get_profile: Get profile

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

Description

To check whether the program is doing a good job or not (an the library is appropriate), it is usually a good idea to recover the expectra of all the pixels that match a given cluster or substance to plot the spectra and compare it to a standard (the library entrance for that cluster/substance for example).

This function allows you to retrieve the spectra of all pixels that match a given cluster/substance and returns a matrix that can then be plotted to do the checking. It also allows the user to plot the object and overlay the points that match a feature. The latter can be achieved also by using the highlight_substance function. However, that function is only implemented for S3 "clipper" objects, so this might be a way to overcome that limitation.

get_profile_all will replace get_profile_sinfo some day. For now it does the same thing BUT it works only for clipper objects and you need to pass the fpa size and the wavenumber (waves) vector. It was designed to run in the cluster. It goes well with sam_write, sam_load.

Usage

get_profile(x, where, ...)

## S4 method for signature 'togetprofile,Tile'
get_profile(x, where, ...)

## S4 method for signature 'togetprofile,list'
get_profile(x, where, ...)

## S4 method for signature 'clipper,character'
get_profile(x, where, dst_cluster, fpa, waves)

get_profile_tile(
  x,
  where,
  dst_cluster,
  plotpol = TRUE,
  plotpt = FALSE,
  cluster = TRUE,
  slice = 1,
  clusternames = NULL,
  ...
)

get_profile_sinfo(
  x,
  where,
  dst_cluster,
  plotpol = TRUE,
  plotpt = FALSE,
  cluster = TRUE,
  slice = 1,
  clusternames = NULL,
  ...
)

get_profile_all(x, where, dst_cluster, fpa, waves)

Arguments

x	Object of class sam, Smooth or clipper that hold the processed tile/mosaic indicated in where.
where	Original object processed. It might by of class Tile or SpectralInfo. However, in the second case, where should be a labeled list of two elements one the SpectralInfo object (labeled "info"), and the other the tarjet dmd file (as a character labeled "dmdfile"). For get_profile_all it is a character vector with the *.dmd files that you want to retrieve.
...	other parameters for plot.raster.
dst_cluster	The expectra of the pixels that match which cluster/substance should be retrieved?
fpa	The fpa size, used in get_profile_all
waves	The wavenumbers, used in get_profile_all
plotpol	If true, the function will plot x and overlay countour lines highlighting dst_cluster. TRUE/FALSE.
plotpt	If true, the function will plot x and draw points over the pixels that match dst_cluster. For mosaics, the points will be only in the chunk selected in where. TRUE/FALSE.
cluster	If class(x) == "SAM", Should the substances or the clusters be used for analysis? TRUE means that the clusters are used, FALSE that the substances. If you set the argument to FALSE, dst_cluster and clusternames should be adjusted. Use the name of the substance and the substances list from the SpectralReference.
slice	If the object is of class sam or Smooth, Which slice of them should be considered when retrieving the pixel locations?
clusternames	if is.character(dst_cluster) you should provide a vector with the clusternames to coerse dst_cluster to numeric.

Value

matrix with the columns matching the wavenumbers of 'where'.

Examples

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)
y <- get_profile_sinfo(y,
                       where = list("info" = x, 
                                    "dmdfile" = "mosaic_0000_0000.dmd"),
                       5, FALSE, FALSE)

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