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utils.py
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utils.py
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import itertools
import textwrap
import warnings
from datetime import datetime
from inspect import getfullargspec
from typing import Any, Iterable, Mapping, Tuple, Union
import numpy as np
import pandas as pd
from ..core.options import OPTIONS
from ..core.utils import is_scalar
try:
import nc_time_axis # noqa: F401
nc_time_axis_available = True
except ImportError:
nc_time_axis_available = False
ROBUST_PERCENTILE = 2.0
_registered = False
def register_pandas_datetime_converter_if_needed():
# based on https://github.com/pandas-dev/pandas/pull/17710
global _registered
if not _registered:
pd.plotting.register_matplotlib_converters()
_registered = True
def import_matplotlib_pyplot():
"""Import pyplot as register appropriate converters."""
register_pandas_datetime_converter_if_needed()
import matplotlib.pyplot as plt
return plt
def _determine_extend(calc_data, vmin, vmax):
extend_min = calc_data.min() < vmin
extend_max = calc_data.max() > vmax
if extend_min and extend_max:
extend = "both"
elif extend_min:
extend = "min"
elif extend_max:
extend = "max"
else:
extend = "neither"
return extend
def _build_discrete_cmap(cmap, levels, extend, filled):
"""
Build a discrete colormap and normalization of the data.
"""
import matplotlib as mpl
if not filled:
# non-filled contour plots
extend = "max"
if extend == "both":
ext_n = 2
elif extend in ["min", "max"]:
ext_n = 1
else:
ext_n = 0
n_colors = len(levels) + ext_n - 1
pal = _color_palette(cmap, n_colors)
new_cmap, cnorm = mpl.colors.from_levels_and_colors(levels, pal, extend=extend)
# copy the old cmap name, for easier testing
new_cmap.name = getattr(cmap, "name", cmap)
# copy colors to use for bad, under, and over values in case they have been
# set to non-default values
try:
# matplotlib<3.2 only uses bad color for masked values
bad = cmap(np.ma.masked_invalid([np.nan]))[0]
except TypeError:
# cmap was a str or list rather than a color-map object, so there are
# no bad, under or over values to check or copy
pass
else:
under = cmap(-np.inf)
over = cmap(np.inf)
new_cmap.set_bad(bad)
# Only update under and over if they were explicitly changed by the user
# (i.e. are different from the lowest or highest values in cmap). Otherwise
# leave unchanged so new_cmap uses its default values (its own lowest and
# highest values).
if under != cmap(0):
new_cmap.set_under(under)
if over != cmap(cmap.N - 1):
new_cmap.set_over(over)
return new_cmap, cnorm
def _color_palette(cmap, n_colors):
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
colors_i = np.linspace(0, 1.0, n_colors)
if isinstance(cmap, (list, tuple)):
# we have a list of colors
cmap = ListedColormap(cmap, N=n_colors)
pal = cmap(colors_i)
elif isinstance(cmap, str):
# we have some sort of named palette
try:
# is this a matplotlib cmap?
cmap = plt.get_cmap(cmap)
pal = cmap(colors_i)
except ValueError:
# ValueError happens when mpl doesn't like a colormap, try seaborn
try:
from seaborn import color_palette
pal = color_palette(cmap, n_colors=n_colors)
except (ValueError, ImportError):
# or maybe we just got a single color as a string
cmap = ListedColormap([cmap], N=n_colors)
pal = cmap(colors_i)
else:
# cmap better be a LinearSegmentedColormap (e.g. viridis)
pal = cmap(colors_i)
return pal
# _determine_cmap_params is adapted from Seaborn:
# https://github.com/mwaskom/seaborn/blob/v0.6/seaborn/matrix.py#L158
# Used under the terms of Seaborn's license, see licenses/SEABORN_LICENSE.
def _determine_cmap_params(
plot_data,
vmin=None,
vmax=None,
cmap=None,
center=None,
robust=False,
extend=None,
levels=None,
filled=True,
norm=None,
_is_facetgrid=False,
):
"""
Use some heuristics to set good defaults for colorbar and range.
