patLanK_HSV: Aligns images usings transformations obtained from fixed...

In patternize: Quantification of Color Pattern Variation

Aligns images usings transformations obtained from fixed landmarks and extracts colors using k-means clustering.

Description

Aligns images usings transformations obtained from fixed landmarks and extracts colors using k-means clustering.

Usage

patLanK_HSV(
  sampleList,
  landList,
  k = 3,
  fixedStartCenter = NULL,
  resampleFactor = NULL,
  crop = FALSE,
  cropOffset = c(0, 0, 0, 0),
  res = 300,
  transformRef = "meanshape",
  transformType = "tps",
  removebgK = NULL,
  adjustCoords = FALSE,
  plot = FALSE,
  focal = FALSE,
  sigma = 3,
  ignoreHSVvalue = FALSE
)

Arguments

sampleList	List of RasterStack objects.
landList	Landmark list as returned by makeList.
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.
crop	Whether to use the landmarks range to crop the image. This can significantly speed up the analysis (default = FALSE).
cropOffset	Vector c(xmin, xmax, ymin, ymax) that specifies the number of pixels you want the cropping to be offset from the landmarks (in case the landmarks do not surround the entire color pattern). The values specified should present the percentage of the maximum landmark value along the x and y axis.
res	Resolution for color pattern raster (default = 300). This should be reduced if the number of pixels in the image is lower than th raster.
transformRef	ID of reference sample for shape to which color patterns will be transformed to. Can be 'meanshape' for transforming to mean shape of Procrustes analysis.
transformType	Transformation type as used by computeTransform (default ='tps').
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.
adjustCoords	Adjust landmark coordinates in case they are reversed compared to pixel coordinates (default = FALSE).
plot	Whether to plot transformed color patterns while processing (default = FALSE).
focal	Whether to perform Gaussian blurring (default = FALSE).
sigma	Size of sigma for Gaussian blurring (default = 3).
ignoreHSVvalue	Whether to ignore the HSV value (~darkness).

Value

List of summed raster for each k-means cluster objects.

Examples

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

extension <- '.jpg'
imageList <- makeList(IDlist, 'image', prepath, extension)
# Note that this example only aligns two images with the target,
# remove [1:2] to run a full examples.
rasterList_lanK <- patLanK(imageList[1:2], landmarkList[1:2], k = 4, crop = TRUE,
res = 100, removebgK = 100, adjustCoords = TRUE, plot = TRUE)

## End(Not run)

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