patRegK: Aligns images using 'niftyreg' utilities for automated image...

In patternize: Quantification of Color Pattern Variation

Aligns images using niftyreg utilities for automated image registration and extracts colors using k-means clustering.

Description

Aligns images using niftyreg utilities for automated image registration and extracts colors using k-means clustering.

Usage

patRegK(
  sampleList,
  target,
  k = 3,
  fixedStartCenter = NULL,
  resampleFactor = NULL,
  useBlockPercentage = 75,
  crop = c(0, 0, 0, 0),
  removebgR = NULL,
  removebgK = NULL,
  maskOutline = NULL,
  maskColor = 0,
  plot = FALSE,
  focal = FALSE,
  sigma = 3
)

Arguments

sampleList	List of RasterStack objects.
target	Image imported as RasterStack used as target for registration.
k	Integere for defining number of k-means clusters (default = 3).
fixedStartCenter	Specify a dataframe with start centers for k-means clustering.
resampleFactor	Integer for downsampling used by redRes (default = NULL).
useBlockPercentage	Block percentage as used in niftyreg (default = 75).
crop	Vector c(xmin, xmax, ymin, ymax) that specifies the pixel coordinates to crop the original image.
removebgR	Integer indicating the range RGB treshold to remove from image (e.g. 100 removes pixels with average RGB > 100; default = NULL) for registration analysis. This works only to remove a white background.
removebgK	Integer indicating the range RGB treshold to remove from image (e.g. 100 removes pixels with average RGB > 100; default = NULL) for k-means analysis. This works only to remove a white background.
maskOutline	When outline is specified, everything outside of the outline will be masked for the color extraction (default = NULL).
maskColor	Color the masked area gets. Set to 0 for black (default) or 255 for white.
plot	Whether to plot k-means clustered image while processing (default = FALSE).
focal	Whether to perform Gaussian blurring (default = FALSE).
sigma	Size of sigma for Gaussian blurring (default = 3).

Value

List of rasters for each k-means cluster objects.

Examples

IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')
prepath <- system.file("extdata",  package = 'patternize')
extension <- '.jpg'

imageList <- makeList(IDlist, 'image', prepath, extension)

target <- imageList[[1]]

## Not run: 
rasterList_regK <- patRegK(imageList[3], target, k = 5,
crop = c(100,400,40,250), removebgR = 100, plot = TRUE)

## End(Not run)

patternize documentation built on Aug. 22, 2023, 5:07 p.m.