"""Plotter for Electrochemistry"""
import warnings
import numpy as np
from . import MPLPlotter, color_axis
from ..tools import deprecate
from ..exceptions import SeriesNotFoundError
[docs]class ECPlotter(MPLPlotter):
"""A matplotlib plotter specialized in electrochemistry measurements."""
def __init__(self, measurement=None):
"""Initiate the ECPlotter with its default Meausurement to plot"""
super().__init__()
self.measurement = measurement
[docs] @deprecate("0.1", "Use `U_name` instead.", "0.3", kwarg_name="V_str")
@deprecate("0.1", "Use `J_name` instead.", "0.3", kwarg_name="J_str")
@deprecate("0.1", "Use `U_color` instead.", "0.3", kwarg_name="V_color")
def plot_measurement(
self,
*,
measurement=None,
tspan=None,
U_name=None,
J_name=None,
U_color=None,
J_color=None,
V_str=None,
J_str=None,
V_color=None,
axes=None,
**plot_kwargs,
):
"""Plot two variables on two y-axes vs time
All arguments are optional. By default it plots potential in black on the left
y-axis and current in red on the right y-axis, using data from its entire
measurement. The axes are colored to match the traces and labeled with the
respective series names.
Args:
measurement (Measurement): The measurement to plot, if not the one the
plotter was initiated with.
tspan (iter of float): The timespan (wrt to measurement.tstamp) to plot.
axes (list of matplotlib.Axis): Two axes to plot on, if not the default
new twinx()'d axes. axes[0] is for `U_name` and axes[1] for `J_name`.
U_name (string): The name of the ValueSeries to plot on the left y-axis.
Defaults to measurement.V_str, which for an ECMeasurement is the name
of its most calibrated/correct potential.
J_name (string): The name of the ValueSeries to plot on the right y-axis.
Defaults to measurement.J_str, which for an ECMeasurement is the name
of its most normalized/correct current.
U_color (str): The color to plot U_name. Defaults to black.
J_color (str): The color to plot J_name. Defaults to red.
V_str (str): DEPRECATED. Use `U_name`.
J_str (str): DEPRECATED. Use `J_name`.
V_color (str): DEPRECATED. Use `U_color`.
**plot_kwargs (dict): Additional key-word arguments are passed to
matplotlib's plot() function. See below for a few examples
Keyword Arguments:
linestle (str): Type of line, e.g. "-" for solid or "--" for dotted
Returns list of matplotlib.pyplot.Axis: The axes plotted on.
"""
measurement = measurement or self.measurement
# apply deprecated arguments (the user will get a warning):
U_name = U_name or V_str
J_name = J_name or J_str
U_color = U_color or V_color
# apply defaults.
U_name = U_name or measurement.U_name
J_name = J_name or measurement.J_name
U_color = U_color or "k"
J_color = J_color or "r"
if axes:
ax1, ax2 = axes
else:
ax1 = self.new_ax()
ax2 = ax1.twinx()
axes = [ax1, ax2]
ax1.set_xlabel("time / [s]")
ax1.set_ylabel(U_name)
ax2.set_ylabel(J_name)
color_axis(ax1, U_color, lr="left")
color_axis(ax2, J_color, lr="right")
try:
t_v, v = measurement.grab(U_name, tspan=tspan)
except SeriesNotFoundError:
warnings.warn(f"No '{U_name}' found in {measurement}")
else:
ax1.plot(t_v, v, "-", color=U_color, label=U_name, **plot_kwargs)
try:
t_j, j = measurement.grab(J_name, tspan=tspan)
except SeriesNotFoundError:
warnings.warn(f"No '{J_name}' found in {measurement}")
else:
ax2.plot(t_j, j, "-", color=J_color, label=J_name, **plot_kwargs)
return axes
[docs] def plot_vs_potential(
self,
measurement=None,
tspan=None,
U_name=None,
J_name=None,
ax=None,
**plot_kwargs,
):
"""Plot an ECMeasurement with electrode potential on the x-axis.
This can actually plot with anything on the x-axis, by specifying what you want
on the x-axis using V_str. The y-axis variable, which can be specified by J_str,
is interpolated onto the time corresponding to the x-axis variable.
.. TODO::
This is a special case of the not-yet-implemented generalized
`plot_vs`. Consider an inheritance structure to reduce redundancy in
future plotters.
sub-TODO: hide or fix TODO's using sphix boxes.
All arguments are optional. By default it will plot current vs potential in
black on a single axis for the whole experiment.
