patRegW: 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 color pattern using watershed segmentation. This function works interactively by allowing to pick a starting pixel within each pattern element from which the watershed will extract the pattern. This function works best for patterns with sharp boundaries.

Description

Aligns images using niftyreg utilities for automated image registration and extracts color pattern using watershed segmentation. This function works interactively by allowing to pick a starting pixel within each pattern element from which the watershed will extract the pattern. This function works best for patterns with sharp boundaries.

Usage

patRegW(
  sampleList,
  target,
  resampleFactor = NULL,
  useBlockPercentage = 75,
  crop = c(0, 0, 0, 0),
  removebgR = NULL,
  maskOutline = NULL,
  cartoonID = NULL,
  correct = FALSE,
  blur = TRUE,
  sigma = 3,
  bucketfill = TRUE,
  cleanP = NULL,
  splitC = NULL,
  plotTransformed = FALSE,
  plotCorrect = FALSE,
  plotEdges = FALSE,
  plotPriority = FALSE,
  plotWS = FALSE,
  plotBF = FALSE,
  plotFinal = FALSE
)

Arguments

sampleList	List of RasterStack objects.
target	Image imported as RasterStack used as target for registration.
resampleFactor	Integer for downsampling image used by redRes.
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.
maskOutline	When outline is specified, everything outside of the outline will be masked for the color extraction (default = NULL).
cartoonID	ID of the sample for which the cartoon was drawn and will be used for masking.
correct	Correct image illumination using a linear model (default = FALSE).
blur	Blur image for priority map extraction (default = TRUE).
sigma	Size of sigma for Gaussian blurring (default = 5).
bucketfill	Use a bucket fill on the background to fill holes (default = TRUE).
cleanP	Integer to remove spurious areas with width smaller than cleanP (default = NULL).
splitC	Integer to split selected patterns into connected components and remove ones with areas smaller than splitC (default = NULL).
plotTransformed	Plot transformed image (default = FALSE).
plotCorrect	Plot corrected image, corrected for illumination using a linear model (default = FALSE).
plotEdges	Plot image gradient (default = FALSE).
plotPriority	Plot priority map (default = FALSE).
plotWS	Plot watershed result (default = FALSE).
plotBF	Plot bucketfill (default = FALSE).
plotFinal	Plot extracted patterns (default = FALSE).

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]]

outline_BC0077 <- read.table(paste(system.file("extdata",  package = 'patternize'),
'/BC0077_outline.txt', sep=''), header = FALSE)

rasterList_regW <- patRegW(imageList, target, plotTransformed = FALSE, cartoonID = 'BC0077',
                          correct = TRUE, plotCorrect = FALSE, blur = FALSE, sigma = 2,
                          bucketfill = FALSE, cleanP = 0, splitC = 10, plotPriority = TRUE,
                          plotWS = FALSE, plotBF = FALSE, plotFinal = TRUE, removebgR = 100,
                          maskOutline = outline_BC0077)

## End(Not run)

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