def plot(self, start=0, end=None, overlay=None):
"""Plots the whole time_signal for each component.
Parameters
----------
start : float
start time for plotting
end : float
end time for plotting
See also
--------
CADETProcess.plot
"""
x = self.time / 60
y = self.solution / 1000
ymax = np.max(y)
fig, ax = plotting.setup_figure()
ax.plot(x, y)
if overlay is not None:
ymax = 1.1 * np.max(overlay)
plotting.add_overlay(ax, overlay)
layout = plotting.Layout()
layout.x_label = '$time~/~min$'
layout.y_label = '$V~/~L$'
layout.xlim = (start, end)
layout.ylim = (0, ymax)
plotting.set_layout(fig, ax, layout)
return ax
def plot_purity(self, start=0, end=None):
"""Plots the local purity for each component of the concentration
profile.
Parameters
----------
start : float
start time for plotting
end : float
ent time for plotting
See also
--------
plotlib
plot
"""
x = self.time / 60
y = self.local_purity * 100
fig, ax = plotting.setup_figure()
ax.plot(x,y)
layout = plotting.Layout()
layout.x_label = '$time~/~min$'
layout.y_label = '$c~/~mol \cdot L^{-1}$'
layout.xlim = (start, end)
layout.ylim = (0, 1.1*np.max(y))
plotting.set_layout(fig, ax, layout)
return ax
def _plot_2D(self, t, comp, state, vmax):
x = self.axial_coordinates
y = self.particle_coordinates
if not self.time[0] <= t <= self.time[-1]:
raise ValueError("Time exceeds bounds.")
t_i = np.where(t <= self.time)[0][0]
c_i = comp * self.n_bound + state
v = self.solution[t_i, :, :, c_i].transpose()
if vmax is None:
vmax = v.max()
fig, ax = plotting.setup_figure()
mesh = ax.pcolormesh(x, y, v, shading='gouraud', vmin=0, vmax=vmax)
plotting.add_text(ax, f'time = {t:.2f} s')
layout = plotting.Layout()
layout.title = f'Solid phase concentration, comp={comp}, state={state}'
layout.x_label = '$z~/~m$'
layout.y_label = '$r~/~m$'
layout.labels = self.component_system.labels[c_i]
plotting.set_layout(fig, ax, layout)
fig.colorbar(mesh)
return fig, ax, mesh
def plot(self, start=0, end=None):
"""Plots the whole time_signal for each component.
Parameters
----------
start : float
start time for plotting
end : float
end time for plotting
See also
--------
plotlib
plot_purity
"""
x = self.time / 60
y = self.signal
fig, ax = plotting.setup_figure()
ax.plot(x,y)
layout = plotting.Layout()
layout.x_label = '$time~/~min$'
layout.y_label = '$c~/~mol \cdot L^{-1}$'
layout.xlim = (start, end)
layout.ylim = (0, 1.1*np.max(y))
plotting.set_layout(fig, ax, layout)
return ax
def plot_events(self):
"""Plot parameter state as function of time.
"""
time = np.linspace(0, self.cycle_time, 1001)
for parameter, tl in self.parameter_timelines.items():
y = tl.value(time)
fig, ax = plotting.setup_figure()
layout = plotting.Layout()
layout.title = str(parameter)
layout.x_label = '$time~/~min$'
layout.y_label = '$state$'
ax.plot(time / 60, y)
plotting.set_layout(fig, ax, layout)
def plot(self):
"""Plot section state over time.
"""
start = self.sections[0].start
end = self.sections[-1].end
time = np.linspace(start, end, 1001) / 60
y = self.value(time)
fig, ax = plotting.setup_figure()
ax.plot(time, y)
layout = plotting.Layout()
layout.x_label = '$time~/~min$'
layout.y_label = '$state$'
layout.xlim = (start / 60, end / 60)
layout.ylim = (0, 1.1 * np.max(y))
plotting.set_layout(fig, ax, layout)
return ax
def plot_at_location(self, z, overlay=None, ymax=None):
"""Plot bulk solution over time at given location.
