aim2dat.plots.spectroscopy¶

Module to plot spectroscopy data.

Module Contents¶

Classes¶

Functions¶

class aim2dat.plots.spectroscopy.SpectrumPlot(detect_peaks=False, smooth_spectra=False, plot_original_spectra=False, plot_unit_x='eV', **kwargs)[source]¶

Bases: aim2dat.plots.base_plot._BasePlot, aim2dat.plots.base_mixin._VLineMixin, aim2dat.plots.base_mixin._PeakDetectionMixin, aim2dat.plots.base_mixin._SmearingMixin

Plot x-ray absorption spectra.

Variables:¶

detect_peaks : bool¶

Whether to detect peaks of the spectra.

smooth_spectra : bool¶

Whether to broaden the spectra.

plot_original_spectra : bool¶

Whether to plot the original spectra (in addition to the broadened spectra).

plot_unit_x : str¶

Unit of the x-values. Imported spectra are transformed to the corresponding unit if the unit of the imported data set is given.

Overview

Properties¶

backend	used backend library to plot the data. Supported values are "matplotlib" and
custom_alpha	Alpha value(s) controlling the opacity of plot elements.
custom_colors	Colors used in the plot.
custom_hatch	Hatch value(s) controlling the hatch of plot elements.
custom_linestyles	Line styles used in the plot (This feature is not supported by all plot
custom_linewidths	Line widths used in the plot (This feature is not supported by all plot
custom_markers	Marker types used in the plot (This feature is not supported by all plot
custom_xticklabels	List of labels for the ticks on the x-axis.
custom_xticks	List of values to set ticks on the x-axis.
custom_yticklabels	List of labels for the ticks on the y-axis.
custom_yticks	List of values to set ticks on the y-axis.
data_labels	List of labels for all data sets.
equal_aspect_ratio	Set equal aspect ratio of the plot(s).
legend_bbox_to_anchor	Shift between box and anchor. The default value is (1, 1).
legend_loc	Location of the legend. The default value is 1.
legend_ncol	Columns of the legend (only supported for the matplotlib backend).
legend_sort_entries	Sort entries of the legend.
peak_color	-
peak_distance	-
peak_height	-
peak_line_style	-
peak_max_factor	-
peak_plateau_size	-
peak_prominence	-
peak_rel_height	-
peak_threshold	-
peak_width	-
peak_wlen	-
peak_y_min	-
peaks	-
plot_grid	Whether to draw a grid in the plot. The default value is False.
plot_unit_x	Set unit of x-axis.
ratio	Length-to-width ratio of the plot given as a tuple of two numbers.
show_colorbar	Show colorbar (not supported by all plots).
show_grid	Whether to draw a grid in the plot. The default value is False.
show_legend	Show legend. The default value is False.
show_plot	Show plot. The default value is False.
smearing_delta	Spacing between two values. If set to None the original function is
smearing_method	Method used to smear out the functions. Supported options are 'gaussian' and
smearing_sigma	Sigma value of the smearing distribution.
store_path	Path of the folder to store the plot. The default value is ./.
store_plot	Store plot. The default value is False.
style_sheet	Custom matplotlib style sheet.
subplot_adjust	Keyword arguments for the matplotlib subplots_adjust function.
subplot_align_ylabels	Align y label of plot. The default value is False.
subplot_gridspec	Grid spec values.
subplot_hspace	Vertical spacing between the subplots.
subplot_ncols	Number of columns. The default value is 1.
subplot_nrows	Number of rows. The default value is 2.
subplot_share_colorbar	Use one common colorbar for all subplots.
subplot_share_legend	Merge legend items of all subplots.
subplot_sharex	Share the x-axis of subplots located in the same column.
subplot_sharey	Share the y-axis of subplots located in the same row.
subplot_sup_title	Title of the whole figure.
subplot_sup_x_label	x-label of the whole figure.
subplot_sup_y_label	y-label of the whole figure.
subplot_tight_layout	Tight layout of plot. The default value is False.
subplot_wspace	Horizontal spacing between the subplots.
x_label	Label of the x-axis. If None is given no label will be shown. The
x_range	Range of the x-axis. The default value is None.
y_label	Label of the y-axis. If None is given no label will be shown. The
y_range	Range of the y-axis. The default value is None.

