11624563836

Committed 01 Nov 2024 04:58AM UTC coverage: 91.367% (-0.2%) from 91.538%

Build # 11624563836

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github

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morganjwilliams

Commit Message

Update get_ionic_radii test

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93.1

/pyrolite/util/plot/style.py

"""
Functions for automated plot styling and argument handling.

Attributes
----------
DEFAULT_CONT_COLORMAP : :class:`matplotlib.colors.ScalarMappable`
    Default continuous colormap.
DEFAULT_DISC_COLORMAP : :class:`matplotlib.colors.ScalarMappable`
    Default discrete colormap.
"""

import itertools
from pathlib import Path

import matplotlib
import matplotlib.axes
import matplotlib.collections
import matplotlib.colors
import matplotlib.lines
import matplotlib.patches
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from matplotlib.legend_handler import HandlerTuple

from ...comp.codata import close
from ..general import copy_file
from ..log import Handle
from ..meta import pyrolite_datafolder, subkwargs
from .helpers import get_centroid
from .transform import xy_to_tlr

logger = Handle(__name__)

DEFAULT_CONT_COLORMAP = plt.cm.viridis
DEFAULT_DISC_COLORMAP = plt.cm.tab10


def _export_mplstyle(
    src=pyrolite_datafolder("_config") / "pyrolite.mplstyle", refresh=False
):
    """
    Export a matplotlib style file to the matplotlib style library such that one can
    use e.g. `matplotlib.style.use("pyrolite")`.

    Parameters
    -----------
    src : :class:`str` | :class:`pathlib.Path`
        File path for the style file to be exported.
    refresh : :class:`bool`
        Whether to re-export a style file (e.g. after updating) even if it
        already exists in the matplotlib style libary.
    """
    src_fn = Path(src)
    dest_dir = Path(matplotlib.get_configdir()) / "stylelib"
    dest_fn = dest_dir / src.name
    if (not dest_fn.exists()) or refresh:
        logger.debug("Exporting pyrolite.mplstyle to matplotlib config folder.")
        if not dest_dir.exists():
            dest_dir.mkdir(parents=True)
        copy_file(src_fn, dest_dir)  # copy to the destination DIR
        logger.debug("Reloading matplotlib")
    matplotlib.style.reload_library()  # needed to load in pyrolite style NOW


def _restyle(f, **_style):
    """
    A decorator to set the default keyword arguments for :mod:`matplotlib`
    functions and classes which are not contained in the `matplotlibrc` file.
    """

    def wrapped(*args, **kwargs):
        return f(*args, **{**_style, **kwargs})

    wrapped.__name__ = f.__name__
    wrapped.__doc__ = f.__doc__
    return wrapped


def _export_nonRCstyles(**kwargs):
    """
    Export default options for parameters not in rcParams using :func:`_restyle`.
    """
    matplotlib.axes.Axes.legend = _restyle(
        matplotlib.axes.Axes.legend, **{"bbox_to_anchor": (1, 1), **kwargs}
    )
    matplotlib.figure.Figure.legend = _restyle(
        matplotlib.figure.Figure.legend, bbox_to_anchor=(1, 1)
    )


_export_mplstyle()
_export_nonRCstyles(handler_map={tuple: HandlerTuple(ndivide=None)})
matplotlib.style.use("pyrolite")


def linekwargs(kwargs):
    """
    Get a subset of keyword arguments to pass to a matplotlib line-plot call.

    Parameters
    -----------
    kwargs : :class:`dict`
        Dictionary of keyword arguments to subset.

    Returns
    --------
    :class:`dict`
    """
    kw = subkwargs(
        kwargs,
        plt.plot,
        matplotlib.axes.Axes.plot,
        matplotlib.lines.Line2D,
        matplotlib.collections.Collection,
    )
    # could trim cmap and norm here, in case they get passed accidentally
    kw.update(
        **dict(
            alpha=kwargs.get("alpha"),
            label=kwargs.get("label"),
            clip_on=kwargs.get("clip_on", True),
        )
    )  # issues with introspection for alpha
    return kw


def scatterkwargs(kwargs):
    """
    Get a subset of keyword arguments to pass to a matplotlib scatter call.

