pycsa.plotting.plotter

Contains the classes and functions for single-cell plots.

Functions

error_bar_abs_plot(errs, lbls[, fs, title, ...])

Bar plot of absolute error values without a y-axis break.

error_bar_plot(idx_name, pmf_diff, params[, ...])

Bar plot of errors.

error_bar_split_plot(errs, lbls, bs, ts, ...)

Function to generate error bar plots with a split in the middle, e.g., when space in limited on a presentation slide or poster.

Classes

fig_obj(fig, nhi, nhj[, cbar, set_label])

A figure object class to plot physical and spectral panels.

plot_3d(cell[, ele, azi, cpad])

Helper class for 3D plots
class pycsa.plotting.plotter.fig_obj(fig, nhi, nhj, cbar=True, set_label=True)

A figure object class to plot physical and spectral panels.

__init__(fig, nhi, nhj, cbar=True, set_label=True)

Initializes the figure object and the methods fill the axes.

Parameters:

  • fig (matplotlib.figure.Figure instance) – matplotlib figure

  • nhi (int) – number of harmonics in the first horizontal direction

  • nhj (int) – number of harmonics in the second horizontal direction

  • cbar (bool, optional) – user-defined colorbar, by default True

  • set_label (bool, optional) – toggle axis labels, by default True

phys_panel(axs, data, title='', extent=None, xlabel='', ylabel='', v_extent=None)

Plots a physical depiction of the input data.

Parameters:

  • axs (plt.Axes) – matplotlib figure axis

  • data (array-like) – 2D image data

  • title (str, optional) – panel title, by default “”

  • extent (list, optional) – [x0,x1,y0,y1], by default “”

  • xlabel (str, optional) – x-axis label, by default “”

  • ylabel (str, optional) – y-axis label, by default “”

  • v_extent (list, optional) – [h0,h1]; vertical extent of the data, by default None

Returns:

matplotlib figure axis

Return type:

plt.Axes

freq_panel(axs, ampls, nhi=None, nhj=None, title='Power spectrum', v_extent=None, show_edge=False)

Plots the spectrum in a dense truncated spectral space.

Parameters:

  • axs (plt.Axes) – matplotlib figure axis

  • ampls (array-like) – 2D (abs.) spectral data

  • nhi (int, optional) – number of harmonics in the first horizontal direction, by default None

  • nhj (int, optional) – number of harmonics in the second horizontal direction, by default None

  • title (str, optional) – user-defined panel title, by default “Power spectrum”

  • v_extent (list, optional) – [h0,h1]; vertical extent of the data, by default None

  • show_edge (bool, optional) – toggle the cell-edge outline on the color mesh, by default False

Returns:

matplotlib figure axis

Return type:

plt.Axes

fft_freq_panel(axs, ampls, kks, lls, title='FFT power spectrum', interval=20, typ='imag')

Plots the spectrum in the full spectral space.

Parameters:

  • axs (plt.Axes) – matplotlib figure axis

  • ampls (array-like) – 2D (abs.) spectral data

  • kks (list) – list of first horizontal wavenumbers

  • lls (list) – list of second horizontal wavenumbers

  • title (str, optional) – user-defined panel title, by default “FFT power spectrum”

  • interval (int, optional) – half-width (in wavenumber indices) of the spectral window cropped around the center before plotting, by default 20

  • typ ({"imag", "real"}, optional) – spectral representation to plot; “imag” crops a symmetric window about the spectral center, “real” keeps the positive first-wavenumber half, by default “imag”

Returns:

matplotlib figure axis

Return type:

plt.Axes

pycsa.plotting.plotter.error_bar_plot(idx_name, pmf_diff, params, comparison=None, title='', gen_title=False, output_fig=False, fn='../output/error_plot.pdf', ylim=[-100, 100], fs=(10.0, 6.0), ylabel='', fontsize=8, show_grid=True)

Bar plot of errors.

