Bug in logic behind roi_type="largest" option inside pcv.roi.filter

[HaleySchuhl]

Describe the bug
A bug was found in some applications of roi_type="largest" within the pcv.roi.filter function recently, uncovered by @sdkenney42 . Instead of returning the largest object in the mask it was consistently returning the second largest object for a specific image. We did a little digging into the function at lab meeting. The logic behind this function is unsound because it is checking the length of a contour rather than actually filtering on contour size. One option for updating _helpers.py instead of checking the length at line 96 we should actually judge by contour area.

To Reproduce

%matplotlib widget 

from plantcv import plantcv as pcv 
import numpy as np 
import cv2

# Make a blank mask
mask = np.zeros((1000,1000), dtype=np.uint8)
start_point = (10, 10) 
end_point = (110,110) 
# Draw 100x100 pixel square 
mask = cv2.rectangle(mask, start_point, end_point, 255, -1) 
#pcv.plot_image(mask) 

# Calculate radius (based on h=100 in our square) that will give nearly equal areas 
circle_r = int(100/np.sqrt(np.pi)) + 1
#print(circle_r)
mask = cv2.circle(mask, (500,500), circle_r, 255, -1) # circle with radius of 3

roi = pcv.roi.rectangle(img=mask, x=1, y=1, h=49, w=49)

pcv.params.debug = "plot" 
filtered_mask = pcv.roi.filter(mask=mask, roi=roi, roi_type='largest')  # Square gets kept 
vis = pcv.visualize.obj_sizes(img=mask, mask=mask)  # But the area of the circle is larger 

Expected behavior
A clear and concise description of what you expected to happen.

Local environment (please complete the following information):

• OS: [macOS]
• Environment [conda.]
• PlantCV Version [main branch 4.2.2.dev432+g8844cfc8.d20240426 ]

Additional context
I believe len(contour) is more equivalent to taking the perimeter vs the area. Instead need to judge which contour to keep with more sound logic, perhaps the solution below.

c = max(contours, key = cv2.contourArea)

or ID the largest contour after filtering on ROI, and then pcv.fill anything smaller than the known largest object size.