Nothing
R/read.spc.modifed.R
In specmine: Metabolomics and Spectral Data Analysis and Mining
Defines functions
.spc.ylab
# This is the implementation of the function read.spc from hyperSpec without creating new hyperSpec
# objects, thus it does not depend anymore from this package. It has the option to read or not the
# header aswell. It returns a list type object.
### read.spc - Import Thermo Galactic's .spc file format into an hyperSpec Object
###
### C. Beleites 2009/11/29
###
#####################################################################################################
## Define constants ---------------------------------------------------------------------------------
.nul <- as.raw (0)
## header sizes
.spc.size <- c (hdr = 512, subhdr = 32, subfiledir = 12, loghdr = 64)
.spc.default.keys.hdr2data <- c('fexper', 'fres', 'fsource')
.spc.default.keys.hdr2log <- c('fdate', 'fpeakpt')
.spc.default.keys.log2data <- FALSE
.spc.default.keys.log2log <- TRUE
## axis labeling ------------------------------------------------------------------------------------
## x-axis units .....................................................................................
.spc.FXTYPE <- c (expression (`/` (x, "a. u.")), #0
expression (`/` (tilde (nu), cm^-1)),
expression (`/` (lambda, (mu * m))),
expression (`/` (lambda, nm)),
expression (`/` (t, s)),
expression (`/` (t, min)),
expression (`/` (f, Hz)),
expression (`/` (f, kHz)),
expression (`/` (f, MHz)),
expression (`/` (frac (m, z), frac (u, e))),
expression (`/` (delta, ppm)), # 10
expression (`/` (t, d)),
expression (`/` (t, a)),
expression (`/` (Delta*tilde (nu), cm^-1)),
expression (`/` (E, eV)),
NA, # old version file uses label in gcatxt
'Diode No',
'Channel',
expression (`/` (x, degree)),
expression (`/` (T, degree*F)),
expression (`/` (T, degree*C)), # 20
expression (`/` (T, K)),
'Data Point',
expression (`/` (t, ms)),
expression (`/` (t, micro*s)),
expression (`/` (t, ns)),
expression (`/` (f, GHz)),
expression (`/` (lambda, cm)),
expression (`/` (lambda, m)),
expression (`/` (lambda, mm)),
expression (`/` (t, h)) # 30
)
.spc.xlab <- function (x) {
## x = 255 is for double interferogram and supposed not to have a label.
## Thus, returning NA is appropriate
if (x <= length (.spc.FXTYPE) + 1)
.spc.FXTYPE [x + 1]
else
NA
}
## y-axis units .....................................................................................
.spc.FYTYPE <- c (expression (`/` (I[Ref], "a. u.")), # -1
expression (`/` (I, "a. u.")),
expression (`/` (I[IGRM], "a. u.")),
'A',
expression (frac ((1 - R)^2, 2 * R)),
'Counts',
expression (`/` (U, V)),
expression (`/` (y, degree)),
expression (`/` (I, mA)),
expression (`/` (l, mm)),
expression (`/` (U, mV)),
expression (-log (R)), # 10
expression (`/` (y, '%')),
expression (`/` (I, 'a. u.')),
expression (I / I[0]),
expression (`/` (E, J)),
NA, # old version file uses label in gcatxt
expression (`/` (G, dB)),
NA, # old version file uses label in gcatxt
NA, # old version file uses label in gcatxt
expression (`/` (T, degree*F)),
expression (`/` (T, degree*C)), # 20
expression (`/` (T, K)),
'n',
'K', # extinction coeaffictient
expression (Re (y)),
expression (Im (y)),
'y (complex)', # complex
'T',
'R',
expression (`/` (I, 'a. u.')),
expression (`/` (I[Emission], 'a. u.'))
