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Add the validate_output_table_type function to check the output_type parameter #2772

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merged 5 commits into from
Oct 30, 2023
Merged

Add the validate_output_table_type function to check the output_type parameter #2772

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cd11f98
Add the validate_output_type function to check the output_type parameter
seisman Oct 27, 2023
1132b8d
Update pygmt/helpers/validators.py
seisman Oct 28, 2023
8f8819b
Merge branch 'main' into validators/output_type
seisman Oct 28, 2023
e60e4df
Merge branch 'main' into validators/output_type
seisman Oct 29, 2023
becbb73
Rename validate_output_type to validate_output_table_type
seisman Oct 30, 2023
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1 change: 1 addition & 0 deletions pygmt/helpers/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,3 +21,4 @@
launch_external_viewer,
non_ascii_to_octal,
)
from pygmt.helpers.validators import validate_output_type
41 changes: 41 additions & 0 deletions pygmt/helpers/validators.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
"""
Functions to check if given arguments are valid.
"""
import warnings

from pygmt.exceptions import GMTInvalidInput


def validate_output_type(output_type, outfile=None):
"""
Check if the 'output_type' and 'outfile' parameters are valid.
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Parameters
----------
output_type : str
The type for a table output. Valid values are "file", "numpy", and
"pandas".
outfile : str
The file name for the output table file. Required if
``output_type="file"``.

Returns
-------
str
The original or corrected output type.
"""
if output_type not in ["file", "numpy", "pandas"]:
raise GMTInvalidInput(
"Must specify 'output_type' either as 'file', 'numpy', or 'pandas'."
)
if output_type == "file" and outfile is None:
raise GMTInvalidInput("Must specify 'outfile' for output_type='file'.")
if output_type != "file" and outfile is not None:
msg = (
f"Changing 'output_type' from '{output_type}' to 'file' "
"since 'outfile' parameter is set. Please use output_type='file' "
"to silence this warning."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
output_type = "file"
return output_type
23 changes: 9 additions & 14 deletions pygmt/src/filter1d.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,17 @@
"""
filter1d - Time domain filtering of 1-D data tables
"""
import warnings

import pandas as pd
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import GMTTempFile, build_arg_string, fmt_docstring, use_alias
from pygmt.helpers import (
GMTTempFile,
build_arg_string,
fmt_docstring,
use_alias,
validate_output_type,
)


@fmt_docstring
Expand Down Expand Up @@ -109,18 +114,8 @@ def filter1d(data, output_type="pandas", outfile=None, **kwargs):
"""
if kwargs.get("F") is None:
raise GMTInvalidInput("Pass a required argument to 'filter_type'.")
if output_type not in ["numpy", "pandas", "file"]:
raise GMTInvalidInput("Must specify format as either numpy, pandas, or file.")
if outfile is not None and output_type != "file":
msg = (
f"Changing `output_type` of filter1d from '{output_type}' to 'file' "
"since `outfile` parameter is set. Please use `output_type='file'` "
"to silence this warning."
)
warnings.warn(msg, category=RuntimeWarning, stacklevel=2)
output_type = "file"
elif output_type == "file" and outfile is None:
raise GMTInvalidInput("Must specify outfile for ASCII output.")

output_type = validate_output_type(output_type, outfile=outfile)

with GMTTempFile() as tmpfile:
with Session() as lib:
Expand Down
18 changes: 2 additions & 16 deletions pygmt/src/grd2xyz.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
"""
grd2xyz - Convert grid to data table
"""
import warnings

import pandas as pd
import xarray as xr
Expand All @@ -13,6 +12,7 @@
fmt_docstring,
kwargs_to_strings,
use_alias,
validate_output_type,
)

__doctest_skip__ = ["grd2xyz"]
Expand Down Expand Up @@ -143,21 +143,7 @@ def grd2xyz(grid, output_type="pandas", outfile=None, **kwargs):
0 10.0 25.0 863.0
1 10.5 25.0 985.5
"""
if output_type not in ["numpy", "pandas", "file"]:
raise GMTInvalidInput(
"Must specify 'output_type' either as 'numpy', 'pandas' or 'file'."
)

if outfile is not None and output_type != "file":
msg = (
f"Changing 'output_type' of grd2xyz from '{output_type}' to 'file' "
"since 'outfile' parameter is set. Please use output_type='file' "
"to silence this warning."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
output_type = "file"
elif outfile is None and output_type == "file":
raise GMTInvalidInput("Must specify 'outfile' for ASCII output.")
output_type = validate_output_type(output_type, outfile=outfile)

