topostats.plottingfuncs

Plotting data.

Attributes

LOGGER

Classes

Images

Plots image arrays.

Functions

add_pixel_to_nm_to_plotting_config(→ dict)	Add the pixel to nanometre scaling factor to plotting configs.
dilate_binary_image(→ numpy.ndarray)	Dilate a supplied binary image a given number of times.
load_mplstyle(→ None)	Load the Matplotlibrc parameter file.
add_bounding_boxes_to_plot(→ None)	Add the bounding boxes to a plot.
set_n_ticks(→ None)	Set the number of ticks along the y and x axes and lets matplotlib assign the values.

Module Contents

topostats.plottingfuncs.LOGGER

topostats.plottingfuncs.add_pixel_to_nm_to_plotting_config(plotting_config: dict, pixel_to_nm_scaling: float) → dict

Add the pixel to nanometre scaling factor to plotting configs.

Ensures plots are in nanometres and not pixels.

Parameters:

• plotting_config (dict) – TopoStats plotting configuration dictionary

• pixel_to_nm_scaling (float) – Pixel to nanometre scaling factor for the image.

Returns:

plotting_config – Updated plotting config with the pixel to nanometre scaling factor applied to all the image configurations.

Return type:

dict

topostats.plottingfuncs.dilate_binary_image(binary_image: numpy.ndarray, dilation_iterations: int) → numpy.ndarray

Dilate a supplied binary image a given number of times.

Parameters:

• binary_image (np.ndarray) – Binary image to be dilated

• dilation_iterations (int) – Number of dilation iterations to be performed

Returns:

binary_image – Dilated binary image

Return type:

np.ndarray

topostats.plottingfuncs.load_mplstyle(style: str | pathlib.Path) → None

Load the Matplotlibrc parameter file.

Parameters:

style (str | Path) – Path to a Matplotlib Style file.

Returns:

Only loads the style file.

Return type:

None

class topostats.plottingfuncs.Images(data: numpy.array, output_dir: str | pathlib.Path, filename: str, style: str | pathlib.Path = None, pixel_to_nm_scaling: float = 1.0, masked_array: numpy.array = None, title: str = None, image_type: str = 'non-binary', image_set: str = 'core', core_set: bool = False, pixel_interpolation: str | None = None, cmap: str | None = None, mask_cmap: str = 'jet_r', region_properties: dict = None, zrange: list = None, colorbar: bool = True, axes: bool = True, num_ticks: list[int | None, int | None] = (None, None), save: bool = True, savefig_format: str | None = None, histogram_log_axis: bool = True, histogram_bins: int | None = None, savefig_dpi: str | float | None = None)

Plots image arrays.

data

output_dir

filename

pixel_to_nm_scaling

masked_array

title

image_type

image_set

core_set

interpolation

cmap

mask_cmap

region_properties

zrange

colorbar

axes

num_ticks

save

savefig_format

histogram_log_axis

histogram_bins

savefig_dpi

plot_histogram_and_save()

Plot and save a histogram of the height map.

Returns:

• fig (plt.figure.Figure) – Matplotlib.pyplot figure object

• ax (plt.axes._subplots.AxesSubplot) – Matplotlib.pyplot axes object

plot_and_save()

Plot and save the images with savefig or imsave depending on config file parameters.

Returns:

• fig (plt.figure.Figure) – Matplotlib.pyplot figure object

• ax (plt.axes._subplots.AxesSubplot) – Matplotlib.pyplot axes object

save_figure()

Save figures as plt.savefig objects.

Returns:

• fig (plt.figure.Figure) – Matplotlib.pyplot figure object

• ax (plt.axes._subplots.AxesSubplot) – Matplotlib.pyplot axes object

save_array_figure() → None

Save the image array as an image using plt.imsave().

topostats.plottingfuncs.add_bounding_boxes_to_plot(fig, ax, shape, region_properties: list, pixel_to_nm_scaling: float) → None

Add the bounding boxes to a plot.

Parameters:

• fig (plt.figure.Figure) – Matplotlib.pyplot figure object

• ax (plt.axes._subplots.AxesSubplot.) – Matplotlib.pyplot axes object

• shape (tuple) – Tuple of the image-to-be-plot’s shape.

• region_properties – Region properties to add bounding boxes from.

• pixel_to_nm_scaling (float) – The scaling factor from px to nm.

Returns:

• fig (plt.figure.Figure) – Matplotlib.pyplot figure object.

• ax (plt.axes._subplots.AxesSubplot) – Matplotlib.pyplot axes object.

topostats.plottingfuncs.set_n_ticks(ax: matplotlib.pyplot.Axes.axes, n_xy: list[int | None, int | None]) → None

Set the number of ticks along the y and x axes and lets matplotlib assign the values.

Parameters:

• ax (plt.Axes.axes) – The axes to add ticks to.

• n_xy (list[int, int]) – The number of ticks.

Returns:

The axes with the new ticks.

Return type:

plt.Axes.axes