Align images using landmarks
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"
)List of aligned RasterStack objects.
List of RasterStack objects.
Landmark list as returned by makeList.
List of sample IDs should be specified when masking outline and transformRef is 'meanshape'.
Adjust landmark coordinates in case they are reversed compared to pixel coordinates (default = FALSE).
Integer for downsampling used by redRes.
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.
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.
Transformation type as used by computeTransform
(default ='tps').
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.
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).
Color offset for color background extraction (default = 0.10).
If TRUE, areas withing the outline will be masked. If maskOutline is a list, this should also be a list.
ID of the sample for which the cartoon was drawn and will be used for masking (should be set when transformRef = 'meanShape').
Image (RasterStack) used for target. Use raster::stack('filename').
Plot transformed image (default = FALSE).
ImageJ (Fiji) or tps format (default = 'imageJ').