mosaic_sam: Mosaic SAM

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

Description

The function performs the spectral angle mapper algorithm chunk by chunk for the mosaics files. It uses the parallel package, and by default all cores -1.

The function uses mosaic_chunk to cast a mosaic tile as a Tile object. Then performs a tile_base_corr, wavealing, and tile_sam to finaly write binary files that hold the Spectral Angle Mapper results in the destination folder (path slot of the SpectralInfo object). The files can be loaded back to R using link{mosaic_compose}.

The function is using the parallel package, as each tile_sam takes a while to complete.

Usage

mosaic_sam(
  info,
  sref,
  derivative = NULL,
  base_corr = TRUE,
  FUN = NULL,
  n_cores = NULL,
  temporal = FALSE
)

Arguments

info	SpectralInfo object.
sref	SpectralReference object.
derivative	whether to apply the first (1) or second (2) derivative before sam. Default NULL.
base_corr	TRUE/FALSE should tile_base_corr be call before processing each chunk?
FUN	A function to be passed to preprocess.It is always applied as if 'data' were a SpectralPack object.
n_cores	The number of cores to parallelize the task. NULL means all cores -1.
temporal	Whether the file should be written in a temporal folder or in the folder where the main file lives.

Value

The folder path where the files where written

See Also

For a single tile application see tile_sam.

Examples

x <- mosaic_info(base::system.file("extdata/mosaic.dmt", package = "uFTIR"))
mosaic_sam(x, primpke, n_cores = 1, temporal = TRUE)

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