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Merge branch 'main' into feature/direction_rose
2 parents 64bf23a + b5eff49 commit 8ba0992

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‎examples/gallery/maps/epsg_codes.py‎

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"""
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EPSG codes
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==========
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Besides one of the :doc:`31 projections supported by GMT </techref/projections>`, users
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can pass an EPSG (European Petroleum Survey Group) code to the ``projection`` parameter.
7+
A commonly used EPSG code is ``EPSG:3857``, that refers to the Web Mercator projection
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WGS84. More information on the EPSG dataset can be found at https://epsg.org and
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https://spatialreference.org/. Please note, that not all EPSG codes are supported by
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GMT / PyGMT.
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"""
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# %%
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import pygmt
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fig = pygmt.Figure()
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# Pass the desired EPSG code and the width of the map (separated by a slash) to the
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# projection parameter
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fig.basemap(region=[-180, 180, -60, 60], projection="EPSG:3857/10c", frame=30)
21+
fig.coast(land="gray", shorelines="1/0.1p,gray10")
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fig.show()

‎pygmt/src/binstats.py‎

Lines changed: 77 additions & 26 deletions
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@@ -2,15 +2,17 @@
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binstats - Bin spatial data and determine statistics per bin.
33
"""
44

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from typing import Literal
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57
import xarray as xr
68
from pygmt._typing import PathLike, TableLike
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from pygmt.alias import Alias, AliasSystem
710
from pygmt.clib import Session
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from pygmt.helpers import build_arg_list, fmt_docstring, kwargs_to_strings, use_alias
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1013

