22# '
33# ' Use this function to import a series of associated ESR spectra into R.
44# '
5- # ' This is a wrapper function for \code{read.table}. The function should be
5+ # ' This is a wrapper function for \code{read.table} and \code{readBin}.
6+ # ' The function should be
67# ' used to read in a series of associated ESR spectrum files. A list with all
78# ' spectrum data is returned, which can be passed to \code{plot_Spectrum}
89# ' for plotting the spectra.
910# '
10- # ' @param file \code{\link{character}} (required): file path or directory where
11- # ' the spectra files are stored.
12- # ' @param ... further arguments (e.g., \code{n} to specify the number of datapoints).
11+ # ' **Binary formats**
12+ # '
13+ # ' This function is able to read in binary spectrum files produced by Bruker
14+ # ' ESR devices. By default (\code{device = 'auto'}), the function assumes the
15+ # ' proper mode of the vector (integer or numeric), endianness and number of
16+ # ' bytes per element based on the file extension. Currently, the following
17+ # ' devices are supported:
18+ # '
19+ # ' - **Bruker ESP300-E** (*.SPC* files): `what = 'int', endian = 'big', size = 4`
20+ # ' - **Bruker ELEXSYS500** (*.DTA* files): `what = 'numeric', endian = 'big', size = 8`
21+ # ' - **Bruker EMXplus** (*.SPC* files): `what = 'numeric', endian = 'little', size = 4`
22+ # '
23+ # ' Note that the Bruker ESP300-E and EMXplus devices share a common file
24+ # ' extension (.SPC) and that `device = 'auto'` (the default) will always
25+ # ' assume that the SPC file is from a ESP300-E. If your SPC file is
26+ # ' from a EMXplus, however, you should manually specify this using
27+ # ' `device = 'EMXplus'`.
28+ # '
29+ # '
30+ # ' @param file \code{\link{character}} (**required**):
31+ # ' file path or directory where the spectra files are stored.
32+ # '
33+ # ' @param device [character] (*with default*):
34+ # ' Manually specify the device the spectrum files were produced by.
35+ # ' By default, the proper binary format is deduced from the file
36+ # ' extension, which may however fail in case of ambiguous file
37+ # ' endings. See details.
38+ # '
39+ # ' Allowed options are:
40+ # ' - `"auto"` (the default)
41+ # ' - `"ESP300-E"` (.SPC)
42+ # ' - `"ELEXSYS500"` (.DTA)
43+ # ' - `"EMXplus"` (.SPC)
44+ # '
45+ # ' @param ... further arguments
46+ # ' (e.g., \code{n} to specify the number of datapoints; \code{sw} to specify
47+ # ' the sweep width).
48+ # '
1349# ' @return Returns a terminal output. In addition an
1450# ' \code{\link{R6Class}} object is returned. \cr
51+ # '
1552# ' @export
53+ # '
1654# ' @author Christoph Burow, University of Cologne (Germany)
55+ # '
1756# ' @seealso \code{\link{read.table}}, \code{\link{readBin}}, \code{\link{read.csv}}
57+ # '
1858# ' @references In progress
59+ # '
1960# ' @examples
2061# '
2162# ' # Import ASCII text file
3879# ' file5 <- system.file("extdata", "quartz.DTA", package = "ESR")
3980# ' spec5 <- read_Spectrum(file5)
4081# '
82+ # ' # Import Bruker EMXplus raw binary spectrum
83+ # ' file6 <- system.file("extdata", "DL_alanine.spc", package = "ESR")
84+ # ' spec6 <- read_Spectrum(file6, device = "EMXplus")
85+ # '
4186# ' # Import all example data sets at once by providing only the directory
4287# ' dir <- system.file("extdata", package = "ESR")
4388# ' specs <- read_Spectrum(dir)
4489# '
90+ # ' @md
4591# ' @export read_Spectrum
46- read_Spectrum <- function (file , ... ) {
92+ read_Spectrum <- function (file , device = " auto" ... ) {
93+
94+ # # SUPPORTED DEVICES ----
95+ devices <- list (bruker = c(" auto" " ESP300-E" " ELEXSYS500" " EMXplus"
96+ if (! is.null(device ))
97+ if (! device %in% unlist(devices ))
98+ stop(" Unknown device. Only the following are supported: " devices ), collapse = " , " call. = FALSE )
4799
48100 # # ADDITIONAL ARGS ----
49101 extraArgs <- list (... )
@@ -66,7 +118,7 @@ read_Spectrum <- function(file, ...) {
66118 if (is.na(val )) {
67119 file_list <- list.files(f , paste0(valid_ext , collapse = " |" ignore.case = TRUE )
68120 if (length(file_list ) == 0 ) {
69- stop(paste(" sInvalid file extension:" ext ), call. = FALSE )
121+ stop(paste(" Invalid file extension:" ext ), call. = FALSE )
70122 }
71123 ext <- list (file_list )
72124 }
@@ -128,7 +180,12 @@ read_Spectrum <- function(file, ...) {
128180 # # SPC
129181 # # -----------------------------------------------
130182 if (type == " spc"
131- df <- as.data.table(readBin(f , " int" n = file.info(f )$ size , endian = " big" size = 4 ))
183+
184+ if (device == " auto" || device == " ESP300-E"
185+ df <- as.data.table(readBin(f , " int" n = file.info(f )$ size , endian = " big" size = 4 ))
186+ else if (device == " EMXplus"
187+ df <- as.data.table(readBin(f , " numeric" n = file.info(f )$ size , endian = " little" size = 4 ))
188+
132189
133190 par <- tryCatch(
134191 read.table(gsub(" .spc" " .par" f , ignore.case = TRUE ), stringsAsFactors = FALSE ),
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