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

In StevenVB12/patternize: Quantification of Color Pattern Variation

Aligns images usings transformations obtained from fixed landmarks and extracts colors using a predefined RGB values and cutoff value.

Description

Aligns images usings transformations obtained from fixed landmarks and extracts colors using a predefined RGB values and cutoff value.

Usage

patLanRGB(
  sampleList,
  landList,
  RGB = NULL,
  sampleRGB = FALSE,
  sampleRGBtype = "point",
  resampleFactor = NULL,
  colOffset = 0.1,
  crop = FALSE,
  cropOffset = c(0, 0, 0, 0),
  res = 300,
  transformRef = "meanshape",
  transformType = "tps",
  adjustCoords = FALSE,
  plot = NULL,
  focal = FALSE,
  sigma = 3,
  iterations = 0,
  imageIDs = NULL,
  patternsToFile = NULL
)

Arguments

sampleList	List of RasterStack objects.
landList	Landmark list as returned by makeList.
RGB	RGB values for color pattern extraction specified as vector.
sampleRGB	Whether to set RGB for each image manually.
sampleRGBtype	Whether to pick a point or area (defined by left bottom and top right) for sampleRGB.
resampleFactor	Integer for downsampling used by redRes.
colOffset	Color offset for color pattern extraction (default = 0.10).
crop	Whether to use the landmarks range to crop the image. This can 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').
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 = NULL). 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.
imageIDs	A list of IDs to match landmarks to images if landmarkList and imageList don't have the same length.
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 <- '_landmarks_LFW.txt'

landmarkList <- makeList(IDlist, 'landmark', prepath, extension)

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

RGB <- c(114,17,0)
rasterList_lanRGB <- patLanRGB(imageList, landmarkList, RGB,
colOffset = 0.15, crop = TRUE, res = 100, adjustCoords = TRUE, plot = 'stack')

## End(Not run)

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