    Parameters
    -----------
    kwargs : :class:`dict`
        Dictionary of keyword arguments to subset.

    Returns
    --------
    :class:`dict`
    """
    kw = subkwargs(
        kwargs,
        plt.scatter,
        matplotlib.axes.Axes.scatter,
        matplotlib.collections.Collection,
    )
    kw.update(
        **dict(
            alpha=kwargs.get("alpha"),
            label=kwargs.get("label"),
            clip_on=kwargs.get("clip_on", True),
        )
    )  # issues with introspection for alpha
    return kw


def patchkwargs(kwargs):
    kw = subkwargs(
        kwargs,
        matplotlib.axes.Axes.fill_between,
        matplotlib.collections.PolyCollection,
        matplotlib.patches.Patch,
    )
    kw.update(
        **dict(
            alpha=kwargs.get("alpha"),
            label=kwargs.get("label"),
            clip_on=kwargs.get("clip_on", True),
        )
    )  # issues with introspection for alpha
    return kw


def _mpl_sp_kw_split(kwargs):
    """
    Process keyword arguments supplied to a matplotlib plot function.

    Returns
    --------
    :class:`tuple` ( :class:`dict`, :class:`dict` )
    """
    sctr_kwargs = scatterkwargs(kwargs)
    # c kwarg is first priority, if it isn't present, use the color arg
    if sctr_kwargs.get("c") is None:
        sctr_kwargs = {**sctr_kwargs, **{"c": kwargs.get("color")}}

    line_kwargs = linekwargs(kwargs)
    return sctr_kwargs, line_kwargs


def marker_cycle(markers=["D", "s", "o", "+", "*"]):
    """
    Cycle through a set of markers.

    Parameters
    ----------
    markers : :class:`list`
        List of markers to provide to matplotlib.
    """
    return itertools.cycle(markers)


def mappable_from_values(values, cmap=DEFAULT_CONT_COLORMAP, norm=None, **kwargs):
    """
    Create a scalar mappable object from an array of values.

    Returns
    -------
    :class:`matplotlib.cm.ScalarMappable`
    """
    if isinstance(values, pd.Series):
        values = values.values
    sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
    sm.set_array(values[np.isfinite(values)])
    return sm


def ternary_color(
    tlr,
    alpha=1.0,
    colors=([1, 0, 0], [0, 1, 0], [0, 0, 1]),
    coefficients=(1, 1, 1),
):
    """
    Color a set of points by their ternary combinations of three specified colors.

    Parameters
    ----------
    tlr : :class:`numpy.ndarray`

    alpha : :class:`float`
        Alpha coefficient for the colors; to be applied *multiplicatively* with
        any existing alpha value (for RGBA colors specified).
    colors : :class:`tuple`
        Set of colours corresponding to the top, left and right verticies,
        respectively.
    coefficients : :class:`tuple`
        Coefficients for the ternary data to adjust the centre.

    Returns
    -------
    :class:`numpy.ndarray`
        Color array for the ternary points.
    """
    colors = np.array([matplotlib.colors.to_rgba(c) for c in colors], dtype=float)
    _tlr = close(np.array(tlr) * np.array(coefficients))
    color = np.atleast_2d(_tlr @ colors)
    color[:, -1] *= alpha * (1 - 10e-7)  # avoid 'greater than 1' issues
    return color


def color_ternary_polygons_by_centroid(
    ax=None,
    patches=None,
    alpha=1.0,
    colors=([1, 0, 0], [0, 1, 0], [0, 0, 1]),
    coefficients=(1, 1, 1),
):
    """
    Color a set of polygons within a ternary diagram by their centroid colors.