Parameters
==========
plot_data: Numpy array
Doesn't handle xarray objects
Returns
=======
cmap_params : dict
Use depends on the type of the plotting function
"""
import matplotlib as mpl
if isinstance(levels, Iterable):
levels = sorted(levels)
calc_data = np.ravel(plot_data[np.isfinite(plot_data)])
# Handle all-NaN input data gracefully
if calc_data.size == 0:
# Arbitrary default for when all values are NaN
calc_data = np.array(0.0)
# Setting center=False prevents a divergent cmap
possibly_divergent = center is not False
# Set center to 0 so math below makes sense but remember its state
center_is_none = False
if center is None:
center = 0
center_is_none = True
# Setting both vmin and vmax prevents a divergent cmap
if (vmin is not None) and (vmax is not None):
possibly_divergent = False
# Setting vmin or vmax implies linspaced levels
user_minmax = (vmin is not None) or (vmax is not None)
# vlim might be computed below
vlim = None
# save state; needed later
vmin_was_none = vmin is None
vmax_was_none = vmax is None
if vmin is None:
if robust:
vmin = np.percentile(calc_data, ROBUST_PERCENTILE)
else:
vmin = calc_data.min()
elif possibly_divergent:
vlim = abs(vmin - center)
if vmax is None:
if robust:
vmax = np.percentile(calc_data, 100 - ROBUST_PERCENTILE)
else:
vmax = calc_data.max()
elif possibly_divergent:
vlim = abs(vmax - center)
if possibly_divergent:
levels_are_divergent = (
isinstance(levels, Iterable) and levels[0] * levels[-1] < 0
)
# kwargs not specific about divergent or not: infer defaults from data
divergent = (
((vmin < 0) and (vmax > 0)) or not center_is_none or levels_are_divergent
)
else:
divergent = False
# A divergent map should be symmetric around the center value
if divergent:
if vlim is None:
vlim = max(abs(vmin - center), abs(vmax - center))
vmin, vmax = -vlim, vlim
# Now add in the centering value and set the limits
vmin += center
vmax += center
# now check norm and harmonize with vmin, vmax
if norm is not None:
if norm.vmin is None:
norm.vmin = vmin
else:
if not vmin_was_none and vmin != norm.vmin:
raise ValueError("Cannot supply vmin and a norm with a different vmin.")
vmin = norm.vmin
if norm.vmax is None:
norm.vmax = vmax
else:
if not vmax_was_none and vmax != norm.vmax:
raise ValueError("Cannot supply vmax and a norm with a different vmax.")
vmax = norm.vmax
# if BoundaryNorm, then set levels
if isinstance(norm, mpl.colors.BoundaryNorm):
levels = norm.boundaries
# Choose default colormaps if not provided
if cmap is None:
if divergent:
cmap = OPTIONS["cmap_divergent"]
else:
cmap = OPTIONS["cmap_sequential"]
# Handle discrete levels
if levels is not None:
if is_scalar(levels):
if user_minmax:
levels = np.linspace(vmin, vmax, levels)
elif levels == 1:
levels = np.asarray([(vmin + vmax) / 2])
else:
# N in MaxNLocator refers to bins, not ticks
ticker = mpl.ticker.MaxNLocator(levels - 1)
levels = ticker.tick_values(vmin, vmax)
vmin, vmax = levels[0], levels[-1]
# GH3734
if vmin == vmax:
vmin, vmax = mpl.ticker.LinearLocator(2).tick_values(vmin, vmax)
if extend is None:
extend = _determine_extend(calc_data, vmin, vmax)
if levels is not None or isinstance(norm, mpl.colors.BoundaryNorm):
cmap, newnorm = _build_discrete_cmap(cmap, levels, extend, filled)
norm = newnorm if norm is None else norm
# vmin & vmax needs to be None if norm is passed
# TODO: always return a norm with vmin and vmax
if norm is not None:
vmin = None
vmax = None
return dict(
vmin=vmin, vmax=vmax, cmap=cmap, extend=extend, levels=levels, norm=norm
)
def _infer_xy_labels_3d(darray, x, y, rgb):
"""
Determine x and y labels for showing RGB images.
Attempts to infer which dimension is RGB/RGBA by size and order of dims.