1114
@fmt_docstring
1215
@use_alias(
13-
C="statistic",
1416
E="empty",
1517
I="spacing",
1618
N="normalize",
@@ -26,7 +28,28 @@
2628
)
2729
@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma")
2830
def binstats(
29-
data: PathLike | TableLike, outgrid: PathLike | None = None, **kwargs
31+
data: PathLike | TableLike,
32+
outgrid: PathLike | None = None,
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statistic: Literal[
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"mean",
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"mad",
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"full",
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"interquartile",
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"min",
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"minpos",
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"median",
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"number",
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"lms",
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"mode",
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"quantile",
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"rms",
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"stddev",
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"max",
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"maxneg",
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"sum",
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] = "number",
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quantile_value: float = 50,
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**kwargs,
3053
) -> xr.DataArray | None:
3154
r"""
3255
Bin spatial data and determine statistics per bin.
@@ -42,35 +65,36 @@ def binstats(
4265
Full GMT docs at :gmt-docs:`gmtbinstats.html`.
4366
4467
{aliases}
68+
- C=statistic
4569
4670
Parameters
4771
----------
4872
data
4973
A file name of an ASCII data table or a 2-D {table-classes}.
5074
{outgrid}
51-
statistic : str
52-
**a**\|\ **d**\|\ **g**\|\ **i**\|\ **l**\|\ **L**\|\ **m**\|\ **n**\
53-
\|\ **o**\|\ **p**\|\ **q**\ [*quant*]\|\ **r**\|\ **s**\|\ **u**\
54-
\|\ **U**\|\ **z**.
55-
Choose the statistic that will be computed per node based on the
56-
points that are within *radius* distance of the node. Select one of:
75+
statistic
76+
Choose the statistic that will be computed per node based on the points that are
77+
within *radius* distance of the node. Select one of:
5778
58-
- **a**: mean (average)
59-
- **d**: median absolute deviation (MAD)
60-
- **g**: full (max-min) range
61-
- **i**: 25-75% interquartile range
62-
- **l**: minimum (low)
63-
- **L**: minimum of positive values only
64-
- **m**: median
65-
- **n**: number of values
66-
- **o**: LMS scale
67-
- **p**: mode (maximum likelihood)
68-
- **q**: selected quantile (append desired quantile in 0-100% range [50])
69-
- **r**: root mean square (RMS)
70-
- **s**: standard deviation
71-
- **u**: maximum (upper)
72-
- **U**: maximum of negative values only
73-
- **z**: sum
79+
- ``"mean"``: Mean (i.e., average).
80+
- ``"mad"``: Median absolute deviation (MAD).
81+
- ``"full"``: The full (max-min) range.
82+
- ``"interquartile"``: The 25-75% interquartile range.
83+
- ``"min"``: Minimum (lowest value).
84+
- ``"minpos"``: Minimum of positive values only.
85+
- ``"median"``: Median value.
86+
- ``"number"``: The number of values per bin.
87+
- ``"lms"``: Least median square (LMS) scale.
88+
- ``"mode"``: Mode (maximum likelihood estimate).
89+
- ``"quantile"``: Selected quantile. The quantile value is specified by the
90+
``quantile_value`` parameter and is in the 0-100% range.
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- ``"rms"``: Root mean square (RMS).
92+
- ``"stddev"``: Standard deviation.
93+
- ``"max"``: Maximum (highest value).
94+
- ``"maxneg"``: Maximum of negative values only.
95+
- ``"sum"``: The sum of the values.
96+
quantile_value
97+
The quantile value if ``statistic="quantile"``.
7498
empty : float
7599
Set the value assigned to empty nodes [Default is NaN].
76100
normalize : bool
@@ -104,13 +128,40 @@ def binstats(
104128
- ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
105129
``outgrid``)
106130
"""
131+
aliasdict = AliasSystem(
132+
C=Alias(
133+
statistic,
134+
name="statistic",
135+
mapping={
136+
"mean": "a",
137+
"mad": "d",
138+
"full": "g",
139+
"interquartile": "i",
140+
"min": "l",
141+
"minpos": "L",
142+
"median": "m",
143+
"number": "n",
144+
"lms": "o",
145+
"mode": "p",
146+
"quantile": "q",
147+
"rms": "r",
148+
"stddev": "s",
149+
"max": "u",
150+
"maxneg": "U",
151+
"sum": "z",
152+
},
153+
),
154+
).merge(kwargs)
155+
if statistic == "quantile":
156+
aliasdict["C"] += f"{quantile_value}"
157+
107158
with Session() as lib:
108159
with (
109160
lib.virtualfile_in(check_kind="vector", data=data) as vintbl,
110161
lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
111162
):
112-
kwargs["G"] = voutgrd
163+
aliasdict["G"] = voutgrd
113164
lib.call_module(
114-
module="binstats", args=build_arg_list(kwargs, infile=vintbl)
165+
module="binstats", args=build_arg_list(aliasdict, infile=vintbl)
115166
)
116167
return lib.virtualfile_to_raster(vfname=voutgrd, outgrid=outgrid)

‎pygmt/src/select.py‎

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@@ -24,7 +24,6 @@
2424
@use_alias(
2525
A="area_thresh",
2626
C="dist2pt",
27-
D="resolution-",
2827
F="polygon",
2928
G="gridmask",
3029
I="reverse",

‎pygmt/src/solar.py‎

Lines changed: 17 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
import pandas as pd
88
from pygmt.alias import Alias, AliasSystem
99
from pygmt.clib import Session
10-
from pygmt.exceptions import GMTInvalidInput, GMTValueError
10+
from pygmt.exceptions import GMTValueError
1111
from pygmt.helpers import build_arg_list, fmt_docstring, kwargs_to_strings, use_alias
1212

1313
__doctest_skip__ = ["solar"]
@@ -18,7 +18,6 @@
1818
B="frame",
1919
G="fill",
2020
R="region",
21-
T="terminator/terminator_datetime-",
2221
V="verbose",
2322
W="pen",
2423
c="panel",
@@ -43,6 +42,7 @@ def solar(
4342
4443
{aliases}
4544
- J=projection
45+
- T=terminator, **+d**: terminator_datetime
4646
4747
Parameters
4848
----------
@@ -99,28 +99,31 @@ def solar(
9999
>>> fig.show()
100100
"""
101101
self._activate_figure()
102-
if kwargs.get("T") is not None:
103-
msg = "Use 'terminator' and 'terminator_datetime' instead of 'T'."
104-
raise GMTInvalidInput(msg)
105102