    Parameters
    ----------
    ax : :class:`matplotlib.axes.Axes`
        Ternary axes to check for patches, if patches is not supplied.
    patches : :class:`list`
        List of ternary-hosted patches to apply color to.
    alpha : :class:`float`
        Alpha coefficient for the colors; to be applied *multiplicatively* with
        any existing alpha value (for RGBA colors specified).
    colors : :class:`tuple`
        Set of colours corresponding to the top, left and right verticies,
        respectively.
    coefficients : :class:`tuple`
        Coefficients for the ternary data to adjust the centre.

    Returns
    -------
    patches : :class:`list`
        List of patches, with updated facecolors.
    """

    if patches is None:
        if ax is None:
            raise NotImplementedError("Either an axis or patches need to be supplied.")
        patches = ax.patches

    for poly in patches:
        xy = get_centroid(poly)
        tlr = xy_to_tlr(np.array([xy]))[0]
        color = ternary_color(
            tlr, alpha=alpha, colors=colors, coefficients=coefficients
        )
        poly.set_facecolor(color)

    return patches

1	"""
2	Functions for automated plot styling and argument handling.
3
4	Attributes
5	----------
6	DEFAULT_CONT_COLORMAP : :class:`matplotlib.colors.ScalarMappable`
7	Default continuous colormap.
8	DEFAULT_DISC_COLORMAP : :class:`matplotlib.colors.ScalarMappable`
9	Default discrete colormap.
10	"""
11
12	import itertools	12✔
13	from pathlib import Path	12✔
14
15	import matplotlib	12✔
16	import matplotlib.axes	12✔
17	import matplotlib.collections	12✔
18	import matplotlib.colors	12✔
19	import matplotlib.lines	12✔
20	import matplotlib.patches	12✔
21	import matplotlib.pyplot as plt	12✔
22	import numpy as np	12✔
23	import pandas as pd	12✔
24	from matplotlib.legend_handler import HandlerTuple	12✔
25
26	from ...comp.codata import close	12✔
27	from ..general import copy_file	12✔
28	from ..log import Handle	12✔
29	from ..meta import pyrolite_datafolder, subkwargs	12✔
30	from .helpers import get_centroid	12✔
31	from .transform import xy_to_tlr	12✔
32
33	logger = Handle(__name__)	12✔
34
35	DEFAULT_CONT_COLORMAP = plt.cm.viridis	12✔
36	DEFAULT_DISC_COLORMAP = plt.cm.tab10	12✔
37
38
39	def _export_mplstyle(	12✔
40	src=pyrolite_datafolder("_config") / "pyrolite.mplstyle", refresh=False
41	):
42	"""
43	Export a matplotlib style file to the matplotlib style library such that one can
44	use e.g. `matplotlib.style.use("pyrolite")`.
45
46	Parameters
47	-----------
48	src : :class:`str` \| :class:`pathlib.Path`
49	File path for the style file to be exported.
50	refresh : :class:`bool`
51	Whether to re-export a style file (e.g. after updating) even if it
52	already exists in the matplotlib style libary.
53	"""
54	src_fn = Path(src)	12✔
55	dest_dir = Path(matplotlib.get_configdir()) / "stylelib"	12✔
56	dest_fn = dest_dir / src.name	12✔
57	if (not dest_fn.exists()) or refresh:	12✔
58	logger.debug("Exporting pyrolite.mplstyle to matplotlib config folder.")	12✔
59	if not dest_dir.exists():	12✔
60	dest_dir.mkdir(parents=True)	12✔
61	copy_file(src_fn, dest_dir) # copy to the destination DIR	12✔
62	logger.debug("Reloading matplotlib")	12✔