"""
assert rgb is None or rgb != x
assert rgb is None or rgb != y
# Start by detecting and reporting invalid combinations of arguments
assert darray.ndim == 3
not_none = [a for a in (x, y, rgb) if a is not None]
if len(set(not_none)) < len(not_none):
raise ValueError(
"Dimension names must be None or unique strings, but imshow was "
"passed x=%r, y=%r, and rgb=%r." % (x, y, rgb)
)
for label in not_none:
if label not in darray.dims:
raise ValueError(f"{label!r} is not a dimension")
# Then calculate rgb dimension if certain and check validity
could_be_color = [
label
for label in darray.dims
if darray[label].size in (3, 4) and label not in (x, y)
]
if rgb is None and not could_be_color:
raise ValueError(
"A 3-dimensional array was passed to imshow(), but there is no "
"dimension that could be color. At least one dimension must be "
"of size 3 (RGB) or 4 (RGBA), and not given as x or y."
)
if rgb is None and len(could_be_color) == 1:
rgb = could_be_color[0]
if rgb is not None and darray[rgb].size not in (3, 4):
raise ValueError(
"Cannot interpret dim %r of size %s as RGB or RGBA."
% (rgb, darray[rgb].size)
)
# If rgb dimension is still unknown, there must be two or three dimensions
# in could_be_color. We therefore warn, and use a heuristic to break ties.
if rgb is None:
assert len(could_be_color) in (2, 3)
rgb = could_be_color[-1]
warnings.warn(
"Several dimensions of this array could be colors. Xarray "
"will use the last possible dimension (%r) to match "
"matplotlib.pyplot.imshow. You can pass names of x, y, "
"and/or rgb dimensions to override this guess." % rgb
)
assert rgb is not None
# Finally, we pick out the red slice and delegate to the 2D version:
return _infer_xy_labels(darray.isel(**{rgb: 0}), x, y)
def _infer_xy_labels(darray, x, y, imshow=False, rgb=None):
"""
Determine x and y labels. For use in _plot2d
darray must be a 2 dimensional data array, or 3d for imshow only.
"""
if (x is not None) and (x == y):
raise ValueError("x and y cannot be equal.")
if imshow and darray.ndim == 3:
return _infer_xy_labels_3d(darray, x, y, rgb)
if x is None and y is None:
if darray.ndim != 2:
raise ValueError("DataArray must be 2d")
y, x = darray.dims
elif x is None:
_assert_valid_xy(darray, y, "y")
x = darray.dims[0] if y == darray.dims[1] else darray.dims[1]
elif y is None:
_assert_valid_xy(darray, x, "x")
y = darray.dims[0] if x == darray.dims[1] else darray.dims[1]
else:
_assert_valid_xy(darray, x, "x")
_assert_valid_xy(darray, y, "y")
if (
all(k in darray._level_coords for k in (x, y))
and darray._level_coords[x] == darray._level_coords[y]
):
raise ValueError("x and y cannot be levels of the same MultiIndex")
return x, y
def _assert_valid_xy(darray, xy, name):
"""
make sure x and y passed to plotting functions are valid
"""
# MultiIndex cannot be plotted; no point in allowing them here
multiindex = {darray._level_coords[lc] for lc in darray._level_coords}
valid_xy = (
set(darray.dims) | set(darray.coords) | set(darray._level_coords)
) - multiindex
if xy not in valid_xy:
valid_xy_str = "', '".join(sorted(valid_xy))
raise ValueError(f"{name} must be one of None, '{valid_xy_str}'")
def get_axis(figsize=None, size=None, aspect=None, ax=None, **kwargs):
try:
import matplotlib as mpl
import matplotlib.pyplot as plt
except ImportError:
raise ImportError("matplotlib is required for plot.utils.get_axis")
if figsize is not None:
if ax is not None:
raise ValueError("cannot provide both `figsize` and " "`ax` arguments")
if size is not None:
raise ValueError("cannot provide both `figsize` and " "`size` arguments")
_, ax = plt.subplots(figsize=figsize)
elif size is not None:
if ax is not None:
raise ValueError("cannot provide both `size` and `ax` arguments")
if aspect is None:
width, height = mpl.rcParams["figure.figsize"]
aspect = width / height
figsize = (size * aspect, size)
_, ax = plt.subplots(figsize=figsize)
elif aspect is not None:
raise ValueError("cannot provide `aspect` argument without `size`")
if kwargs and ax is not None:
raise ValueError("cannot use subplot_kws with existing ax")
if ax is None:
ax = plt.gca(**kwargs)
return ax
def label_from_attrs(da, extra=""):
""" Makes informative labels if variable metadata (attrs) follows
CF conventions. """
if da.attrs.get("long_name"):
name = da.attrs["long_name"]
elif da.attrs.get("standard_name"):
name = da.attrs["standard_name"]
elif da.name is not None:
name = da.name
else:
name = ""
if da.attrs.get("units"):
units = " [{}]".format(da.attrs["units"])
else:
units = ""
return "\n".join(textwrap.wrap(name + extra + units, 30))
def _interval_to_mid_points(array):
"""
Helper function which returns an array
with the Intervals' mid points.
