patRegK {patternize} | R Documentation |
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 |
useBlockPercentage |
Block percentage as used in |
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)