63	matplotlib.style.reload_library() # needed to load in pyrolite style NOW	12✔
64
65
66	def _restyle(f, **_style):	12✔
67	"""
68	A decorator to set the default keyword arguments for :mod:`matplotlib`
69	functions and classes which are not contained in the `matplotlibrc` file.
70	"""
71
72	def wrapped(args, *kwargs):	12✔
73	return f(args, {_style, *kwargs})	12✔
74
75	wrapped.__name__ = f.__name__	12✔
76	wrapped.__doc__ = f.__doc__	12✔
77	return wrapped	12✔
78
79
80	def _export_nonRCstyles(**kwargs):	12✔
81	"""
82	Export default options for parameters not in rcParams using :func:`_restyle`.
83	"""
84	matplotlib.axes.Axes.legend = _restyle(	12✔
85	matplotlib.axes.Axes.legend, {"bbox_to_anchor": (1, 1), kwargs}
86	)
87	matplotlib.figure.Figure.legend = _restyle(	12✔
88	matplotlib.figure.Figure.legend, bbox_to_anchor=(1, 1)
89	)
90
91
92	_export_mplstyle()	12✔
93	_export_nonRCstyles(handler_map={tuple: HandlerTuple(ndivide=None)})	12✔
94	matplotlib.style.use("pyrolite")	12✔
95
96
97	def linekwargs(kwargs):	12✔
98	"""
99	Get a subset of keyword arguments to pass to a matplotlib line-plot call.
100
101	Parameters
102	-----------
103	kwargs : :class:`dict`
104	Dictionary of keyword arguments to subset.
105
106	Returns
107	--------
108	:class:`dict`
109	"""
110	kw = subkwargs(	12✔
111	kwargs,
112	plt.plot,
113	matplotlib.axes.Axes.plot,
114	matplotlib.lines.Line2D,
115	matplotlib.collections.Collection,
116	)
117	# could trim cmap and norm here, in case they get passed accidentally
118	kw.update(	12✔
119	**dict(
120	alpha=kwargs.get("alpha"),
121	label=kwargs.get("label"),
122	clip_on=kwargs.get("clip_on", True),
123	)
124	) # issues with introspection for alpha
125	return kw	12✔
126
127
128	def scatterkwargs(kwargs):	12✔
129	"""
130	Get a subset of keyword arguments to pass to a matplotlib scatter call.
131
132	Parameters
133	-----------
134	kwargs : :class:`dict`
135	Dictionary of keyword arguments to subset.
136
137	Returns
138	--------
139	:class:`dict`
140	"""
141	kw = subkwargs(	12✔
142	kwargs,
143	plt.scatter,
144	matplotlib.axes.Axes.scatter,
145	matplotlib.collections.Collection,
146	)
147	kw.update(	12✔
148	**dict(
149	alpha=kwargs.get("alpha"),
150	label=kwargs.get("label"),
151	clip_on=kwargs.get("clip_on", True),
152	)
153	) # issues with introspection for alpha
154	return kw	12✔
155
156
157	def patchkwargs(kwargs):	12✔
158	kw = subkwargs(	12✔
159	kwargs,
160	matplotlib.axes.Axes.fill_between,
161	matplotlib.collections.PolyCollection,
162	matplotlib.patches.Patch,
163	)
164	kw.update(	12✔
165	**dict(
166	alpha=kwargs.get("alpha"),
167	label=kwargs.get("label"),
168	clip_on=kwargs.get("clip_on", True),
169	)
170	) # issues with introspection for alpha
171	return kw	12✔
172
173
174	def _mpl_sp_kw_split(kwargs):	12✔
175	"""
176	Process keyword arguments supplied to a matplotlib plot function.
177
178	Returns
179	--------
180	:class:`tuple` ( :class:`dict`, :class:`dict` )
181	"""
182	sctr_kwargs = scatterkwargs(kwargs)	12✔
183	# c kwarg is first priority, if it isn't present, use the color arg
184	if sctr_kwargs.get("c") is None:	12✔
185	sctr_kwargs = {sctr_kwargs, {"c": kwargs.get("color")}}	×
186
187	line_kwargs = linekwargs(kwargs)	12✔
188	return sctr_kwargs, line_kwargs	12✔
189
190
