locpix.visualise.vis_img.visualise_seg#
- visualise_seg(image, segmentation, bin_sizes, axes, label_map, threshold=0, how='linear', alphas=[1, 0.5, 0.2, 0.1], alpha_seg=0.8, blend_overlays=False, cmap_img=None, cmap_seg=['m', 'g', 'lightsalmon', 'r', 'b'], figsize=(10, 10), origin='upper', save=False, save_loc=None, save_name=None, four_colour=True, background_one_colour=False, legend=True, show=False, vmin_img=0, vmax_img=255, sum_chans=False)[source]#
Take in image and the associated segmentation and plot it, with option to convert to 4 colours and also option to choose to plot background as one particular colour (only relevant if four colour is true)
- Parameters:
image (array) – Shape C x H x W Therefore to plot the first axis of the image we would just want to consider image[0]
segmentation (np.ndarray) – Array of integers where each represents unique label in the segmentation
bin_sizes (list) – List of sizes of the bins of the histogram
axes (list) – List of axes to plot
label_map (list) – List of labels associated with each axis
threshold (int) – Threshold applied to images when plotting
how (string) – Interpolation applied to image when plotting
alphas (list) – List of alpha to be used in plt.imshow
alpha_seg (float) – Value of alpha for segmentation
blend_overlays (bool) – Whether to blend img and seg
cmap_img (list) – List of cmaps to plot images (transpose of histograms)
cmap_seg (list) – List of cmaps to plot segmentations
figsize (tuple) – Tuple of figure size in 2D (x,y) sizes
origin (string) – Location of origin in plot, image convention is ‘upper’ but for cartesian use ‘lower’
save (bool) – Whether to save
save_loc (string) – Where to save if chosen to save
save_name (string) – Name of file
four_colour (bool) – Whether to convert localisations to 4 colour
background_one_colour (bool) – Whether to keep background as all same colour when doing 4 colour conversion
legend (bool) – Whether to include a legend
show (bool) – Whether to show img to screen
vmin_img (int) – vmin for plotting image
vmax_img (int) – vmax for plotting image
sum_chans (bool) – If true all image channels are summed and one image is plotted