"""
return np.array([x.mid for x in array])
def _interval_to_bound_points(array):
"""
Helper function which returns an array
with the Intervals' boundaries.
"""
array_boundaries = np.array([x.left for x in array])
array_boundaries = np.concatenate((array_boundaries, np.array([array[-1].right])))
return array_boundaries
def _interval_to_double_bound_points(xarray, yarray):
"""
Helper function to deal with a xarray consisting of pd.Intervals. Each
interval is replaced with both boundaries. I.e. the length of xarray
doubles. yarray is modified so it matches the new shape of xarray.
"""
xarray1 = np.array([x.left for x in xarray])
xarray2 = np.array([x.right for x in xarray])
xarray = list(itertools.chain.from_iterable(zip(xarray1, xarray2)))
yarray = list(itertools.chain.from_iterable(zip(yarray, yarray)))
return xarray, yarray
def _resolve_intervals_1dplot(xval, yval, xlabel, ylabel, kwargs):
"""
Helper function to replace the values of x and/or y coordinate arrays
containing pd.Interval with their mid-points or - for step plots - double
points which double the length.
"""
# Is it a step plot? (see matplotlib.Axes.step)
if kwargs.get("drawstyle", "").startswith("steps-"):
# Convert intervals to double points
if _valid_other_type(np.array([xval, yval]), [pd.Interval]):
raise TypeError("Can't step plot intervals against intervals.")
if _valid_other_type(xval, [pd.Interval]):
xval, yval = _interval_to_double_bound_points(xval, yval)
if _valid_other_type(yval, [pd.Interval]):
yval, xval = _interval_to_double_bound_points(yval, xval)
# Remove steps-* to be sure that matplotlib is not confused
del kwargs["drawstyle"]
# Is it another kind of plot?
else:
# Convert intervals to mid points and adjust labels
if _valid_other_type(xval, [pd.Interval]):
xval = _interval_to_mid_points(xval)
xlabel += "_center"
if _valid_other_type(yval, [pd.Interval]):
yval = _interval_to_mid_points(yval)
ylabel += "_center"
# return converted arguments
return xval, yval, xlabel, ylabel, kwargs
def _resolve_intervals_2dplot(val, func_name):
"""
Helper function to replace the values of a coordinate array containing
pd.Interval with their mid-points or - for pcolormesh - boundaries which
increases length by 1.
"""
label_extra = ""
if _valid_other_type(val, [pd.Interval]):
if func_name == "pcolormesh":
val = _interval_to_bound_points(val)
else:
val = _interval_to_mid_points(val)
label_extra = "_center"
return val, label_extra
def _valid_other_type(x, types):
"""
Do all elements of x have a type from types?
"""
return all(any(isinstance(el, t) for t in types) for el in np.ravel(x))
def _valid_numpy_subdtype(x, numpy_types):
"""
Is any dtype from numpy_types superior to the dtype of x?
