hyperSpec: textio – R documentation

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textio

Import/export of hyperSpec objects to/from ASCII files A detailed discussion of hyperSpec's file import and export capabilities is given in vignette “fileio”.

Description

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

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

Usage

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,
  ...
)

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

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,
  ...
)

Arguments

`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.
`check.names`	handed to `read.table`. Make sure this is `FALSE`, if the column names of the spectra are the wavelength values.
`...`	arguments handed to `read.table` and `write.table`, respectively.
`header`	the file has (shall have) a header line
`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`

Details

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.

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, vignette ("fileio") and the documentation of R.matlab.

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.

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.

Author(s)

C. Beleites

Examples

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

## export & import matlab files
if (require (R.matlab)) {
   # export to matlab file
   writeMat (paste0 (tempdir(), "/test.mat"),
             x = flu[[]], wavelength = flu@wavelength,
             label = lapply (flu@label, as.character))

   # reading a matlab file
   data <- readMat (paste0 (tempdir(), "/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 = paste0 (tempdir(), "/flu.txt"),
    cols = c(".wavelength", "spc", "c"),
		order = c("c", ".wavelength"),
		decreasing = c(FALSE, TRUE))

read.txt.long (file = paste0 (tempdir(), "/flu.txt"),
      cols = list (.wavelength = expression (lambda / nm),
      spc = "I / a.u", c = expression ("/" (c, (mg/l)))))

write.txt.wide (flu,  file = paste0 (tempdir(), "/flu.txt"),
    cols = c("c", "spc"),
		col.labels = TRUE, header.lines = 2, row.names = TRUE)

write.txt.wide (flu,  file = paste0 (tempdir(), "/flu.txt"),
                col.labels = FALSE, row.names = FALSE)

read.txt.wide (file = paste0 (tempdir(), "/flu.txt"),
    # give columns in same order as they are in the file
    cols = list (spc = "I / a.u",
                 c = expression ("/"("c", "mg/l")),
                 filename = "filename",
                 # plus wavelength label last
                 .wavelength = "lambda / nm"),
		header = TRUE)

hyperSpec

Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

v0.100.0

GPL (>= 3)

Authors

Claudia Beleites [aut, cre, dtc] (<https://orcid.org/0000-0003-1626-154X>), Valter Sergo [aut], Alois Bonifacio [ctb, dtc], Marcel Dahms [ctb], Björn Egert [ctb], Simon Fuller [ctb], Vilmantas Gegzna [ctb], Rustam Guliev [ctb], Bryan A. Hanson [ctb], Michael Hermes [ctb], Martin Kammer [dtc], Roman Kiselev [ctb], Sebastian Mellor [ctb]

Initial release

2021-09-13