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

Description Usage Arguments Value See Also Examples

There are to ways to process a mosaic. One way -which should be the standard- is to do it internally in R by calling first mosaic_info and later mosaic_sam.

The function will write in the path specified in the SpectralInfo object returned by mosaic_info a series of binary files holding the SAM results. In other words, the function does not load the results to R automaticaly. You can call this function to load them back to R in a single object, which will be of class SAM.

mosaic_compose(
  path = ".",
  clusterlist = NULL,
  nslices = NULL,
  drop_raw = FALSE
)

`path`	Where are the binary files? you can use the 'path' slot of the `SpectralInfo` instead of enter it manually.
`clusterlist`	The clusterlist vector that you passed along with the `SpectralReference` in the call to `mosaic_sam`.
`nslices`	If you deal with large mosaics, you might want to load only a few of the sam matches. This argument allows you to define up to which match you want to load to R.
`drop_raw`	If you are not interested in the angles you can set this argument to TRUE and avoid load them to R.

An object of class SAM.

mosaic_sam

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x <- mosaic_info(base::system.file("extdata/mosaic.dmt", package = "uFTIR"))
mosaic_sam(x, primpke, n_cores = 1)
y <- mosaic_compose(x@path, primpke@clusterlist)