106-
valid_terminators = ["day_night", "civil", "nautical", "astronomical"]
107-
if terminator not in valid_terminators and terminator not in "dcna":
108-
raise GMTValueError(
109-
terminator, description="solar terminator type", choices=valid_terminators
110-
)
111-
kwargs["T"] = terminator[0]
103+
datetime_string = None
112104
if terminator_datetime:
113105
try:
114106
datetime_string = pd.to_datetime(terminator_datetime).strftime(
115107
"%Y-%m-%dT%H:%M:%S.%f"
116108
)
117109
except ValueError as verr:
118-
msg = "Unrecognized datetime format."
119-
raise GMTInvalidInput(msg) from verr
120-
kwargs["T"] += f"+d{datetime_string}"
110+
raise GMTValueError(terminator_datetime, description="datetime") from verr
121111

122112
aliasdict = AliasSystem(
123113
J=Alias(projection, name="projection"),
114+
T=[
115+
Alias(
116+
terminator,
117+
name="terminator",
118+
mapping={
119+
"day_night": "d",
120+
"civil": "c",
121+
"nautical": "n",
122+
"astronomical": "a",
123+
},
124+
),
125+
Alias(datetime_string, name="terminator_datetime", prefix="+d"),
126+
],
124127
).merge(kwargs)
125128

126129
with Session() as lib:

‎pygmt/tests/test_binstats.py‎

Lines changed: 24 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ def test_binstats_outgrid():
2020
data="@capitals.gmt",
2121
outgrid=tmpfile.name,
2222
spacing=5,
23-
statistic="z",
23+
statistic="sum",
2424
search_radius="1000k",
2525
aspatial="2=population",
2626
region="g",
@@ -37,7 +37,7 @@ def test_binstats_no_outgrid():
3737
temp_grid = binstats(
3838
data="@capitals.gmt",
3939
spacing=5,
40-
statistic="z",
40+
statistic="sum",
4141
search_radius="1000k",
4242
aspatial="2=population",
4343
region="g",
@@ -49,3 +49,25 @@ def test_binstats_no_outgrid():
4949
npt.assert_allclose(temp_grid.min(), 53)
5050
npt.assert_allclose(temp_grid.median(), 1232714.5)
5151
npt.assert_allclose(temp_grid.mean(), 4227489)
52+
53+
54+
def test_binstats_quantile():
55+
"""
56+
Test binstats quantile statistic functionality.
57+
"""
58+
temp_grid = binstats(
59+
data="@capitals.gmt",
60+
spacing=5,
61+
statistic="quantile",
62+
quantile_value=75,
63+
search_radius="1000k",
64+
aspatial="2=population",
65+
region="g",
66+
)
67+
assert temp_grid.dims == ("y", "x")
68+
assert temp_grid.gmt.gtype is GridType.CARTESIAN
69+
assert temp_grid.gmt.registration is GridRegistration.GRIDLINE
70+
npt.assert_allclose(temp_grid.max(), 15047685)
71+
npt.assert_allclose(temp_grid.min(), 53)
72+
npt.assert_allclose(temp_grid.median(), 543664.5)
73+
npt.assert_allclose(temp_grid.mean(), 1661363.6)

‎pygmt/tests/test_solar.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -96,7 +96,7 @@ def test_invalid_datetime():
9696
Test if solar fails when it receives an invalid datetime string.
9797
"""
9898
fig = Figure()
99-
with pytest.raises(GMTInvalidInput):
99+
with pytest.raises(GMTValueError):
100100
fig.solar(
101101
region="d",
102102
projection="W0/15c",

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