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Vectorize a SpatRaster mask to an sf object

Source: R/utils_mosaic.R
mosaic_vectorize.Rd

Converts a raster mask into a vectorized sf object, with various options for morphological operations and filtering.

Usage

mosaic_vectorize(
  mask,
  aggregate = NULL,
  watershed = TRUE,
  tolerance = 1,
  extension = 1,
  opening = FALSE,
  closing = FALSE,
  filter = FALSE,
  erode = FALSE,
  dilate = FALSE,
  fill_hull = FALSE,
  lower_size = NULL,
  upper_size = NULL,
  topn_lower = NULL,
  topn_upper = NULL
)

Arguments

mask

An optional mask (SpatRaster) to mask the mosaic.

aggregate

The size as a fraction (percentage) of the input image size. Either a scalar (eg., 50), or a length-two numeric vector. In the last, different percentage reduction/expansion can be used for columns, and rows, respectively.

watershed

If TRUE (default), performs watershed-based object detection. This will detect objects even when they are touching one another. If FALSE, all pixels for each connected set of foreground pixels are set to a unique object. This is faster but is not able to segment touching objects.

tolerance

The minimum height of the object in the units of image intensity between its highest point (seed) and the point where it contacts another object (checked for every contact pixel). If the height is smaller than the tolerance, the object will be combined with one of its neighbors, which is the highest.

extension

Radius of the neighborhood in pixels for the detection of neighboring objects. A higher value smooths out small objects.

opening, closing, filter, erode, dilate

Morphological operations (brush size)

  • dilate puts the mask over every background pixel, and sets it to foreground if any of the pixels covered by the mask is from the foreground.

  • erode puts the mask over every foreground pixel, and sets it to background if any of the pixels covered by the mask is from the background.

  • opening performs an erosion followed by a dilation. This helps to remove small objects while preserving the shape and size of larger objects.

  • closing performs a dilatation followed by an erosion. This helps to fill small holes while preserving the shape and size of larger objects.

  • filter performs median filtering in the binary image. Provide a positive integer > 1 to indicate the size of the median filtering. Higher values are more efficient to remove noise in the background but can dramatically impact the perimeter of objects, mainly for irregular perimeters such as leaves with serrated edges.

fill_hull

Fill holes in the binary image? Defaults to FALSE.

lower_size, upper_size

Lower and upper limits for size for the image analysis. Plant images often contain dirt and dust. Upper limit is set to NULL, i.e., no upper limit used. One can set a known area or use lower_size = 0 to select all objects (not advised). Objects that matches the size of a given range of sizes can be selected by setting up the two arguments. For example, if lower_size = 120 and upper_size = 140, objects with size greater than or equal 120 and less than or equal 140 will be considered.

topn_lower, topn_upper

Select the top n objects based on its area. topn_lower selects the n elements with the smallest area whereas topn_upper selects the n objects with the largest area.

Value

An sf object containing vectorized features from the raster mask, with added area measurements.

Examples

if (interactive() && requireNamespace("EBImage")) {
library(pliman)
mask <- image_pliman("mask.tif")
shp <- mosaic_vectorize(mask, watershed = FALSE)
mosaic_plot(mask)
shapefile_plot(shp, add = TRUE, lwd = 3)
}