"""
# If any of the types given in numpy_types is understood as numpy.generic,
# all possible x will be considered valid. This is probably unwanted.
for t in numpy_types:
assert not np.issubdtype(np.generic, t)
return any(np.issubdtype(x.dtype, t) for t in numpy_types)
def _ensure_plottable(*args):
"""
Raise exception if there is anything in args that can't be plotted on an
axis by matplotlib.
"""
numpy_types = [np.floating, np.integer, np.timedelta64, np.datetime64, np.bool_]
other_types = [datetime]
try:
import cftime
cftime_datetime = [cftime.datetime]
except ImportError:
cftime_datetime = []
other_types = other_types + cftime_datetime
for x in args:
if not (
_valid_numpy_subdtype(np.array(x), numpy_types)
or _valid_other_type(np.array(x), other_types)
):
raise TypeError(
"Plotting requires coordinates to be numeric, boolean, "
"or dates of type numpy.datetime64, "
"datetime.datetime, cftime.datetime or "
f"pandas.Interval. Received data of type {np.array(x).dtype} instead."
)
if (
_valid_other_type(np.array(x), cftime_datetime)
and not nc_time_axis_available
):
raise ImportError(
"Plotting of arrays of cftime.datetime "
"objects or arrays indexed by "
"cftime.datetime objects requires the "
"optional `nc-time-axis` (v1.2.0 or later) "
"package."
)
def _is_numeric(arr):
numpy_types = [np.floating, np.integer]
return _valid_numpy_subdtype(arr, numpy_types)
def _add_colorbar(primitive, ax, cbar_ax, cbar_kwargs, cmap_params):
cbar_kwargs.setdefault("extend", cmap_params["extend"])
if cbar_ax is None:
cbar_kwargs.setdefault("ax", ax)
else:
cbar_kwargs.setdefault("cax", cbar_ax)
# dont pass extend as kwarg if it is in the mappable
if hasattr(primitive, "extend"):
cbar_kwargs.pop("extend")
fig = ax.get_figure()
cbar = fig.colorbar(primitive, **cbar_kwargs)
return cbar
def _rescale_imshow_rgb(darray, vmin, vmax, robust):
assert robust or vmin is not None or vmax is not None
# Calculate vmin and vmax automatically for `robust=True`
if robust:
if vmax is None:
vmax = np.nanpercentile(darray, 100 - ROBUST_PERCENTILE)
if vmin is None:
vmin = np.nanpercentile(darray, ROBUST_PERCENTILE)
# If not robust and one bound is None, calculate the default other bound
# and check that an interval between them exists.
elif vmax is None:
vmax = 255 if np.issubdtype(darray.dtype, np.integer) else 1
if vmax < vmin:
raise ValueError(
"vmin=%r is less than the default vmax (%r) - you must supply "
"a vmax > vmin in this case." % (vmin, vmax)
)
elif vmin is None:
vmin = 0
if vmin > vmax:
raise ValueError(
"vmax=%r is less than the default vmin (0) - you must supply "
"a vmin < vmax in this case." % vmax
)
# Scale interval [vmin .. vmax] to [0 .. 1], with darray as 64-bit float
# to avoid precision loss, integer over/underflow, etc with extreme inputs.
# After scaling, downcast to 32-bit float. This substantially reduces
# memory usage after we hand `darray` off to matplotlib.
darray = ((darray.astype("f8") - vmin) / (vmax - vmin)).astype("f4")
return np.minimum(np.maximum(darray, 0), 1)
def _update_axes(
ax,
xincrease,
yincrease,
xscale=None,
yscale=None,
xticks=None,
yticks=None,
xlim=None,
ylim=None,
):
"""
Update axes with provided parameters
"""
if xincrease is None:
pass
elif xincrease and ax.xaxis_inverted():
ax.invert_xaxis()
elif not xincrease and not ax.xaxis_inverted():
ax.invert_xaxis()
if yincrease is None:
pass
elif yincrease and ax.yaxis_inverted():
ax.invert_yaxis()
elif not yincrease and not ax.yaxis_inverted():
ax.invert_yaxis()
