vignettes/read.ENVI.Nicolet.R

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

# The contents of "read.ENVI.Nicolet.R"

read.ENVI.Nicolet <- function(
  file = stop("read.ENVI: file name needed"),
  headerfile = NULL,
  header = list(),
  ..., # goes to read.ENVI
  x = NA, y = NA, # NA means: use the specifications from the header file if possible
  nicolet.correction = FALSE) {


  ## 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
    }
  }

  spc
}