TODO: color gradient (cmap=inferno) from first to last cycle.
Args:
measurement (Measurement): What to plot. Defaults to the measurement the
plotter was initialized with
tspan (iter of float): The timespan, relative to vs measurement.tstamp, on
which to plot.
U_name (str): Name of the x-axis variable. Defaults to calibrated potential
J_name (str): Name of the y-axis variable. Defaults to normalized current.
ax (matplotlib.pyplot.Axis): The axis to plot on, if not a new one.
**plot_kwargs (dict): Additional key-word arguments are passed to
matplotlib's plot() function. See below for a few examples
Keyword Arguments:
color (color): Color of the trace, e.g. "r", "blue", or RGB like [0, 0, 1]
linestle (str): Type of line, e.g. "-" for solid or "--" for dotted
Returns matplotlib.pyplot.axis: The axis plotted on.
"""
measurement = measurement or self.measurement
U_name = U_name or measurement.U_name
J_name = J_name or measurement.J_name
t_v, v = measurement.grab(U_name, tspan=tspan)
t_j, j = measurement.grab(J_name, tspan=tspan)
j_v = np.interp(t_v, t_j, j)
if not ax:
ax = self.new_ax()
if "color" not in plot_kwargs:
plot_kwargs["color"] = "k"
ax.plot(v, j_v, **plot_kwargs)
ax.set_xlabel(U_name)
ax.set_ylabel(J_name)
return ax
[docs]class CVDiffPlotter(MPLPlotter):
"""A matplotlib plotter for highlighting the difference between two cv's."""
def __init__(self, measurement=None):
"""Initiate the ECPlotter with its default CyclicVoltammagramDiff to plot"""
super().__init__()
self.measurement = measurement
[docs] def plot(self, measurement=None, ax=None):
"""Plot the two cycles of the CVDiff measurement and fill in the areas between
example: https://ixdat.readthedocs.io/en/latest/_images/cv_diff.svg
"""
measurement = measurement or self.measurement
# FIXME: This is probably the wrong use of plotter functions.
# see https://github.com/ixdat/ixdat/pull/30/files#r810926968
ax = ECPlotter.plot_vs_potential(
self, measurement=measurement.cv_compare_1, ax=ax, color="g"
)
ax = ECPlotter.plot_vs_potential(
self, measurement=measurement.cv_compare_2, ax=ax, color="k", linestyle="--"
)
t1, U1 = measurement.cv_compare_1.grab("potential")
J1 = measurement.cv_compare_1.grab_for_t("current", t=t1)
J_diff = measurement.grab_for_t("current", t=t1)
# a mask which is true when cv_1 had bigger current than cv_2:
v_scan = measurement.grab_for_t("scan_rate", t=t1)
mask = np.logical_xor(0 < J_diff, v_scan < 0)
ax.fill_between(U1, J1 - J_diff, J1, where=mask, alpha=0.2, color="g")
ax.fill_between(
U1,
J1 - J_diff,
J1,
where=np.logical_not(mask),
alpha=0.1,
hatch="//",
color="g",
)
return ax
[docs] def plot_measurement(self, measurement=None, axes=None, **kwargs):
"""Plot the difference between the two cv's vs time"""
measurement = measurement or self.measurement
# FIXME: not correct useage of
return ECPlotter.plot_measurement(
self, measurement=measurement, axes=axes, **kwargs
)
[docs] def plot_diff(self, measurement=None, tspan=None, ax=None):
"""Plot the difference between the two cv's vs potential.
The trace is solid where the current in cv_2 is greater than cv_1 in the anodic
scan or the current cv_2 is more negative than cv_1 in the cathodic scan.
"""
measurement = measurement or self.measurement
t, U = measurement.grab("potential", tspan=tspan, include_endpoints=False)
j_diff = measurement.grab_for_t("current", t)
v_scan = measurement.grab_for_t("scan_rate", t)
# a mask which is true when cv_1 had bigger current than cv_2:
mask = np.logical_xor(0 < j_diff, v_scan < 0)
if not ax:
ax = self.new_ax()
ax.plot(U[mask], j_diff[mask], "k-", label="cv1 > cv2")
ax.plot(
U[np.logical_not(mask)],
j_diff[np.logical_not(mask)],
"k--",
label="cv1 < cv2",
)
return ax
[docs] def plot_vs_potential(self):
"""FIXME: This is needed to satisfy ECMeasurement.__init__"""
pass