toClip: Visual clipper

In uFTIR: Process and Analyze Agilent Cary 620 FTIR Microscope Images

Description

Visual aid to find the right center and radius for the clipper function. It does not clip, but return an usable (plotable) object.

Since the samples are placed under the uFTIR Microscope by hand, the cropping area to pass to clipper is not always the same and (usually) it has to be adjusted. To have a visual aid, you can use this function. It returns an S4 object of class clipmask which can be over-plotted on top of a SAM or Smooth object by calling polygon and using the xycoords slot of the returned object. Using that process you can test manually different center points and radius for the clipping circle.

Usage

toClip(rad = 1, segments = 5, centre = c(0, 0))

Arguments

rad	The circle radius.
segments	How many segments should the resulting polygon have? (because it is not a circle, 20 is ok).
centre	The coordinates of the polygon centre (x,y).

Value

An object of class clipmask.

See Also

clipper

Examples

toClip(1, 5, c(0,0))

x <- tile_read(base::system.file("extdata/tile.bsp", package = "uFTIR"))
x <- tile_base_corr(x)
x <- wavealign(x, primpke)
x <- tile_sam(x)
x <- smooth_sam(x, as.integer(length(primpke@clusternames)), window = 3, 1)

clip <- toClip(8,20,c(10,10))
polygon(clip@xycoords)

x <- clipper(x, clip@centre, clip@rad, 1)

uFTIR documentation built on Oct. 25, 2021, 9:08 a.m.