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

In StevenVB12/patternize: Quantification of Color Pattern Variation

Aligns images using niftyreg utilities for automated image registration and extracts colors using a predefined HSV values and cutoff value.

Description

Aligns images using niftyreg utilities for automated image registration and extracts colors using a predefined HSV values and cutoff value.

Usage

patRegHSV(
  sampleList,
  target,
  HSV,
  resampleFactor = NULL,
  useBlockPercentage = 75,
  colOffset = 0.1,
  crop = c(0, 0, 0, 0),
  removebgR = NULL,
  maskOutline = NULL,
  plot = FALSE,
  focal = FALSE,
  sigma = 3,
  iterations = 0,
  ignoreHSVvalue = FALSE,
  patternsToFile = NULL
)

Arguments

sampleList	List of RasterStack objects.
target	Image imported as RasterStack used as target for registration.
HSV	Values for color pattern extraction specified as HSV vector.
resampleFactor	Integer for downsampling used by redRes (default = NULL).
useBlockPercentage	Block percentage as used in niftyreg (default = 75).
colOffset	Color offset for color pattern extraction (default = 0.10).
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.
maskOutline	When outline is specified, everything outside of the outline will be masked for the color extraction (default = NULL).
plot	Whether to plot transformed color patterns while processing (default = FALSE). Transformed color patterns can be plot on top of each other ('stack') or next to the original image for each sample ('compare').
focal	Whether to perform Gaussian blurring (default = FALSE).
sigma	Size of sigma for Gaussian blurring (default = 3).
iterations	Number of iterations for recalculating average color (default = 0). If set, the RGB value for pattern extraction will be iteratively recalculated to be the average of the extracted area. This may improve extraction of distinct color pattern, but fail for more gradually distributed (in color space) patterns.
ignoreHSVvalue	Whether to ignore the HSV value (~darkness).
patternsToFile	Name of directory to which the color pattern of each individual will be outputted (default = NULL).

Value

List of raster objects.

Examples

## Not run: 
IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')
prepath <- system.file("extdata",  package = 'patternize')
extension <- '.jpg'

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

target <- imageList[[1]]

HSV <- c(0.025,1,0.45)

# Note that this example only aligns one image with the target,
# remove [2] to run a full examples.
rasterList_regHSV <- patRegRGB(imageList[2], target, HSV,
colOffset= 0.15, crop = c(100,400,40,250), removebgR = 100, plot = 'stack')

## End(Not run)

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