def get_isotope_string(atom_number, atom_mass):
"""Get the isotope string in the format e.g. Ni56
Parameters
----------
atom_number : int
Atomic number
atom_mass : int
Atomic mass
Returns
-------
str
Isotope string in the format e.g. Ni56
"""
return atomic_number2element_symbol(atom_number) + str(atom_mass)
def _plot_absorption_ply(self):
"""Plot absorption part of the SDEC Plot using plotly."""
elements_z = self.absorption_luminosities_df.columns
nelements = len(elements_z)
for i, atomic_num in enumerate(elements_z):
self.fig.add_trace(
go.Scatter(
x=self.absorption_luminosities_df.index,
# to plot absorption luminosities along negative y-axis
y=self.absorption_luminosities_df[atomic_num] * -1,
mode="none",
name=atomic_number2element_symbol(atomic_num),
fillcolor=self.to_rgb255_string(self.cmap(i / nelements)),
stackgroup="absorption",
showlegend=False,
))
def _show_colorbar_ply(self):
"""Show plotly colorbar with labels of elements mapped to colors."""
# Interpolate [0, 1] range to create bins equal to number of elements
colorscale_bins = np.linspace(0, 1, num=self.elements.size + 1)
# Create a categorical colorscale [a list of (reference point, color)]
# by mapping same reference points (excluding 1st and last bin edge)
# twice in a row (https://plotly.com/python/colorscales/#constructing-a-discrete-or-discontinuous-color-scale)
categorical_colorscale = []
for i in range(self.elements.size):
color = self.to_rgb255_string(self.cmap(colorscale_bins[i]))
categorical_colorscale.append((colorscale_bins[i], color))
categorical_colorscale.append((colorscale_bins[i + 1], color))
coloraxis_options = dict(
colorscale=categorical_colorscale,
showscale=True,
cmin=0,
cmax=self.elements.size,
colorbar=dict(
title="Elements",
tickvals=np.arange(0, self.elements.size) + 0.5,
ticktext=[
atomic_number2element_symbol(atomic_num)
for atomic_num in self.elements
],
# to change length and position of colorbar
len=0.75,
yanchor="top",
y=0.75,
),
)
# Plot an invisible one point scatter trace, to make colorbar show up
scatter_point_idx = pu.get_mid_point_idx(self.plot_wavelength)
self.fig.add_trace(
go.Scatter(
x=self.plot_wavelength[scatter_point_idx],
y=[0],
mode="markers",
showlegend=False,
hoverinfo="skip",
marker=dict(color=[0], opacity=0, **coloraxis_options),
)
)
def _show_colorbar_mpl(self):
"""Show matplotlib colorbar with labels of elements mapped to colors."""
color_values = [
self.cmap(i / self.elements.size) for i in range(self.elements.size)
]
custcmap = clr.ListedColormap(color_values)
norm = clr.Normalize(vmin=0, vmax=self.elements.size)
mappable = cm.ScalarMappable(norm=norm, cmap=custcmap)
mappable.set_array(np.linspace(1, self.elements.size + 1, 256))
cbar = plt.colorbar(mappable, ax=self.ax)
bounds = np.arange(self.elements.size) + 0.5
cbar.set_ticks(bounds)
elements_name = [
atomic_number2element_symbol(atomic_num)
for atomic_num in self.elements
]
cbar.set_ticklabels(elements_name)
def _plot_emission_ply(self):
"""Plot emission part of the SDEC Plot using plotly."""
# By specifying a common stackgroup, plotly will itself add up
# luminosities, in order, to created stacked area chart
self.fig.add_trace(
go.Scatter(
x=self.emission_luminosities_df.index,
y=self.emission_luminosities_df.noint,
mode="none",
name="No interaction",
fillcolor="black",
stackgroup="emission",
)
)
self.fig.add_trace(
go.Scatter(
x=self.emission_luminosities_df.index,
y=self.emission_luminosities_df.escatter,
mode="none",
name="Electron Scatter Only",
fillcolor="grey",
stackgroup="emission",
)
)
elements_z = self.emission_luminosities_df.columns[2:]
nelements = len(elements_z)
for i, atomic_num in enumerate(elements_z):
self.fig.add_trace(
go.Scatter(
x=self.emission_luminosities_df.index,
y=self.emission_luminosities_df[atomic_num],
mode="none",
name=atomic_number2element_symbol(atomic_num),
fillcolor=self.to_rgb255_string(self.cmap(i / nelements)),
stackgroup="emission",
showlegend=False,
)
)
def test_atomic_number2element_symbol():
assert atomic_number2element_symbol(14) == 'Si'
def test_atomic_number2element_symbol():
assert atomic_number2element_symbol(14) == 'Si'