)
.spc.ylab <- function(x){
if (x <= 26)
.spc.FYTYPE [x + 2]
else if (x %in% 128 : 131)
.spc.FYTYPE [x - 99]
else
NA
}
## helper functions ---------------------------------------------------------------------------------
### raw.split.nul - rawToChar conversion, splitting at \0
raw.split.nul <- function (raw, trunc = c (TRUE, TRUE), firstonly = FALSE) {
# todo make better truncation
trunc <- rep (trunc, length.out = 2)
if (trunc [1] && raw [1] == .nul)
raw <- raw [-1]
if (trunc [2]) {
tmp <- which (raw > .nul)
if (length (tmp) == 0)
return ("")
raw <- raw [1 : tail (tmp, 1)]
}
if (raw [length (raw)] != .nul)
raw <- c (raw , .nul)
tmp <- c (0, which (raw == .nul))
out <- character (length (tmp) - 1)
for (i in 1 : (length (tmp) - 1))
if (tmp [i] + 1 < tmp [i + 1] - 1)
out [i] <- rawToChar (raw [(tmp [i] + 1) : (tmp [i + 1] - 1)])
if (length (out) > 1L & firstonly){
warning ("multiple strings encountered: ", paste (out, collapse = ", "), " but using only the first one.")
out <- out [1]
}
out
}
## file part reading functions ----------------------------------------------------------------------
## read file header .................................................................................
##
##
.spc.filehdr <- function (raw.data) {
## check file format
## NEW.LSB = 75 supported,
## NEW.MSB = 76 not supported (neither by many Grams software according to spc doc)
## OLD = 77 not supported (replaced by new format in 1996)
if (raw.data [2] != 75)
stop ("Wrong spc file format version.\n",
"Only 'new' spc files (1996 file format) with LSB word order are supported.")
hdr <- list (ftflgs = readBin (raw.data [ 1], "integer", 1, 1, signed = FALSE),
## byte 2 is already interpreted
fexper = readBin (raw.data [ 3], "integer", 1, 1, signed = TRUE ),
fexp = readBin (raw.data [ 4], "integer", 1, 1, signed = TRUE ),
fnpts = readBin (raw.data [ 5 : 8], "integer", 1, 4 ),
ffirst = readBin (raw.data [ 9 : 16], "double", 1, 8 ),
flast = readBin (raw.data [ 17 : 24], "double", 1, 8 ),
fnsub = readBin (raw.data [ 25 : 28], "integer", 1, 4 ),
fxtype = readBin (raw.data [ 29], "integer", 1, 1, signed = FALSE),
fytype = readBin (raw.data [ 30], "integer", 1, 1, signed = FALSE),
fztype = readBin (raw.data [ 31], "integer", 1, 1, signed = FALSE),
fpost = readBin (raw.data [ 32], "integer", 1, 1, signed = TRUE ),
fdate = readBin (raw.data [ 33 : 36], "integer", 1, 4 ),
fres = raw.split.nul (raw.data [ 37 : 45], firstonly = TRUE),
fsource = raw.split.nul (raw.data [ 46 : 54], firstonly = TRUE),
fpeakpt = readBin (raw.data [ 55 : 56], "integer", 1, 2, signed = FALSE),
fspare = readBin (raw.data [ 57 : 88], "numeric", 8, 4 ),
fcmnt = raw.split.nul (raw.data [ 89 : 218], firstonly = TRUE),
fcatxt = raw.split.nul (raw.data [219 : 248], trunc = c (FALSE, TRUE) ),
flogoff = readBin (raw.data [249 : 252], "integer", 1, 4), #, signed = FALSE),
fmods = readBin (raw.data [253 : 256], "integer", 1, 4), #, signed = FALSE),
fprocs = readBin (raw.data [ 257], "integer", 1, 1, signed = TRUE ),
flevel = readBin (raw.data [ 258], "integer", 1, 1, signed = TRUE ),
fsampin = readBin (raw.data [259 : 260], "integer", 1, 2, signed = FALSE),
ffactor = readBin (raw.data [261 : 264], "numeric", 1, 4 ),
fmethod = raw.split.nul (raw.data [265 : 312]),
fzinc = readBin (raw.data [313 : 316], "numeric", 1, 4), #, signed = FALSE),
fwplanes = readBin (raw.data [317 : 320], "integer", 1, 4), #, signed = FALSE),
fwinc = readBin (raw.data [321 : 324], "numeric", 1, 4 ),
fwtype = readBin (raw.data [ 325], "integer", 1, 1, signed = TRUE ),
## 187 bytes reserved
.last.read = .spc.size ['hdr']
)