Methods¶

add_vline(x, y_min, y_max, color, line_style, scaled, foreground, subplot_assignment, data_label)	Add a vertical line to the plot.
auto_set_axis_properties(set_x_label, set_y_label)	Whether the axis labels and other axis properties are auto-generated.
create_default_gridspec(nrows, ncols, nplots, heights, widths, center_last_row)	Create default grid for multiple plots.
import_spectrum(data_label, x_values, y_values, unit_x)	Import spectrum.
plot(data_labels, plot_title, plot_name, subplot_assignment)	Plot the data sets.
remove_additional_plot_elements()	Remove all added plot elements.
reset_gridspec()	Reset gridspec settings.
return_data_labels()	Return the labels of all data sets.

property backend¶

used backend library to plot the data. Supported values are "matplotlib" and "plotly".

Type:¶

str

property custom_alpha¶

Alpha value(s) controlling the opacity of plot elements.

Type:¶

float, list or tuple

property custom_colors¶

Colors used in the plot.

Type:¶

list or tuple

property custom_hatch¶

Hatch value(s) controlling the hatch of plot elements.

Type:¶

float, list or tuple

property custom_linestyles¶

Line styles used in the plot (This feature is not supported by all plot types).

Type:¶

list or tuple

property custom_linewidths¶

Line widths used in the plot (This feature is not supported by all plot types).

Type:¶

list or tuple

property custom_markers¶

Marker types used in the plot (This feature is not supported by all plot types).

Type:¶

list or tuple

property custom_xticklabels¶

List of labels for the ticks on the x-axis.

Type:¶

list

property custom_xticks¶

List of values to set ticks on the x-axis.

Type:¶

list

property custom_yticklabels¶

List of labels for the ticks on the y-axis.

Type:¶

list

property custom_yticks¶

List of values to set ticks on the y-axis.

Type:¶

list

property data_labels¶

List of labels for all data sets.

Type:¶

list

property equal_aspect_ratio¶

Set equal aspect ratio of the plot(s).

Type:¶

bool

property legend_bbox_to_anchor¶

Shift between box and anchor. The default value is (1, 1).

Type:¶

tuple or list

property legend_loc¶

Location of the legend. The default value is 1.

Type:¶

int

property legend_ncol¶

Columns of the legend (only supported for the matplotlib backend).

Type:¶

int

property legend_sort_entries¶

Sort entries of the legend.

Type:¶

bool

property peak_color¶

property peak_distance¶

property peak_height¶

property peak_line_style¶

property peak_max_factor¶

property peak_plateau_size¶

property peak_prominence¶

property peak_rel_height¶

property peak_threshold¶

property peak_width¶

property peak_wlen¶

property peak_y_min¶

property peaks¶

property plot_grid¶

Whether to draw a grid in the plot. The default value is False.

Type:¶

bool

property plot_unit_x¶

Set unit of x-axis.

property ratio¶

Length-to-width ratio of the plot given as a tuple of two numbers.

Type:¶

tuple or list

property show_colorbar¶

Show colorbar (not supported by all plots).

Type:¶

bool

property show_grid¶

Whether to draw a grid in the plot. The default value is False.

Type:¶

bool

property show_legend¶

Show legend. The default value is False.

Type:¶

bool

property show_plot¶

Show plot. The default value is False.

Type:¶

bool

property smearing_delta¶

Spacing between two values. If set to None the original function is used.

Type:¶

float or None

property smearing_method¶

Method used to smear out the functions. Supported options are 'gaussian' and 'lorentzian'.

Type:¶

str

property smearing_sigma¶

Sigma value of the smearing distribution.

Type:¶

float

property store_path¶

Path of the folder to store the plot. The default value is ./.

Type:¶

str

property store_plot¶

Store plot. The default value is False.

Type:¶

bool

property style_sheet¶

Custom matplotlib style sheet.

Type:¶

str

property subplot_adjust¶

Keyword arguments for the matplotlib subplots_adjust function.

Type:¶

dict

property subplot_align_ylabels¶

Align y label of plot. The default value is False.

