textio: Import and Export of hyperSpec objects Besides 'save' and...
In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Description Usage Arguments Details Author(s) See Also Examples

Firstly, hyperSpec objects can be imported and exported as ASCII files.

Besides save and load, two general ways to import and export data into hyperSpec objects exist.

read.txt.long(file = stop("file is required"), cols = list(.wavelength =
  expression(lambda/nm), spc = "I / a.u."), header = TRUE, ...)

read.txt.wide(file = stop("file is required"), cols = list(spc = "I / a.u.",
  .wavelength = expression(lambda/nm)), sep = "\t", row.names = NULL,
  check.names = FALSE, ...)

write.txt.long(object, file = "", order = c(".rownames", ".wavelength"),
  na.last = TRUE, decreasing = FALSE, quote = FALSE, sep = "\t",
  row.names = FALSE, cols = NULL, col.names = TRUE, col.labels = FALSE,
  append = FALSE, ...)

write.txt.wide(object, file = "", cols = NULL, quote = FALSE,
  sep = "\t", row.names = FALSE, col.names = TRUE, header.lines = 1,
  col.labels = if (header.lines == 1) FALSE else TRUE, append = FALSE, ...)

`file`	filename or connection
`cols`	the column names specifying the column order. For data import, a list with elements `colname = label`; for export a character vector with the colnames. Use `wavelength` to specify the wavelengths.
`header`	the file has (shall have) a header line
`...`	arguments handed to `read.table` and `write.table`, respectively.
`check.names`	handed to `read.table`. Make sure this is `FALSE`, if the column names of the spectra are the wavelength values.
`object`	the `hyperSpec` object
`order`	which columns should be `order`ed? `order` is used as index vector into a `data.frame` with columns given by `cols`.
`na.last`	handed to `order` by `write.txt.long`.
`decreasing`	logical vector giving the sort order
`quote,sep,col.names,row.names`	have their usual meaning (see `read.table` and `write.table`), but different default values. For file import, `row.names` should usually be `NULL` so that the first column becomes a extra data column (as opposed to row names of the extra data).
`col.labels`	Should the column labels be used rather than the colnames?
`append`	Should the output be appended to an existing file?
`header.lines`	Toggle one or two line header (wavelengths in the second header line) for `write.txt.wide`

A second option is using the package R.matlab which provides the functions readMat and writeMat.

hyperSpec comes with a number of pre-defined functions to import manufacturer specific file formats. For details, see vignette ("file-io").

read.spc imports Thermo Galactic's .spc file format, and ENVI files may be read using read.ENVI.

These functions are very flexible and provide lots of arguments.

If you use them to read or write manufacturer specific ASCII formats, please consider writing a wrapper function and contributing this function to hyperSpec. An example is in the “flu” vignette (see vignette ("flu", package = "hyperSpec").

Note that R accepts many packed formats for ASCII files, see connections. For .zip files, see unzip.

For further information, see the examples below and the documentation of R.matlab.

Firstly, hyperSpec objects can be imported and exported as ASCII files.

A second option is using the package R.matlab which provides the functions readMat and writeMat.

hyperSpec comes with a number of pre-defined functions to import manufacturer specific file formats. For details, see vignette ("fileio").

read.spc imports Thermo Galactic's .spc file format, and ENVI files may be read using read.ENVI.

These functions are very flexible and provide lots of arguments.

Note that R accepts many packed formats for ASCII files, see connections. For .zip files, see unzip.

For further information, see the examples below, vignette ("fileio") and the documentation of R.matlab.

C. Beleites

read.table and write.table

R.matlab for .mat files

read.ENVI for ENVI data

read.spc for .spc files

Manufacturer specific file formats: scan.txt.Renishaw

vignette ("fileio") and http://hyperspec.r-forge.r-project.org/blob/fileio.pdf, respectively

## Not run: vignette  ("file-io")

## export & import matlab files
if (require (R.matlab)){
   # export to matlab file
   writeMat ("test.mat", x = flu[[]], wavelength = flu@wavelength,
             label = lapply (flu@label, as.character))

   # reading a matlab file
   data <- readMat ("test.mat")
   print (data)
   mat <- new ("hyperSpec", spc = data$x,
               wavelength = as.numeric(data$wavelength),
               label = data$label[,,1])
}

## ascii export & import


write.txt.long (flu,  file = "flu.txt", cols = c(".wavelength", "spc", "c"),
		order = c("c", ".wavelength"),
		decreasing = c(FALSE, TRUE))

read.txt.long (file = "flu.txt", cols = list (.wavelength = expression (lambda / nm),
      spc= "I / a.u", c = expression ("/" (c, (mg/l)))))

write.txt.wide (flu,  file = "flu.txt", cols = c("c", "spc"),
		col.labels = TRUE, header.lines = 2, row.names = TRUE)

write.txt.wide (flu,  file = "flu.txt", col.labels = FALSE, row.names = FALSE)

read.txt.wide (file = "flu.txt",
      cols = list (c=expression ("/"("c", "mg/l")), spc="I / a.u", .wavelength = "lambda / nm"),
		header = TRUE)