## R doesn't have unsigned long int .................................
if (any (unlist (hdr [c ("flogoff", "fmods", "fzinc", "fwplanes")]) < 0))
stop ("error reading header: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
## do some post processing ..........................................
experiments <- c ("General", "Gas Chromatogram", "General Chromatogram", "HPLC Chromatogram",
"NIR Spectrum", "UV-VIS Spectrum", "* reserved *", "X-ray diffraction spectrum",
"Mass Spectrum", "NMR Spectrum", "Raman Spectrum", "Fluorescence Spectrum",
"Atomic Spectrum", "Chroatography Diode Array Data")
hdr$fexper <- factor (hdr$fexper + 1, levels = seq_along (experiments))
levels (hdr$fexper) <- experiments
hdr$ftflgs <- .spc.ftflags (hdr$ftflgs)
hdr$fdate <- ISOdate (year = hdr$fdate %/% 1048560,
month = hdr$fdate %/% 65536 %% 16,
day = hdr$fdate %/% 2048 %% 32,
hour = hdr$fdate %/% 64 %% 32,
min = hdr$fdate %% 64)
## interferogram ?
## if not, hdr$fpeakpt is set to NULL
if (hdr$fytype == 1){
if (hdr$fpeakpt != 0)
hdr$fpeakpt <- hdr$fpeakpt + 1
} else {
hdr$fpeakpt <- NULL
}
## set the axis labels
if (hdr$ftflgs ['TALABS']) {
# TODO: find test data
tmp <- rep (0, 4)
tmp [seq_along (hdr$fcatxt)] <- nchar (hdr$fcatxt)
if (tmp [1] > 0) hdr$fxtype <- hdr$fcatxt[1]
if (tmp [2] > 0) hdr$fytype <- hdr$fcatxt[2]
if (tmp [3] > 0) hdr$fztype <- hdr$fcatxt[3]
if (tmp [4] > 0) hdr$fwtype <- hdr$fcatxt[4]
}
hdr$fxtype <- .spc.xlab (hdr$fxtype)
hdr$fytype <- .spc.ylab (hdr$fytype)
hdr$fztype <- .spc.xlab (hdr$fztype)
hdr$fwtype <- .spc.xlab (hdr$fwtype)
## File with subfiles with individual x axes?
## Then there should be a subfile directory:
if (hdr$ftflgs ['TXYXYS'] && hdr$ftflgs ['TMULTI']){
## try to reject impossible values for the subfiledir offset
if (hdr$fnpts > length (raw.data) ||
(hdr$fnpts > hdr$flogoff && hdr$flogoff > 0) ||
hdr$fnpts < 512)
.spc.error (".spc.read.hdr", list (hdr = hdr),
"file header flags specify TXYXYS and TMULTI, ",
"but fnpts does not give a valid offset for the subfile directory.\n hdr$ftflgs = ",
paste (names (hdr$ftflgs)[hdr$ftflgs], collapse = " | "),
" (", sum (2^(0:7) [hdr$ftflgs]) , ")\n",
"You can try to read the file using hdr$ftflgs & ! TXYXYS (",
sum (2^(0 : 7) [hdr$ftflgs & c (TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)]),
"). This assumes that all subfiles do have the same x axis.\n\n")
hdr$subfiledir <- hdr$fnpts
hdr$fnpts <- 0
} else {
hdr$subfiledir <- 0
}
## some checks ......................................................
if (hdr$ftflgs ['TMULTI']){
## multiple spectra in file
if (hdr$fnsub <= 1)
warning ("spc file header specifies multiple spectra but only zero or one subfile.")
} else {
## single spectrum file
if (hdr$fnsub == 0)
hdr$fnsub <- 1
if (hdr$fnsub > 1) {
warning ("spc file header specifies single spectrum file but", hdr$fnsub,
"subfiles (spectra).\nOnly first subfile will be read.")
hdr$fnsub <- 1
}
if (hdr$ftflgs ['TRANDM'])
warning ("spc file header: file type flag TRANDM does not make sense without TMULTI.")
if (hdr$ftflgs ['TORDRD'])
warning ("spc file header: file type flag TORDRD does not make sense without TMULTI.")
