roi_select {colocr}

Select regions of interest

Description

Select regions of interest in an image using different morphological operations

Usage

roi_select(
  img,
  threshold,
  shrink = 5,
  grow = 5,
  fill = 5,
  clean = 5,
  tolerance = 0.1,
  n = 1
)

Arguments

img

An object of class cimg or a list of multiple cimg items

threshold

A numeric to be passed to threshold or a vector of values for each image in img

shrink

A numeric to be passed to shrink or a vector of values for each image in img

grow

A numeric to be passed to grow or a vector of values for each image in img

fill

A numeric to be passed to fill or a vector of values for each image in img

clean

A numeric to be passed to clean or a vector of values for each image in img

tolerance

A numeric to be passed to label or a vector of values for each image in img

n

A numeric of the number of regions of interest or a vector of values for each image in img

Details

The function applies several imager morphological manipulations to select the regions of interest. These include threshold which sets all values below certain cut to 0; shrink/grow for pixel set dilation and erosion; fill/clean for removing isolated regions and holes. When n is provided, the individual regions (connected components) are selected where tolerance is used to determine if two pixels belong to the same region.

Value

A cimg. The original input img with an additional attribute label. label is a vector of integers. The labels for the selected regions of interests starts from 1 and 0 is ignored. When img is a list, a list is returned.

Examples

# load images
fl <- system.file('extdata', 'Image0001_.jpg', package = 'colocr')
img <- image_load(fl)

# choose ROI
newimg <- roi_select(img, threshold = 90)

# check the ROI labels
unique(attr(newimg, 'label'))