binarize_fisheye {hemispheR}

Compute the threshold of a single-channel fisheye image, and return a binary fisheye image of canopy (0) and gap (1) pixels

Description

The function calculates a single threshold of a single-channel raster image using the autothresholdr::auto_thresh() functionality. The single thresholding is also applied at sub-image level if zonal=TRUE. The available methods are described at https://imagej.net/plugins/auto-threshold. The thresholding value is then used to make a binary raster image of canopy (0) and gap (1) pixels.

Usage

binarize_fisheye(
  img,
  method = "Otsu",
  zonal = FALSE,
  manual = NULL,
  display = FALSE,
  export = FALSE
)

Arguments

img

SpatRaster. A single layer fisheye image imported by import_fisheye() using the terra::rast() functionality.

method

Character. The method used to threshold the image, using the autothresholdr::auto_thresh() function. For details, see https://imagej.net/plugins/auto-threshold. Default = 'Otsu'.

zonal

Logical. If is set to TRUE, it divides the images in four (N, W, S, E) regions and classify each region separately. Useful in case of uneven illumination condition in the image.

manual

Numeric. It uses a manual thresholding instead of automatic one. If selected, it overrides automatic thresholding.

display

Logical. If is set to TRUE, it plots the classified binary image. Default to FALSE.

export

Logical. If is set to TRUE, it saves the binary fisheye image as tif file. Default to FALSE.

Value

A binary single-layer image (SpatRaster)

See Also

https://imagej.net/plugins/auto-threshold

Examples

c.im<-system.file('extdata/circular_coolpix4500+FC-E8_chestnut.jpg',package='hemispheR')

c.im |>
import_fisheye(circ.mask=camera_fisheye('Coolpix4500+FC-E8')) |>
 binarize_fisheye(display=TRUE)

#zonal thresholding:
c.im |>
import_fisheye(circ.mask=camera_fisheye('Coolpix4500+FC-E8')) |>
 binarize_fisheye(zonal=TRUE,display=TRUE)

#manual thresholding:
c.im |>
import_fisheye(circ.mask=camera_fisheye('Coolpix4500+FC-E8')) |>
binarize_fisheye(manual=55,display=TRUE)