if ((hdr$ftflgs ['TRANDM'] || hdr$ftflgs ['TORDRD']) && hdr$fnsub > 1)
hdr$ftflgs ['TMULTI'] <- TRUE
}
if (hdr$ftflgs ['TXYXYS'] && ! hdr$ftflgs ['TXVALS']) {
warning ("spc file header: file type flag TXYXYS does not make sense without TXVALS.")
hdr$ftflgs ['TXVALS'] <- TRUE
}
if (hdr$fwplanes > 0)
warning ("w planes found! This is not yet tested as the developer didn't have access to such files.\n",
"Please contact the package maintainer (cbeleites@units.it)",
"stating whether the file was imported successfully or not.")
hdr
}
## read sub file header .............................................................................
##
## needs header for consistency checks
##
.spc.subhdr <- function (raw.data, pos, hdr) {
subhdr <- list (subflgs = raw.data [pos + ( 1)],
subexp = readBin (raw.data [pos + ( 2)], "integer", 1, 1, signed = FALSE),
subindx = readBin (raw.data [pos + ( 3 : 4)], "integer", 1, 2, signed = FALSE),
subtime = readBin (raw.data [pos + ( 5 : 8)], "numeric", 1, 4),
subnext = readBin (raw.data [pos + ( 9 : 12)], "numeric", 1, 4),
subnois = readBin (raw.data [pos + (13 : 16)], "numeric", 1, 4),
subnpts = readBin (raw.data [pos + (17 : 20)], "integer", 1, 4), #, signed = FALSE),
subscan = readBin (raw.data [pos + (21 : 24)], "integer", 1, 4), #, signed = FALSE),
subwlevel = readBin (raw.data [pos + (25 : 28)], "numeric", 1, 4))
## 4 bytes reserved
## R doesn't have unsigned long int .................................
if (any (unlist (subhdr [c ("subnpts", "subscan")]) < 0))
stop ("error reading subheader: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
hdr$.last.read <- pos + .spc.size ['subhdr']
## checking
if (subhdr$subexp == -128 && hdr$fexp != -128)
warning ("subfile ", subhdr$subindx, " specifies data type float, but file header doesn't.",
"\nData will be interpreted as float.")
if (subhdr$subnpts > 0 && subhdr$subnpts != hdr$fnpts && ! hdr$ftflgs ['TXYXYS'])
warning ('subfile ', subhdr$subindx, ": number of points in subfile should be 0 if file",
" header flags do not specify TXYXYS.")
if (subhdr$subnpts == 0){
if (hdr$ftflgs ['TXYXYS'])
warning ('subfile ', subhdr$subindx, ': number of data points per spectrum not specified. ',
'Using fnpts (', hdr$fnpts, ').')
subhdr$subnpts <- hdr$fnpts
}
if (! hdr$ftflgs ['TXYXYS'])
if (hdr$fnpts != subhdr$subnpts) {
.spc.error (".spc.read.subhdr", list (hdr = hdr, subhdr = subhdr),
"hdr and subhdr differ in number of points per spectrum, ",
"but TXYXYS is not specified.\n hdr$ftflgs = ",
paste (names (hdr$ftflgs)[hdr$ftflgs], collapse = " | "),
" (", sum (2^(0:7) [hdr$ftflgs]) , ")\n",
"You can try to read the file using hdr$ftflgs | TMULTI | TXYXYS (",
sum (2^(0 : 7) [hdr$ftflgs |
c (FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE)]),
").\n\n")
}
# str (subhdr)
## according to .spc file documentation:
if (! hdr$ftflgs ['TMULTI'])
subhdr$subexp <- hdr$fexp
else if (hdr$fexp == -128 && subhdr$subexp != -128) {
warning ("Header file specifies float data format, but subfile uses integer exponent.",
" Subfile settings are overwritten.")
subhdr$subexp <- -128
}
## the z values
if (hdr$fzinc == 0) # should only happen for the first subfile...