Type:¶

bool

property subplot_gridspec¶

Grid spec values.

Type:¶

list or tuple

property subplot_hspace¶

Vertical spacing between the subplots.

Type:¶

float

property subplot_ncols¶

Number of columns. The default value is 1.

Type:¶

int

property subplot_nrows¶

Number of rows. The default value is 2.

Type:¶

int

property subplot_share_colorbar¶

Use one common colorbar for all subplots.

Type:¶

bool

property subplot_share_legend¶

Merge legend items of all subplots.

Type:¶

bool

property subplot_sharex¶

Share the x-axis of subplots located in the same column.

Type:¶

bool

property subplot_sharey¶

Share the y-axis of subplots located in the same row.

Type:¶

bool

property subplot_sup_title¶

Title of the whole figure.

Type:¶

str

property subplot_sup_x_label¶

x-label of the whole figure.

Type:¶

str

property subplot_sup_y_label¶

y-label of the whole figure.

Type:¶

str

property subplot_tight_layout¶

Tight layout of plot. The default value is False.

Type:¶

bool

property subplot_wspace¶

Horizontal spacing between the subplots.

Type:¶

float

property x_label¶

Label of the x-axis. If None is given no label will be shown. The default value is None.

Type:¶

str or None

property x_range¶

Range of the x-axis. The default value is None.

Type:¶

tuple or list

property y_label¶

Label of the y-axis. If None is given no label will be shown. The default value is None.

Type:¶

str or None

property y_range¶

Range of the y-axis. The default value is None.

Type:¶

tuple or list

add_vline(x, y_min, y_max, color=None, line_style=None, scaled=False, foreground=False, subplot_assignment=None, data_label=None)¶

Add a vertical line to the plot.

Parameters:¶

• x (float) – x-position of the line.

• y_min (float) – Bottom y-position of the line.

• y_max (float) – Top y-position of the line.

• color (str or None) – Color of the line.

• line_style (str or None) – Line style of the line.

• scaled (bool) – Whether the input is given in scaled positions.

• foreground (bool) – Whether to plot the line in front of the other elements.

• subplot_assignment (list or None) – Assignment of the line to individual subplots.

auto_set_axis_properties(set_x_label=True, set_y_label=True)¶

Whether the axis labels and other axis properties are auto-generated.

Parameters:¶

• set_x_label (bool) – Set x-axis label automatically.

• set_y_label (bool) – Set y-axis label automatically.

create_default_gridspec(nrows, ncols, nplots, heights=1, widths=1, center_last_row=True)¶

Create default grid for multiple plots.

Parameters:¶

• nrows (Int) – Number of rows.

• ncols (int) – Number columns.

• nplots (int) – Number of subplots.

• heights (int (optional)) – Height of subplots.

• widths (int (optional)) – Width of subplots.

• center_last_row (bool (optional)) – Center the plots of the last row.

import_spectrum(data_label, x_values, y_values, unit_x)[source]¶

Import spectrum.

Parameters:¶

• data_label (str) – Internal label of the data set.

• x_values (list) – x-values of the spectrum.

• y_values (list) – y-values of the spectrum.

• unit_x (str) – Unit of the x-values.

plot(data_labels, plot_title=None, plot_name='plot.png', subplot_assignment=None)¶

Plot the data sets.

Parameters:¶

• data_labels (list or str) – List of data labels of the data sets that are plotted or in case only one data set is plotted a string.

• plot_title (list or str (optional)) – Title of the plots or subplots.

• plot_name (str (optional)) – The file name of the plot.

• subplot_assignment (list or None (optional)) – Assignment of the data sets to individual subplots.

Returns:¶

fig (matplotlib.pyplot.figure or plotly.graph_objects.Figure) – Figure object of the plot.

remove_additional_plot_elements()¶

Remove all added plot elements.

reset_gridspec()¶

Reset gridspec settings.

return_data_labels()¶

Return the labels of all data sets.

Returns:¶

data_labels (list) – List of the labels of all data sets.

aim2dat.plots.spectroscopy.Spectrum(*args, **kwargs)[source]¶

Depreciated Spectrum class.