Printing Images From cluster_contours

[JodC58972]

Hello, I am running a batch script and would like to print the image of the following line:

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

I want to print images from this step in an output folder but I am having trouble with the implementation.
I tried using the debug = "print", filename, file parameters but none have produced the desired results.
How can I print the images from this step and provide filenames in a batch run?

[nfahlgren]

Hi @JodC58972, thanks for reaching out!

Are you wanting to save the multi-colored image like this?

Or do you want to save the individually segmented plant images like these:

[JodC58972]

Like that but with the gird

[nfahlgren]

Awesome, thanks!

It is possible to save that specific image from pcv.cluster_contours by configuring debug mode:

pcv.params.debug = "print"
pcv.params.debug_outdir = "./output_images"

But the way we name debug images is not unique, so if you batch process more than one image and the debug_outdir is the same, it will overwrite the image each time.

That being said, we have a visualization tool that creates an image almost like the one you are looking for that can be saved with a unique name.

import os
from plantcv import plantcv as pcv

# Hardcoded output directory as an example
outdir = "./output_images"

# Read image and get filename
img, imgpath, filename = pcv.readimage("input-image-filename")

# Other workflow steps

# Cluster contours
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")

[JodC58972]

Thanks, so I can run this separately over my data set to get the images I need?

[nfahlgren]

If you add the pcv.visualize.clustered_contours and pcv.print_image code to your existing workflow after running pcv.cluster_contours I think that would work. The print_image part might need some tweaking to match your existing code. Happy to help get it working though!

[JodC58972]

That worked thank you but how do I remove the circle?