patRegW {patternize}

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)