Find Objects within a Region of Interest¶

Find objects within a region of interest, either cut those objects to the region of interest or include objects that overlap with the region of interest.

plantcv.roi_objects(img, roi_type, roi_contour, roi_hierarchy, object_contour, obj_hierarchy)

returns kept objects, object hierarchy, object mask, object area

Important Note: If your ROI object detection does not perform first check that the ROI is completely within the image.

• Parameters:

  • img = RGB or grayscale image data to display kept objects on
  • roi_type = 'cutto' or 'partial' (include objects that are partially inside or overlapping with ROI)
  • roi_contour = contour of roi, output from "define_roi" function
  • roi_hierarchy = contour of roi, output from "define_roi" function
  • object_contour = contours of objects, output from "find_objects" function
  • obj_hierarchy = hierarchy of objects, output from "find_objects" function

• Context:

  • Used to find objects within a region of interest and decide which ones to keep.
• Example use:
  • Use In VIS Tutorial
  • Use In NIR Tutorial
  • Use In PSII Tutorial


from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file), or "plot" (Jupyter Notebooks or X11)
pcv.params.debug = "print"

# ROI objects allows the user to define if objects partially inside ROI are included or if objects are cut to ROI.
roi_objects, hierarchy, kept_mask, obj_area = pcv.roi_objects(img, 'partial', roi, roi_hierarchy, objects, obj_hierarchy)

Object (green) that is identified as partially inside ROI

Mask of identified object

Kept objects

from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file), or "plot" (Jupyter Notebooks or X11)
pcv.params.debug = "print"

# Define region of interest in an image, there is a futher function 'ROI Objects' that allows the user to define if you want to include objects partially inside ROI or if you want to do cut objects to ROI.
roi_objects, hierarchy, kept_mask, obj_area = pcv.roi_objects(img, 'cutto', roi, roi_hierarchy, objects, obj_hierarchy)

Object (green) that is cut to the ROI

Mask of identified object

Kept objects