Plotting

Plot processed images.

Functions:

Name	Description
generate_gif	Generate a GIF of all slices through the image.
plot_all_layers	Plot a three-dimensional numpy array.
plot_area_by_layer	Plot the layer v total area of pores within it.
plot_layer	Plot a two-dimensional numpy array.
plot_pores_by_layer	Plot the layer v number of pores within it.

generate_gif

generate_gif(
    sliced_segments, outdir, img_name, duration=100, loop=0
)

Generate a GIF of all slices through the image.

Parameters:

Name	Type	Description	Default
sliced_segments	NDArray	A three-dimensional array of slices through the image.	required
outdir	Path	Where to save the image to.	required
img_name	str	The original image filename, will have .gif extension added.	required
duration	int	Duration between frames in the GIF, default is 100.	100
loop	int	Whether to loop the image, default is 0 which doesn't loop.	0

plot_all_layers

plot_all_layers(
    array,
    img_name=None,
    outdir=None,
    format=None,
    cmap=None,
)

Plot a three-dimensional numpy array.

This function calls plot_layer() for each "slice" of a three-dimensional array.

Parameters:

Name	Type	Description	Default
array	NDArray	Two-dimensional numpy array to be plotted, may be labelled or unlabelled data.	required
img_name	str	The image name from which the data is derived.	None
outdir	str | Path	Target output directory, will be created if it does not exist.	None
format	str	Image format for creating image. Default is png.	None
cmap	str | ColorType	Colormap to plot as, defaults to black for binary images, viridis for heights. Labelled images are plotted as is.	None

Returns:

Type	Description
dict[int, tuple[Figure, Axes]]	Dictionary of Matplotlib Figure and Axes indexed by layer.

plot_area_by_layer

plot_area_by_layer(
    area_per_layer,
    img_name=None,
    min_size=None,
    outdir=None,
    format=None,
    fwhm=None,
    log=False,
    grid=False,
)

Plot the layer v total area of pores within it.

Parameters:

Name	Type	Description	Default
area_per_layer	list[list[float]]	A list of the total area of pores within each layer.	required
img_name	str	Image name.	None
min_size	float	Minimum size of objects to include when summing the area by layer.	None
outdir	str | Path	Output directory, if no None the image is saved there as <img_name>_pores_per_layer_[log].<format>.	None
format	str	Output file format as a string, defaults to png if not specified.	None
fwhm	tuple[int, int]	Full width half max limits for subsetting the data.	None
log	bool	Whether to plot with the logarithm (base10) of the number of pores.	False
grid	bool	Whether to include a grid on the plot.	False

Returns:

Type	Description
tuple[Figure, Axes]	Returns a tuple of Matplotlib fig and ax.

plot_layer

plot_layer(
    array,
    img_name=None,
    layer=None,
    outdir=None,
    format=None,
    cmap=None,
)

Plot a two-dimensional numpy array.

Parameters:

Name	Type	Description	Default
array	NDArray	Two-dimensional numpy array to be plotted, may be labelled or unlabelled data.	required
img_name	str	The image name from which the data is derived.	None
layer	int	The layer that is being plotted.	None
outdir	str | Path	Target output directory, will be created if it does not exist.	None
format	str	Image format for creating image. Default is png.	None
cmap	str	Colormap to plot as, defaults to black for binary images, viridis for heights. Labelled images are plotted as is.	None

Returns:

Type	Description
tuple[Figure, Axes]	Matplotlib Figure and Axes.

plot_pores_by_layer

plot_pores_by_layer(
    pores_per_layer,
    img_name=None,
    outdir=None,
    format=None,
    log=False,
    grid=False,
)

Plot the layer v number of pores within it.

Parameters:

Name	Type	Description	Default
pores_per_layer	list[int]	A list of the number of pores in each layer.	required
img_name	str	Image name.	None
outdir	str | Path	Output directory, if no None the image is saved there as <img_name>_pores_per_layer_[log].<format>.	None
format	str	Output file format as a string, defaults to png if not specified.	None
log	bool	Whether to plot with the logarithm (base10) of the number of pores.	False
grid	bool	Whether to include a grid on the plot.	False

Returns:

Type	Description
tuple[Figure, Axes]	Returns a tuple of Matplotlib fig and ax.