if kwargs.get("o") is not None and output_type == "pandas":
raise GMTInvalidInput(
Expand Down
16 changes: 2 additions & 14 deletions pygmt/src/grdhisteq.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
"""
grdhisteq - Perform histogram equalization for a grid.
"""
import warnings

import numpy as np
import pandas as pd
Expand All @@ -13,6 +12,7 @@
fmt_docstring,
kwargs_to_strings,
use_alias,
validate_output_type,
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Just on the naming, should we specify that this applies to tabular outputs? E.g. use something like validate_output_table_type? There are some functions like pygmt.grdhisteq.equalize_grid that has code looking like this:

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("Must specify 'outgrid' as a string or None.")

If we ever decide to have more output_types for grids (e.g. NetCDF or TIFF or xarray or ???), then there might be a validate_output_grid_type.

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I was thinking about adding a new parameter kind (valid values are dataset/grid) to make the function working for both tables and grids.

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There would a lot of if-thens, and the error/warning messages would be different between tables and grids though.

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Ah right, tables use outfile but grids use outgrid.

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Just on the naming, should we specify that this applies to tabular outputs? E.g. use something like validate_output_table_type?

Renamed in becbb73.

)
from pygmt.io import load_dataarray

Expand Down Expand Up @@ -321,23 +321,11 @@ def compute_bins(
This method does a weighted histogram equalization for geographic
grids to account for node area varying with latitude.
"""
# Return a pandas.DataFrame if ``outfile`` is not set
if output_type not in ["numpy", "pandas", "file"]:
raise GMTInvalidInput(
"Must specify 'output_type' either as 'numpy', 'pandas' or 'file'."
)
output_type = validate_output_type(output_type, outfile=outfile)

if header is not None and output_type != "file":
raise GMTInvalidInput("'header' is only allowed with output_type='file'.")
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if isinstance(outfile, str) and output_type != "file":
msg = (
f"Changing 'output_type' from '{output_type}' to 'file' "
"since 'outfile' parameter is set. Please use output_type='file' "
"to silence this warning."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
output_type = "file"
with GMTTempFile(suffix=".txt") as tmpfile:
if output_type != "file":
outfile = tmpfile.name
Expand Down
9 changes: 2 additions & 7 deletions pygmt/src/grdvolume.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,13 @@
"""
import pandas as pd
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
GMTTempFile,
build_arg_string,
fmt_docstring,
kwargs_to_strings,
use_alias,
validate_output_type,
)

__doctest_skip__ = ["grdvolume"]
Expand Down Expand Up @@ -101,12 +101,7 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
3 350 2.018302e+12 5.222640e+14 258.764032
4 400 1.857370e+12 4.252699e+14 228.963499
"""
if output_type not in ["numpy", "pandas", "file"]:
raise GMTInvalidInput(
"""Must specify format as either numpy, pandas, or file."""
)
if output_type == "file" and outfile is None:
raise GMTInvalidInput("""Must specify outfile for ASCII output.""")
output_type = validate_output_type(output_type, outfile=outfile)

with GMTTempFile() as tmpfile:
with Session() as lib:
Expand Down
17 changes: 2 additions & 15 deletions pygmt/src/triangulate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
triangulate - Delaunay triangulation or Voronoi partitioning and gridding of
Cartesian data.
"""
import warnings

import pandas as pd
from pygmt.clib import Session
Expand All @@ -13,6 +12,7 @@
fmt_docstring,
kwargs_to_strings,
use_alias,
validate_output_type,
)
from pygmt.io import load_dataarray

Expand Down Expand Up @@ -357,20 +357,7 @@ def delaunay_triples( # pylint: disable=too-many-arguments,too-many-locals
``triangulate`` is a Cartesian or small-geographic area operator and is
unaware of periodic or polar boundary conditions.
"""
# Return a pandas.DataFrame if ``outfile`` is not set
if output_type not in ["numpy", "pandas", "file"]:
raise GMTInvalidInput(
"Must specify 'output_type' either as 'numpy', 'pandas' or 'file'."
)

if isinstance(outfile, str) and output_type != "file":
msg = (
f"Changing 'output_type' from '{output_type}' to 'file' "
"since 'outfile' parameter is set. Please use output_type='file' "
"to silence this warning."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
output_type = "file"
output_type = validate_output_type(output_type, outfile)

# Return a pandas.DataFrame if ``outfile`` is not set
with GMTTempFile(suffix=".txt") as tmpfile:
Expand Down