hdr$fzinc = subhdr$subnext - subhdr$subtime
if (subhdr$subindx == 0)
hdr$firstz <- subhdr$subtime
if (subhdr$subtime == 0)
subhdr$subtime = subhdr$subindx * hdr$fzinc + hdr$firstz
## the w values
if (hdr$fwplanes > 0) {
if (subhdr$subwlevel != 0) {
subhdr$w <- subhdr$subwlevel
} else if (subhdr$subindx %% hdr$fwplanes == 1)
subhdr$w <- hdr$subhdr$w + hdr$fwinc
else
subhdr$w <- hdr$subhdr$w
}
hdr$subhdr <- subhdr
hdr
}
## read subfile directory ...........................................................................
##
.spc.subfiledir <- function (raw.data, pos, nsub) {
dir <- data.frame (ssfposn = rep (NA, nsub),
ssfsize = rep (NA, nsub),
ssftime = rep (NA, nsub))
for (s in seq_len (nsub)){
dir [s,] <- c (readBin (raw.data [pos + ( 1 : 4)], "integer", 1, 4), # , signed = FALSE),
readBin (raw.data [pos + ( 5 : 8)], "integer", 1, 4), # , signed = FALSE),
readBin (raw.data [pos + ( 9 : 12)], "numeric", 1, 4))
pos <- pos + .spc.size ['subfiledir']
}
## R doesn't have unsigned long int .................................
if (any (dir [, 1:2] < 0))
stop ("error reading subfiledir: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
# dir$ssfposn <- dir$ssfposn
dir
}
## read log block header ............................................................................
##
.spc.log <- function (raw.data, pos, log.bin, log.disk, log.txt, keys.log2data, keys.log2log,
replace.nul = as.raw (255), iconv.from = "latin1", iconv.to = "utf8") {
if (pos == 0) # no log block exists
return (list (data = list (),
log = list ()))
loghdr <- list (logsizd = readBin (raw.data [pos + ( 1 : 4)], "integer", 1, 4), # , signed = FALSE),
logsizm = readBin (raw.data [pos + ( 5 : 8)], "integer", 1, 4), # , signed = FALSE),
logtxto = readBin (raw.data [pos + ( 9 : 12)], "integer", 1, 4), # , signed = FALSE),
logbins = readBin (raw.data [pos + (13 : 16)], "integer", 1, 4), # , signed = FALSE),
logdsks = readBin (raw.data [pos + (17 : 20)], "integer", 1, 4), # , signed = FALSE),
## 44 bytes reserved
.last.read = pos + .spc.size ['loghdr']
)
## R doesn't have unsigned long int .................................
if (any (unlist (loghdr) < 0))
stop ("error reading log: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
log <- list ()
data <- list ()
## read binary part of log
if (log.bin)
log$.log.bin <- raw.data [loghdr$.last.read + seq_len (loghdr$logbins)]
## read binary on-disk-only part of log
if (log.disk)
log$.log.disk <- raw.data [loghdr$.last.read + loghdr$logbins + seq_len (loghdr$logdsks)]
## read text part of log
if (log.txt) {
log.txt <- raw.data [pos + loghdr$logtxto + seq_len (loghdr$logsizd - loghdr$logtxto)]
if (tail (log.txt, 1) == .nul) # throw away nul at the end
log.txt <- head (log.txt, -1)
log.txt [log.txt == .nul] <- replace.nul
log.txt <- readChar (log.txt, length (log.txt), useBytes=T)
log.txt <- gsub (rawToChar (replace.nul), '\r\n', log.txt)
log.txt <- iconv (log.txt, iconv.from, iconv.to)
# log.txt <- paste (rawToChar (log.txt, multiple = TRUE), collapse = "")
log.txt <- split.string (log.txt, "\r\n") ## spc file spec says \r\n regardless of OS
log.txt <- split.line (log.txt, "=")
data <- getbynames (log.txt, keys.log2data)
log <- c (log, getbynames (log.txt, keys.log2log))
}
list (log.long = log, extra.data = data)
}
## read y data ......................................................................................
##
.spc.read.y <- function (raw.data, pos, npts, exponent, word) {
if (exponent == -128) { # 4 byte float
list (y = readBin (raw.data [pos + seq_len (npts * 4)], "numeric", npts, 4),
.last.read = pos + npts * 4)
} else if (word) { # 2 byte fixed point integer = word
list (y = readBin (raw.data [pos + seq_len (npts * 2)], "integer", npts, 2, signed = TRUE) *
2 ^ (exponent - 16),
.last.read = pos + npts * 2)
} else { # 4 byte fixed point integer = dword
list (y = readBin (raw.data [pos + seq_len (npts * 4)], "integer", npts, 4) *
2 ^ (exponent - 32),
.last.read = pos + npts * 4)
