alignLan {patternize}

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').

Value

List of aligned RasterStack objects.