itrax_image {itraxR}

Read an Itrax Image File

Description

Reads an Itrax image file and trims it according to the metadata provided.

Usage

itrax_image(
  file = "optical.tif",
  meta = "document.txt",
  plot = FALSE,
  trim = TRUE
)

Arguments

file

defines the name of the datafile to parse

meta

defines the relating metadata

plot

would you like to create a plot as a side-effect?

trim

defines custom trim parameters. The default behaviour uses the limits from the metadata file. Set the false for no trimming, or set the position limits by passing a two element vector.

Value

a matrix of RGB values, and the relevant data from the metadata file relating to the image.

Examples

itrax_image(file = system.file("extdata",
                         "CD166_19_S1_optical_lowres.tif",
                         package = "itraxR",
                         mustWork = TRUE),
            meta = system.file("extdata",
                         "CD166_19_S1_xrf_document.txt",
                         package = "itraxR",
                         mustWork = TRUE),
            plot = TRUE)