}
}
## read x data ......................................................................................
##
.spc.read.x <- function (raw.data, pos, npts) {
list (x = readBin (raw.data [pos + seq_len (npts * 4)], "numeric", npts, 4),
.last.read = pos + 4 * npts)
}
## error .............................................................................................
.spc.error <- function (fname, objects, ...) {
cat ('ERROR in read.spc function ', fname, '\n\n')
for (i in seq_along (objects)) {
cat (names (objects) [i], ":\n")
str (objects [[i]], vec.len = 20)
}
stop (...)
}
.spc.ftflags <- function (x) {
ftflgs <- as.logical (x %/% 2^(0 : 7) %% 2)
names (ftflgs) <- c ('TSPREC', 'TCGRAM', 'TMULTI', 'TRANDM',
'TORDRD', 'TALABS', 'TXYXYS', 'TXVALS')
ftflgs
}
#####################################################################################################
##' Import for Thermo Galactic's spc file format
##' These functions allow to import .spc files.
##' A detailed description of the .spc file format is available at
##' \url{https://ftirsearch.com/features/converters/SPCFileFormat.htm}.
##'
##' @param filename The complete file name of the .spc file.
##' @param files If \code{glob = TRUE}, \code{filename} can contain wildcards.
##' Thus all files matching the name pattern in \code{filename} can be
##' specified.
##' @param keys.hdr2data,keys.hdr2log,keys.log2data,keys.log2log character
##' vectors with the names of parameters in the .spc file's log block
##' (log2xxx) or header (hdr2xxx) that should go into the extra data
##' (yyy2data) or into the \code{long.description} field of the returned
##' hyperSpec object's log (yyy2log).
##'
##' All header fields specified in the .spc file format specification (see
##' below) are imported and can be referred to by their de-capitalized names.
##' @param log.txt Should the text part of the .spc file's log block be read?
##' @param log.bin,log.disk Should the normal and on-disk binary parts of the
##' .spc file's log block be read? If so, they will be put as raw vectors
##' into the hyperSpec object's log.
##' @param hdr A list with fileheader fields that overwrite the settings of
##' actual file's header.
##' @param nosubhdr Boolean value to decide if the header should be read or not.
##' Default to TRUE.
##'
##' Use with care, and look into the source code for detailed insight on the
##' elements of this list.
##' @param no.object If \code{TRUE}, a list with wavelengths, spectra, labels,
##' log and data are returned instead of a hyperSpec object.
##'
##' This parameter will likely be subject to change in future - use with care.
##' @return If the file contains multiple spectra with individual wavelength
##' axes, \code{read.spc} returns a list of hyperSpec objects. Otherwise the
##' result is a hyperSpec object.
##'
##' \code{read.spc.KaiserMap} returns a hyperSpec object with data columns x,
##' y, and z containing the stage position as recorded in the .spc files'
##' log.
##' @note Only a restricted set of test files was available for development.
##' Particularly, the w-planes feature could not be tested.
##'
##' If you have .spc files that cannot be read with these function, don't
##' hesitate to contact the package maintainer with your code patch or asking
##' advice.
##' @author C. Beleites
##' @rdname read-spc
##' @seealso \code{\link[hyperSpec]{textio}}
##' @references Source development kit and file format specification of .spc
##' files:
##' \url{https://ftirsearch.com/features/converters/SPCFileFormat.htm}.
