alignLan: Align images using landmarks
In StevenVB12/patternize: Quantification of Color Pattern Variation

alignLan

R Documentation

Align images using landmarks

Description

Align images using landmarks

Usage

alignLan(
  imageList,
  landList,
  IDlist = NULL,
  adjustCoords = FALSE,
  resampleFactor = NULL,
  res = c(300, 300),
  transformRef = "meanshape",
  transformType = "tps",
  maskOutline = NULL,
  removebg = NULL,
  removebgColOffset = 0.1,
  inverse = FALSE,
  cartoonID = NULL,
  refImage = NULL,
  plotTransformed = FALSE,
  format = "imageJ"
)

Arguments

`imageList`	List of RasterStack objects.
`landList`	Landmark list as returned by `makeList`.
`IDlist`	List of sample IDs should be specified when masking outline and transformRef is 'meanshape'.
`adjustCoords`	Adjust landmark coordinates in case they are reversed compared to pixel coordinates (default = FALSE).
`resampleFactor`	Integer for downsampling used by `redRes`.
`res`	Resolution vector c(x,y) for output rasters (default = c(300,300)). This should be reduced if the number of pixels in the image is lower than th raster.
`transformRef`	ID or landmark matrix 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').
`maskOutline`	When outline is specified, everything outside of the outline will be masked for the color extraction (default = NULL). This can be a list of multiple outlines.
`removebg`	Integer or RGB vector indicating the range of RGB threshold to remove from image (e.g. 100 removes pixels with average RGB > 100; default = NULL).
`removebgColOffset`	Color offset for color background extraction (default = 0.10).
`inverse`	If TRUE, areas withing the outline will be masked. If maskOutline is a list, this should also be a list.
`cartoonID`	ID of the sample for which the cartoon was drawn and will be used for masking (should be set when transformRef = 'meanShape').
`refImage`	Image (RasterStack) used for target. Use raster::stack('filename').
`plotTransformed`	Plot transformed image (default = FALSE).
`format`	ImageJ (Fiji) or tps format (default = 'imageJ').