R/DEPRECATED-read.ENVI.Nicolet.R

In r-hyperspec/hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

#' @details
#' Nicolet uses some more keywords in their header file.
#' They are interpreted as follows:
#' \tabular{ll}{
#' description   \tab giving the position of the first spectrum \cr
#' z plot titles \tab wavelength and intensity axis units, comma separated \cr
#' pixel size    \tab interpreted as x and y step size
#'                    (specify `x = NA` and `y = NA`)
#' }
#' These parameters can be overwritten by giving a list with the respective
#' elements in parameter `header`.
#'
#' The values in header line description seem to be microns while the pixel
#' size seems to be in microns. If `nicolet.correction` is true, the
#' pixel size values (i.e. the step sizes) are multiplied by 1000.
#'
#' @param nicolet.correction see details
#' @describeIn  DEPRECATED-read.ENVI
#' @export
#'
#' @importFrom utils modifyList
read.ENVI.Nicolet <- function(file = stop("read.ENVI: file name needed"),
                              headerfile = NULL, header = list(), ...,
                              x = NA, y = NA,
                              nicolet.correction = FALSE) {
  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  deprecated_read_envi()
  # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  ## the additional keywords to interprete must be read from headerfile
  headerfile <- .find.ENVI.header(file, headerfile)
  keys <- readLines(headerfile)
  keys <- .read.ENVI.split.header(keys)
  keys <- keys[c("description", "z plot titles", "pixel size")]

  header <- modifyList(keys, header)

  ## most work is done by read.ENVI
  spc <- read.ENVI(
    file = file, headerfile = headerfile, header = header, ...,
    x = if (is.na(x)) 0:1 else x,
    y = if (is.na(y)) 0:1 else y
  )

  ### From here on processing the additional keywords in Nicolet's ENVI header *

  ## z plot titles -------------------------------------------------------------
  ## default labels
  label <- list(
    x = expression(`/`(x, micro * m)),
    y = expression(`/`(y, micro * m)),
    spc = "I / a.u.",
    .wavelength = expression(tilde(nu) / cm^-1)
  )

  ## get labels from header information
  if (!is.null(header$"z plot titles")) {
    pattern <- "^[[:blank:]]*([[:print:]^,]+)[[:blank:]]*,.*$"
    tmp <- sub(pattern, "\\1", header$"z plot titles")

    if (grepl("Wavenumbers (cm-1)", tmp, ignore.case = TRUE)) {
      label$.wavelength <- expression(tilde(nu) / cm^(-1))
    } else {
      label$.wavelength <- tmp
    }

    pattern <- "^[[:blank:]]*[[:print:]^,]+,[[:blank:]]*([[:print:]^,]+).*$"
    tmp <- sub(pattern, "\\1", header$"z plot titles")
    if (grepl("Unknown", tmp, ignore.case = TRUE)) {
      label$spc <- "I / a.u."
    } else {
      label$spc <- tmp
    }
  }

  ## modify the labels accordingly
  spc@label <- modifyList(label, spc@label)

  ## set up spatial coordinates ------------------------------------------------
  ## look for x and y in the header only if x and y are NULL
  ## they are in `description` and `pixel size`

  ## set up regular expressions to extract the values
  p.description <- paste(
    "^Spectrum position[[:digit:]]+ of[[:digit:]]+ positions,",
    "X = ([[:digit:].-]+), Y = ([[:digit:].-]+)$"
  )
  p.pixel.size <- "^[[:blank:]]*([[:digit:].-]+),[[:blank:]]*([[:digit:].-]+).*$"

  if (is.na(x) && is.na(y) &&
    !is.null(header$description) && grepl(p.description, header$description) &&
    !is.null(header$"pixel size") && grepl(p.pixel.size, header$"pixel size")) {
    x[1] <- as.numeric(sub(p.description, "\\1", header$description))
    y[1] <- as.numeric(sub(p.description, "\\2", header$description))

    x[2] <- as.numeric(sub(p.pixel.size, "\\1", header$"pixel size"))
    y[2] <- as.numeric(sub(p.pixel.size, "\\2", header$"pixel size"))

    ## it seems that the step size is given in mm while the offset is in micron
    if (nicolet.correction) {
      x[2] <- x[2] * 1000
      y[2] <- y[2] * 1000
    }

    ## now calculate and set the x and y coordinates
    x <- x[2] * spc$x + x[1]
    if (!any(is.na(x))) {
      spc@data$x <- x
    }

    y <- y[2] * spc$y + y[1]
    if (!any(is.na(y))) {
      spc@data$y <- y
    }
  }

  ## consistent file import behaviour across import functions
  ## .spc_io_postprocess_optional is called already by read.ENVI

  spc
}

hySpc.testthat::test(read.ENVI.Nicolet) <- function() {
  context("read.ENVI.Nicolet")

  test_that(
    "deprecated",
    expect_warning(
      expect_error(read.ENVI.Nicolet(file = ""), "Cannot guess header"),
      "deprecated"
    )
  )
}