##' @export
##' @keywords IO file
##' @examples
##'
##' ## get the sample .spc files from ftirsearch.com (see above)
##' \donttest{
##' # single spectrum
##' spc <- read.spc ("BENZENE.SPC")
##' plot (spc)
##'
##' # multi-spectra .spc file with common wavelength axis
##' spc <- read.spc ('IG_MULTI.SPC')
##' spc
##'
##' # multi-spectra .spc file with individual wavelength axes
##' spc <- read.spc ("BARBITUATES.SPC")
##' plot (spc [[1]], lines.args = list (type = "h"))
##' }
##'
read_spc_nosubhdr <- function (filename,
keys.hdr2data = c('fexper', 'fres', 'fsource'), keys.hdr2log = c('fdate', 'fpeakpt'),
keys.log2data = FALSE, keys.log2log = TRUE,
log.txt = TRUE, log.bin = FALSE, log.disk = FALSE,
hdr = list (), nosubhdr = TRUE,
no.object = FALSE){
## f contains the raw bytes of the file
## fpos marks the position of the last read byte
## this is the same as the offset from beginning of the file (count 0) in the .spc definition
f <- readBin (filename, "raw", file.info (filename)$size, 1)
hdr <- modifyList (.spc.filehdr (f), hdr)
fpos <- hdr$.last.read
if (! hdr$ftflgs ['TXYXYS']) {
if (! hdr$ftflgs ['TXVALS']) {
## spectra with common evenly spaced wavelength axis
wavelength <- seq (hdr$ffirst, hdr$flast, length.out = hdr$fnpts)
} else {
## spectra with common unevenly spaced wavelength axis
if (! hdr$ftflgs ['TMULTI']) {
tmp <- .spc.read.x (f, fpos, hdr$fnpts)
wavelength <- tmp$x
fpos <- tmp$.last.read
}
}
}
## otherwise (TXYXYS set) hdr$fnpts gives offset to subfile directory if that exists
## obtain labels from file hdr or from parameter
if (hdr$fwplanes > 0)
label <- modifyList (list (w = hdr$fwtype), label)
label <- list (.wavelength = hdr$fxtype, spc = hdr$fytype,
z = hdr$fztype, z.end = hdr$fztype)
## prepare list for hyperSpec log and data.frame for extra data
data <- list (z = NA, z.end = NA)
if (hdr$fwplanes > 0)
data <- c (data, w = NA)
## process the log block
tmp <- .spc.log (f, hdr$flogoff,
log.bin, log.disk, log.txt,
keys.log2data, keys.log2log)
log <- list (short = "read.spc",
long = list (call = match.call (),
log = tmp$log.long,
header = getbynames (hdr, keys.hdr2log)))
data <- c (data, tmp$extra.data, getbynames (hdr, keys.hdr2data))
## try to preallocate spectra matrix and extra data data.frame
## if multispectra file with separate wavelength axes, prepare a list
if (hdr$ftflgs ['TXYXYS'] && hdr$ftflgs ['TMULTI']) {
spc <- list ()
data <- as.data.frame (data)
} else {
spc <- matrix (NA, nrow = hdr$fnsub, ncol = hdr$fnpts)
data <- as.data.frame (lapply (data, rep, hdr$fnsub))
}
## read subfiles
if (hdr$subfiledir){ ## TXYXYS
hdr$subfiledir <- .spc.subfiledir (f, hdr$subfiledir, hdr$fnsub)
for (s in seq_len (hdr$fnsub)) {
if (!nosubhdr){
hdr <- .spc.subhdr (f, hdr$subfiledir$ssfposn [s], hdr)
}
#hdr <- .spc.subhdr (f, hdr$subfiledir$ssfposn [s], hdr)
fpos <- hdr$.last.read
wavelength <- .spc.read.x (f, fpos, hdr$fnpts)
fpos <- wavelength$.last.read
y <- .spc.read.y (f, fpos, npts = hdr$fnpts, exponent = hdr$fexp,
word = hdr$ftflgs ['TSPREC'])
fpos <- y$.last.read
if (!nosubhdr) {
data$z <- hdr$subhdr$subtime
data$z.end <- hdr$subhdr$subnext
if (hdr$fwplanes > 0)
data$w <- hdr$subhdr$w
}
if (! exists ('wavelength'))
.spc.error ("read.spc", list (hdr = hdr),
"wavelength not read. This may be caused by wrong header information.")
