Removing Circles From Segmentation Image

[JodC58972]

Hello I am looking to remove the circle from an image similar to this with the code below ,

`
clusters_i, contours, hierarchy = pcv.cluster_contours(img, roi_objects, roi_obj_hierarchy, 1,9, show_grid=True)

# Visualize clustered contours
clust_img = pcv.visualize.clustered_contours(img=img, grouped_contour_indices=clusters_i, roi_objects=roi_objects, roi_obj_hierarchy=roi_obj_hierarchy, nrow=1, ncol=9)

# Save clust_img in outdir with the name filename (minus extension) plus suffix
pcv.print_image(clust_img, os.path.join(outdir, filename[:-4] + "_clustered_img.png"))

`

[nfahlgren]

Hi @JodC58972,

It looks like we have the circles hardcoded right now but I think we can definitely add an input to turn them on/off. It should be something we could do pretty quickly.

[JodC58972]

Hello, @nfahlgren

On the website in https://plantcv.readthedocs.io/en/latest/multi-plant_tutorial/ there is this image that does not have the circles. I was looking for a way to recreate this image. Thank you

[nfahlgren]

Hi @JodC58972,

@GrantKonkel updated pcv.visualize.clustered_contours to add a new input parameter bounding that can be set to True or False to turn the circles on/off. If you have installed PlantCV from the source on GitHub and you update now the new version should be available to you. Otherwise, we can release v3.12 soon so that it's available through conda/PyPI.