# The default xscale, yscale needs to be None.
# If we set a scale it resets the axes formatters,
# This means that set_xscale('linear') on a datetime axis
# will remove the date labels. So only set the scale when explicitly
# asked to. https://github.com/matplotlib/matplotlib/issues/8740
if xscale is not None:
ax.set_xscale(xscale)
if yscale is not None:
ax.set_yscale(yscale)
if xticks is not None:
ax.set_xticks(xticks)
if yticks is not None:
ax.set_yticks(yticks)
if xlim is not None:
ax.set_xlim(xlim)
if ylim is not None:
ax.set_ylim(ylim)
def _is_monotonic(coord, axis=0):
"""
>>> _is_monotonic(np.array([0, 1, 2]))
True
>>> _is_monotonic(np.array([2, 1, 0]))
True
>>> _is_monotonic(np.array([0, 2, 1]))
False
"""
if coord.shape[axis] < 3:
return True
else:
n = coord.shape[axis]
delta_pos = coord.take(np.arange(1, n), axis=axis) >= coord.take(
np.arange(0, n - 1), axis=axis
)
delta_neg = coord.take(np.arange(1, n), axis=axis) <= coord.take(
np.arange(0, n - 1), axis=axis
)
return np.all(delta_pos) or np.all(delta_neg)
def _infer_interval_breaks(coord, axis=0, check_monotonic=False):
"""
>>> _infer_interval_breaks(np.arange(5))
array([-0.5, 0.5, 1.5, 2.5, 3.5, 4.5])
>>> _infer_interval_breaks([[0, 1], [3, 4]], axis=1)
array([[-0.5, 0.5, 1.5],
[ 2.5, 3.5, 4.5]])
"""
coord = np.asarray(coord)
if check_monotonic and not _is_monotonic(coord, axis=axis):
raise ValueError(
"The input coordinate is not sorted in increasing "
"order along axis %d. This can lead to unexpected "
"results. Consider calling the `sortby` method on "
"the input DataArray. To plot data with categorical "
"axes, consider using the `heatmap` function from "
"the `seaborn` statistical plotting library." % axis
)
deltas = 0.5 * np.diff(coord, axis=axis)
if deltas.size == 0:
deltas = np.array(0.0)
first = np.take(coord, [0], axis=axis) - np.take(deltas, [0], axis=axis)
last = np.take(coord, [-1], axis=axis) + np.take(deltas, [-1], axis=axis)
trim_last = tuple(
slice(None, -1) if n == axis else slice(None) for n in range(coord.ndim)
)
return np.concatenate([first, coord[trim_last] + deltas, last], axis=axis)
def _process_cmap_cbar_kwargs(
func,
data,
cmap=None,
colors=None,
cbar_kwargs: Union[Iterable[Tuple[str, Any]], Mapping[str, Any]] = None,
levels=None,
_is_facetgrid=False,
**kwargs,
):
"""
Parameters
==========
func : plotting function
data : ndarray,
Data values
Returns
=======
cmap_params
cbar_kwargs
"""
cbar_kwargs = {} if cbar_kwargs is None else dict(cbar_kwargs)
if "contour" in func.__name__ and levels is None:
levels = 7 # this is the matplotlib default
# colors is mutually exclusive with cmap
if cmap and colors:
raise ValueError("Can't specify both cmap and colors.")
# colors is only valid when levels is supplied or the plot is of type
# contour or contourf
if colors and (("contour" not in func.__name__) and (levels is None)):
raise ValueError("Can only specify colors with contour or levels")
# we should not be getting a list of colors in cmap anymore
# is there a better way to do this test?
if isinstance(cmap, (list, tuple)):
raise ValueError(
"Specifying a list of colors in cmap is deprecated. "
"Use colors keyword instead."
)
cmap_kwargs = {
"plot_data": data,
"levels": levels,
"cmap": colors if colors else cmap,
"filled": func.__name__ != "contour",
}
cmap_args = getfullargspec(_determine_cmap_params).args
cmap_kwargs.update((a, kwargs[a]) for a in cmap_args if a in kwargs)
if not _is_facetgrid:
cmap_params = _determine_cmap_params(**cmap_kwargs)
else:
cmap_params = {
k: cmap_kwargs[k]
for k in ["vmin", "vmax", "cmap", "extend", "levels", "norm"]
}
return cmap_params, cbar_kwargs