191	def marker_cycle(markers=["D", "s", "o", "+", "*"]):	12✔
192	"""
193	Cycle through a set of markers.
194
195	Parameters
196	----------
197	markers : :class:`list`
198	List of markers to provide to matplotlib.
199	"""
200	return itertools.cycle(markers)	12✔
201
202
203	def mappable_from_values(values, cmap=DEFAULT_CONT_COLORMAP, norm=None, **kwargs):	12✔
204	"""
205	Create a scalar mappable object from an array of values.
206
207	Returns
208	-------
209	:class:`matplotlib.cm.ScalarMappable`
210	"""
211	if isinstance(values, pd.Series):	12✔
212	values = values.values	12✔
213	sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)	12✔
214	sm.set_array(values[np.isfinite(values)])	12✔
215	return sm	12✔
216
217
218	def ternary_color(	12✔
219	tlr,
220	alpha=1.0,
221	colors=([1, 0, 0], [0, 1, 0], [0, 0, 1]),
222	coefficients=(1, 1, 1),
223	):
224	"""
225	Color a set of points by their ternary combinations of three specified colors.
226
227	Parameters
228	----------
229	tlr : :class:`numpy.ndarray`
230
231	alpha : :class:`float`
232	Alpha coefficient for the colors; to be applied multiplicatively with
233	any existing alpha value (for RGBA colors specified).
234	colors : :class:`tuple`
235	Set of colours corresponding to the top, left and right verticies,
236	respectively.
237	coefficients : :class:`tuple`
238	Coefficients for the ternary data to adjust the centre.
239
240	Returns
241	-------
242	:class:`numpy.ndarray`
243	Color array for the ternary points.
244	"""
245	colors = np.array([matplotlib.colors.to_rgba(c) for c in colors], dtype=float)	12✔
246	_tlr = close(np.array(tlr) * np.array(coefficients))	12✔
247	color = np.atleast_2d(_tlr @ colors)	12✔
248	color[:, -1] = alpha (1 - 10e-7) # avoid 'greater than 1' issues	12✔
249	return color	12✔
250
251
252	def color_ternary_polygons_by_centroid(	12✔
253	ax=None,
254	patches=None,
255	alpha=1.0,
256	colors=([1, 0, 0], [0, 1, 0], [0, 0, 1]),
257	coefficients=(1, 1, 1),
258	):
259	"""
260	Color a set of polygons within a ternary diagram by their centroid colors.
261
262	Parameters
263	----------
264	ax : :class:`matplotlib.axes.Axes`
265	Ternary axes to check for patches, if patches is not supplied.
266	patches : :class:`list`
267	List of ternary-hosted patches to apply color to.
268	alpha : :class:`float`
269	Alpha coefficient for the colors; to be applied multiplicatively with
270	any existing alpha value (for RGBA colors specified).
271	colors : :class:`tuple`
272	Set of colours corresponding to the top, left and right verticies,
273	respectively.
274	coefficients : :class:`tuple`
275	Coefficients for the ternary data to adjust the centre.
276
277	Returns
278	-------
279	patches : :class:`list`
280	List of patches, with updated facecolors.
281	"""
282
283	if patches is None:	12✔
284	if ax is None:	12✔
285	raise NotImplementedError("Either an axis or patches need to be supplied.")	×
286	patches = ax.patches	12✔
287
288	for poly in patches:	12✔
289	xy = get_centroid(poly)	×
290	tlr = xy_to_tlr(np.array([xy]))[0]	×
291	color = ternary_color(	×
292	tlr, alpha=alpha, colors=colors, coefficients=coefficients
293	)
294	poly.set_facecolor(color)	×
295
296	return patches	12✔

morganjwilliams / pyrolite / 11624563836

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