Parameters:

  • idx_name (list) – labels of the error plots, e.g., cell index

  • pmf_diff (list) – list containing the errors. Same size as idx_name.

  • params (pycsa.config.params.params) – user parameter class

  • comparison (list, optional) – a second error list to be compared to pmf_diff. Same size as pmf_diff, by default None

  • title (str, optional) – user-defined panel title, by default “”

  • gen_title (bool, optional) – automatically generate panel title from params, by default False

  • output_fig (bool, optional) – toggle writing figure output, by default False

  • fn (str, optional) – path to write output figure, by default “../output/error_plot.pdf”

  • ylim (list, optional) – extent of the error bar plot, by default [-100,100]

  • fs (tuple, optional) – figure size, by default (10.0,6.0)

  • ylabel (str, optional) – y-axis label, by default “”

  • fontsize (int, optional) – by default 8

  • show_grid (bool, optional) – toggles grid in output, by default True

pycsa.plotting.plotter.error_bar_split_plot(errs, lbls, bs, ts, ts_ticks, color, fs=(3.5, 3.5), title='', output_fig=False, fn='output/errors.pdf')

Function to generate error bar plots with a split in the middle, e.g., when space in limited on a presentation slide or poster.

Parameters:

  • errs (list) – list of error values, one per bar (rounded to 2 d.p. internally)

  • lbls (list) – bar labels, used as the x-axis tick labels. Same size as errs.

  • bs (float) – upper limit of the lower (bottom) axis; the y-axis break occurs here

  • ts (list) – [t0, t1] y-limits of the upper (top) axis above the break

  • ts_ticks (list) – explicit y-tick locations for the upper axis

  • color (color or list) – bar color(s) passed to matplotlib.axes.Axes.bar()

  • fs (tuple, optional) – figure size, by default (3.5, 3.5)

  • title (str, optional) – figure title, by default “”

  • output_fig (bool, optional) – toggle writing figure output, by default False

  • fn (str, optional) – path to write output figure, by default “output/errors.pdf”

pycsa.plotting.plotter.error_bar_abs_plot(errs, lbls, fs=(3.5, 3.5), title='', output_fig=False, fn='output/errors.pdf', color=None, ylims=None, fontsize=10)

Bar plot of absolute error values without a y-axis break.

Parameters:

  • errs (list) – list of error values, one per bar (rounded to 2 d.p. internally)

  • lbls (list) – bar labels, used as the x-axis tick labels. Same size as errs.

  • fs (tuple, optional) – figure size, by default (3.5, 3.5)

  • title (str, optional) – figure title, by default “”

  • output_fig (bool, optional) – toggle writing figure output, by default False

  • fn (str, optional) – path to write output figure, by default “output/errors.pdf”

  • color (color or list, optional) – bar color(s) passed to matplotlib.axes.Axes.bar(), by default None

  • ylims (list, optional) – [y0, y1] y-axis limits; left unset when None, by default None

  • fontsize (int, optional) – title font size, by default 10

class pycsa.plotting.plotter.plot_3d(cell, ele=5, azi=230, cpad=0.01)

Helper class for 3D plots

__init__(cell, ele=5, azi=230, cpad=0.01)
Parameters:

  • cell (pycsa.data.cell.topo_cell) – instance of a cell object

  • ele (int, optional) – elevation angle, by default 5

  • azi (int, optional) – azimuthal angle, by default 230

  • cpad (float, optional) – color bar padding, by default 0.01

plot(Z, output_fig=True, output_fn='plot_3D', lbls=None, fs=(10, 10))

Does the plotting

Parameters:

  • Z (array-like) – 2D elevation array

  • output_fig (bool, optional) – toggles output of figure, by default True

  • output_fn (str, optional) – output filename, by default “plot_3D”. The figure is always written to ./outputs/<output_fn>.pdf (the ./outputs/ directory and .pdf suffix are hardcoded).

  • lbls (list, optional) – list of axis labels containing [x_label, y_label, z_label], by default None

  • fs (tuple, optional) – figure size, by default (10,10)