maskOutline: Intersects a RasterStack with an outline. Everything outside...

In StevenVB12/patternize: Quantification of Color Pattern Variation

Intersects a RasterStack with an outline. Everything outside of the outline will be removed from the raster.

Description

Intersects a RasterStack with an outline. Everything outside of the outline will be removed from the raster.

Usage

maskOutline(
  RasterStack,
  outline,
  refShape,
  landList = NULL,
  adjustCoords = FALSE,
  cartoonID = NULL,
  IDlist = NULL,
  crop = c(0, 0, 0, 0),
  flipRaster = NULL,
  flipOutline = NULL,
  imageList = NULL,
  maskColor = 0,
  inverse = FALSE
)

Arguments

RasterStack	RasterStack to be masked.
outline	xy coordinates that define outline.
refShape	This can be 'target' in case the reference shape is a single sample (for registration analysis) or 'mean' if the images were transformed to a mean shape (only for meanshape when using landmark transformation)
landList	Landmark list to be given when type = 'mean'.
adjustCoords	Adjust landmark coordinates in case they are reversed compared to pixel coordinates (default = FALSE).
cartoonID	ID of the sample for which the cartoon was drawn. Only has to be given when refShape is 'mean'.
IDlist	List of sample IDs should be specified when refShape is 'mean'.
crop	Vector c(xmin, xmax, ymin, ymax) that specifies the pixel coordinates to crop the original image used in landmark or registration analysis.
flipRaster	Whether to flip raster along xy axis (in case there is an inconsistency between raster and outline coordinates).
flipOutline	Whether to flip plot along x, y or xy axis.
imageList	List of image as obtained from makeList should be given if one wants to flip the outline or adjust landmark coordinates.
maskColor	Color the masked area gets. Set to 0 for black (default) or 255 for white.
inverse	If TRUE, areas withing the outline will be masked.

Examples

## Not run: 
data(imageList)
outline_BC0077 <- read.table(paste(system.file("extdata",  package = 'patternize'),
'/BC0077_outline.txt', sep=''), header = FALSE)

masked <- maskOutline(imageList[[1]], outline_BC0077, refShape = 'target', flipOutline = 'y')

## End(Not run)

StevenVB12/patternize documentation built on Nov. 2, 2023, 8:01 p.m.