topostats.plottingfuncs

Plotting data.

Attributes

LOGGER

Classes

Images

Plots image arrays

Functions

add_bounding_boxes_to_plot(→ None)

Add the bounding boxes to a plot.

Module Contents

topostats.plottingfuncs.LOGGER

class topostats.plottingfuncs.Images(data: numpy.array, output_dir: str | pathlib.Path, filename: str, pixel_to_nm_scaling: float = 1.0, data2: numpy.array = None, title: str = None, image_type: str = 'non-binary', image_set: str = 'core', core_set: bool = False, interpolation: str = 'nearest', cmap: str = 'nanoscope', region_properties: dict = None, zrange: list = [None, None], colorbar: bool = True, axes: bool = True, save: bool = True, save_format: str = 'png', histogram_log_axis: bool = True)

Plots image arrays

data

output_dir

filename

pixel_to_nm_scaling

data2

title

image_type

image_set

core_set

interpolation

cmap

region_properties

zrange

colorbar

axes

save

save_format

histogram_log_axis

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()

This function saves 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

This function saves only 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.