinates and values z of the data points.
data : str, {table-like}
Pass in (x, y, z) or (longitude, latitude, elevation) values by
providing a file name to an ASCII data table, a 2-D
{table-classes}.
{projection}
{region}
{spacing}
{outgrid}
The interpolation is performed in the original coordinates, so if
your triangles are close to the poles you are better off projecting
all data to a local coordinate system before using ``triangulate``
(this is true of all gridding routines) or instead select
:gmt-docs:`sphtriangulate <sphtriangulate.html>`.
outfile : str, bool or None
The name of the output ASCII file to store the results of the
histogram equalization in.
output_type: str
Determine the output type. Use "file", "xarray", "pandas", or
"numpy".
{verbose}
{binary}
{nodata}
{find}
{coltypes}
{header}
{incols}
{registration}
Only valid with ``outgrid``.
{skiprows}
{wrap}

Returns
-------
ret: numpy.ndarray or pandas.DataFrame or xarray.DataArray or None
Return type depends on the ``output_type`` parameter:

- numpy.ndarray if ``output_type`` is "numpy"
- pandas.DataFrame if ``output_type`` is "pandas"
- xarray.DataArray if ``output_type`` is "xarray""
- None if ``output_type`` is "file" (output is stored in
``outgrid`` or ``outfile``)
"""
with Session() as lib:
table_context = lib.virtualfile_from_data(
check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
)
with table_context as infile:
# table output if outgrid is unset, else output to outgrid
if (outgrid := kwargs.get("G")) is None:
kwargs.update({">": outfile})
lib.call_module(
module="triangulate", args=build_arg_string(kwargs, infile=infile)
)

if output_type == "file":
return None
if output_type == "xarray":
return load_dataarray(outgrid)

result = pd.read_csv(outfile, sep="\t", header=None)
if output_type == "numpy":
return result.to_numpy()
return result

@staticmethod
@fmt_docstring
def regular_grid( # noqa: PLR0913
data=None,
x=None,
y=None,
z=None,
outgrid=None,
spacing=None,
projection=None,
region=None,
verbose=None,
binary=None,
nodata=None,
find=None,
coltypes=None,
header=None,
incols=None,
registration=None,
skiprows=None,
wrap=None,
**kwargs,
):
def regular_grid(data=None, x=None, y=None, z=None, **kwargs):
"""
Delaunay triangle based gridding of Cartesian data.

Expand All @@ -190,6 +87,8 @@ def regular_grid( # noqa: PLR0913

Full option list at :gmt-docs:`triangulate.html`

{aliases}

Parameters
----------
x/y/z : np.ndarray
Expand Down Expand Up @@ -236,58 +135,45 @@ def regular_grid( # noqa: PLR0913
"""
# Return an xarray.DataArray if ``outgrid`` is not set
with GMTTempFile(suffix=".nc") as tmpfile:
if isinstance(outgrid, str):
output_type = "file"
elif outgrid is None:
output_type = "xarray"
outgrid = tmpfile.name
else:
raise GMTInvalidInput(
"'outgrid' should be a proper file name or `None`"
)

return triangulate._triangulate(
data=data,
x=x,
y=y,
z=z,
output_type=output_type,
outgrid=outgrid,
spacing=spacing,
projection=projection,
region=region,
verbose=verbose,
binary=binary,
nodata=nodata,
find=find,
coltypes=coltypes,
header=header,
incols=incols,
registration=registration,
skiprows=skiprows,
wrap=wrap,
**kwargs,
)
with Session() as lib:
with lib.virtualfile_from_data(
check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
) as vintbl:
if (outgrid := kwargs.get("G")) is None:
kwargs["G"] = outgrid = tmpfile.name # output to tmpfile
lib.call_module(
module="triangulate",
args=build_arg_string(kwargs, infile=vintbl),
)

return load_dataarray(outgrid) if outgrid == tmpfile.name else None

@staticmethod
@fmt_docstring
def delaunay_triples( # noqa: PLR0913
@use_alias(
I="spacing",
J="projection",
R="region",
V="verbose",
b="binary",
d="nodata",
e="find",
f="coltypes",
h="header",
i="incols",
r="registration",
s="skiprows",
w="wrap",
)
@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma")
def delaunay_triples(
data=None,
x=None,
y=None,
z=None,
*,
output_type="pandas",
outfile=None,
projection=None,
verbose=None,
binary=None,
nodata=None,
find=None,
coltypes=None,
header=None,
incols=None,
skiprows=None,
wrap=None,
**kwargs,
):
"""
Expand All @@ -306,6 +192,8 @@ def delaunay_triples( # noqa: PLR0913

Full option list at :gmt-docs:`triangulate.html`

{aliases}

Parameters
----------
x/y/z : np.ndarray
Expand All @@ -316,7 +204,7 @@ def delaunay_triples( # noqa: PLR0913
{table-classes}.
{projection}
{region}
outfile : str or bool or None
outfile : str or None
The name of the output ASCII file to store the results of the
histogram equalization in.
output_type : str
Expand Down Expand Up @@ -355,26 +243,25 @@ def delaunay_triples( # noqa: PLR0913
"""
output_type = validate_output_table_type(output_type, outfile)

# Return a pandas.DataFrame if ``outfile`` is not set
with GMTTempFile(suffix=".txt") as tmpfile:
if output_type != "file":
outfile = tmpfile.name
return triangulate._triangulate(
data=data,
x=x,
y=y,
z=z,
output_type=output_type,
outfile=outfile,
projection=projection,
verbose=verbose,
binary=binary,
nodata=nodata,
find=find,
coltypes=coltypes,
header=header,
incols=incols,
skiprows=skiprows,
wrap=wrap,
**kwargs,
)
with Session() as lib:
with lib.virtualfile_from_data(
check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
) as vintbl:
if outfile is None:
outfile = tmpfile.name
lib.call_module(
module="triangulate",
args=build_arg_string(kwargs, infile=vintbl, outfile=outfile),
)

if outfile == tmpfile.name:
# if user did not set outfile, return pd.DataFrame
result = pd.read_csv(outfile, sep="\t", header=None)
elif outfile != tmpfile.name:
# return None if outfile set, output in outfile
result = None

if output_type == "numpy":
result = result.to_numpy()
return result
9 changes: 0 additions & 9 deletions pygmt/tests/test_triangulate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,12 +157,3 @@ def test_regular_grid_with_outgrid_param(dataframe, expected_grid):
assert grid.gmt.registration == 0 # Gridline registration
assert grid.gmt.gtype == 0 # Cartesian type
xr.testing.assert_allclose(a=grid, b=expected_grid)


def test_regular_grid_invalid_format(dataframe):
"""
Test that triangulate.regular_grid fails with outgrid that is not None or a proper
file name.
"""
with pytest.raises(GMTInvalidInput):
triangulate.regular_grid(data=dataframe, outgrid=True)
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