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Segment a mosaic

Source: R/utils_mosaic.R
mosaic_segment.Rd

Segment a SpatRaster using a computed image index. By default, values greater than threshold are kept in the mask.

Usage

mosaic_segment(
  mosaic,
  index = "R",
  r = 3,
  g = 2,
  b = 1,
  re = NA,
  nir = NA,
  swir = NA,
  tir = NA,
  threshold = "Otsu",
  invert = FALSE,
  return = c("mosaic", "mask")
)

Arguments

mosaic

A mosaic of class SpatRaster, generally imported with mosaic_input().

index

A character value (or a vector of characters) specifying the target mode for conversion to a binary image. Use pliman_indexes_rgb() and pliman_indexes_me() to see the available RGB and multispectral indexes, respectively. Users can also calculate their own index using R, G, B, RE, NIR, SWIR, and TIR bands (eg., index = "R+B/G") or using the names of the mosaic's layers (ex., "(band_1 + band_2) / 2").

r, g, b, re, nir, swir, tir

The red, green, blue, red-edge, near-infrared, shortwave Infrared, and thermal infrared bands of the image, respectively. By default, the function assumes a BGR as input (b = 1, g = 2, r = 3). If a multispectral image is provided up to seven bands can be used to compute built-in indexes. There are no limitation of band numbers if the index is computed using the band name.

threshold

By default (threshold = "Otsu"), a threshold value based on Otsu's method is used to reduce the grayscale image to a binary image. If a numeric value is provided, this value will be used as a threshold.

invert

Logical, indicating whether to invert the mask. Defaults to FALSE, i.e., pixels with intensity greater than the threshold values are selected.

return

The output of the function. Either 'mosaic' (the segmented mosaic), or 'mask' (the binary mask).

Value

The segmented mosaic (SpatRaster object)

Examples

if (interactive() && requireNamespace("EBImage")) {
library(pliman)
mosaic <- mosaic_input(system.file("ex/elev.tif", package="terra"))
seg <-
mosaic_segment(mosaic,
               index = "elevation",
               threshold = 350)
mosaic_plot(seg)
}
#> Warning: The current raster is in the lat/lon coordinate system, which may result in processing errors when trying to segment individuals in the `mosaic_analyze()` function. It is highly suggested to reproject the raster using mosaic_project() with EPSG:32632
#> class       : SpatRaster 
#> dimensions  : 90, 95, 1  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 5.741667, 6.533333, 49.44167, 50.19167  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : elev.tif 
#> name        : elevation 
#> min value   :       141 
#> max value   :       547 
#> Index 'elevation' is not available. Trying to compute your own index.