Parameters
----------
z : float
space for plotting
See also
--------
plot_at_time
CADETProcess.plotting
"""
x = self.time
if not self.axial_coordinates[0] <= z <= self.axial_coordinates[-1]:
raise ValueError("Axial coordinate exceets boundaries.")
z_i = np.where(z <= self.axial_coordinates)[0][0]
y = self.solution[:, z_i]
if ymax is None:
ymax = 1.1 * np.max(y)
fig, ax = plotting.setup_figure()
ax.plot(x, y)
plotting.add_text(ax, f'z = {z:.2f} m')
if overlay is not None:
ymax = np.max(overlay)
plotting.add_overlay(ax, overlay)
layout = plotting.Layout()
layout.x_label = '$time~/~min$'
layout.y_label = '$c~/~mM$'
layout.ylim = (0, ymax)
plotting.set_layout(fig, ax, layout)
return ax
def plot_at_time(self, t, overlay=None, ymax=None):
"""Plot bulk solution over space at given time.
Parameters
----------
t : float
time for plotting
See also
--------
plot_at_location
CADETProcess.plotting
"""
x = self.axial_coordinates
if not self.time[0] <= t <= self.time[-1]:
raise ValueError("Time exceeds bounds.")
t_i = np.where(t <= self.time)[0][0]
y = self.solution[t_i, :]
if ymax is None:
ymax = 1.1 * np.max(y)
fig, ax = plotting.setup_figure()
ax.plot(x, y)
plotting.add_text(ax, f'time = {t:.2f} s')
if overlay is not None:
ymax = np.max(overlay)
plotting.add_overlay(ax, overlay)
layout = plotting.Layout()
layout.x_label = '$z~/~m$'
layout.y_label = '$c~/~mM$'
layout.ylim = (0, ymax)
plotting.set_layout(fig, ax, layout)
return ax
def _plot_1D(self, t, ymax):
x = self.axial_coordinates
if not self.time[0] <= t <= self.time[-1]:
raise ValueError("Time exceeds bounds.")
t_i = np.where(t <= self.time)[0][0]
y = self.solution[t_i, :]
if ymax is None:
ymax = 1.1 * np.max(y)
fig, ax = plotting.setup_figure()
ax.plot(x, y)
plotting.add_text(ax, f'time = {t:.2f} s')
layout = plotting.Layout()
layout.x_label = '$z~/~m$'
layout.y_label = '$c~/~mM$'
layout.ylim = (0, ymax)
plotting.set_layout(fig, ax, layout)
return fig, ax
def plot_solution_1D(solution,
ax=None,
layout=None,
only_plot_total_concentrations=False,
alpha=1,
hide_labels=False,
hide_species_labels=True,
secondary_axis=None,
secondary_layout=None,
show_legend=True):
time = solution.time / 60
sol = solution.solution
if ax is None:
fig, ax = plotting.setup_figure()
total_concentration = solution.total_concentration()
if secondary_axis is not None:
ax_secondary = ax.twinx()
else:
ax_secondary = None
species_index = 0
for i, comp in enumerate(solution.component_system.components):
color = next(ax._get_lines.prop_cycler)['color']
if hide_labels:
label = None
else:
label = comp.name
if secondary_axis is not None and i in secondary_axis.component_indices:
a = ax_secondary
else:
a = ax
if secondary_axis is not None \
and secondary_axis.transform is not None \
and i in secondary_axis.component_indices:
y = secondary_axis.transform(total_concentration[..., i])
else:
y = total_concentration[..., i]
a.plot(time, y, label=label, color=color, alpha=alpha)
if not only_plot_total_concentrations:
if comp.n_species == 1:
species_index += 1
continue
for s, species in enumerate(comp.species):
if hide_species_labels:
label = None
else:
label = s
if secondary_axis is not None and i in secondary_axis.component_indices:
a = ax_secondary
else:
a = ax
if secondary_axis is not None \
and secondary_axis.transform is not None \
and i in secondary_axis.component_indices:
y = secondary_axis.transform(sol[..., species_index])
else:
y = sol[..., species_index]
a.plot(time, y, '--', label=label, color=color, alpha=alpha)
species_index += 1
if layout is not None:
plotting.set_layout(fig, ax, layout, show_legend, ax_secondary,
secondary_layout)
return ax, fig