spc [[s]] <- list (spc = y$y,
wavelength = wavelength$x,
data = data,
log = log,
labels = label)
}
} else { ## multiple y data blocks behind each other
for (s in seq_len (hdr$fnsub)) {
if (!nosubhdr) {
hdr <- .spc.subhdr (f, fpos, hdr)
}
fpos <- hdr$.last.read
tmp <- .spc.read.y (f, fpos, npts = hdr$fnpts, exponent = hdr$fexp,
word = hdr$ftflgs ['TSPREC'])
fpos <- tmp$.last.read
spc [s, ] <- tmp$y
if (!nosubhdr) {
data [s, c('z', 'z.end')] <- unlist (hdr$subhdr [c('subtime', 'subnext')])
if (hdr$fwplanes > 0)
data [s, "w"] <- hdr$subhdr$w
}
}
}
if (hdr$ftflgs ['TXYXYS'] && hdr$ftflgs ['TMULTI'])
spc
else if (no.object)
list (spc = spc, wavelength = wavelength, data = data, log = log, labels = label)
else
list (spc = spc, wavelength = wavelength,
data = data [rep (1, hdr$fnsub), ], log = log, labels = label)
}
getbynames = function (x, e) {
x <- x [e]
if (length (x) > 0) {
if (is.character (e))
names (x) <- e
x [sapply (x, is.null)] <- NA
x
} else {
list ()
}
}
###-----------------------------------------------------------------------------
###
### split.line - split line into list of key-value pairs
###
###
split.line <- function (x, separator, trim.blank = TRUE) {
tmp <- regexpr (separator, x)
#if (length (tmp) == 1 && tmp [[1]] == -1)
# warning ("line without separator", separator)
key <- substr (x, 1, tmp - 1)
value <- substr (x, tmp + 1, nchar (x))
if (trim.blank){
blank.pattern <- "^[[:blank:]]*([^[:blank:]]+.*[^[:blank:]]+)[[:blank:]]*$"
key <- sub (blank.pattern, "\\1", key)
value <- sub (blank.pattern, "\\1", value)
}
value <- as.list (value)
names (value) <- key
value
}
###-----------------------------------------------------------------------------
###
### split.string - split string at pattern
###
###
split.string <- function (x, separator, trim.blank = TRUE, remove.empty = TRUE) {
pos <- gregexpr (separator, x)
if (length (pos) == 1 && pos [[1]] == -1)
return (x)
pos <- pos [[1]]
pos <- matrix (c (1, pos + attr (pos, "match.length"),
pos - 1, nchar (x)),
ncol = 2)
if (pos [nrow (pos), 1] > nchar (x))
pos <- pos [- nrow (pos), ]
x <- apply (pos, 1, function (p, x) substr (x, p [1], p [2]), x)
if (trim.blank){
blank.pattern <- "^[[:blank:]]*([^[:blank:]]+.*[^[:blank:]]+)[[:blank:]]*$"
x <- sub (blank.pattern, "\\1", x)
}
if (remove.empty){
x <- x [sapply (x, nchar) > 0]
}
x
}
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Defines functions .spc.ylab
# This is the implementation of the function read.spc from hyperSpec without creating new hyperSpec
# objects, thus it does not depend anymore from this package. It has the option to read or not the
# header aswell. It returns a list type object.
### read.spc - Import Thermo Galactic's .spc file format into an hyperSpec Object
###
### C. Beleites 2009/11/29
###
#####################################################################################################
## Define constants ---------------------------------------------------------------------------------
.nul <- as.raw (0)
## header sizes
.spc.size <- c (hdr = 512, subhdr = 32, subfiledir = 12, loghdr = 64)
.spc.default.keys.hdr2data <- c('fexper', 'fres', 'fsource')
.spc.default.keys.hdr2log <- c('fdate', 'fpeakpt')
.spc.default.keys.log2data <- FALSE
.spc.default.keys.log2log <- TRUE
## axis labeling ------------------------------------------------------------------------------------
## x-axis units .....................................................................................
.spc.FXTYPE <- c (expression (`/` (x, "a. u.")), #0
expression (`/` (tilde (nu), cm^-1)),
expression (`/` (lambda, (mu * m))),
expression (`/` (lambda, nm)),
expression (`/` (t, s)),
expression (`/` (t, min)),
expression (`/` (f, Hz)),
expression (`/` (f, kHz)),
expression (`/` (f, MHz)),
expression (`/` (frac (m, z), frac (u, e))),
expression (`/` (delta, ppm)), # 10
expression (`/` (t, d)),
expression (`/` (t, a)),
expression (`/` (Delta*tilde (nu), cm^-1)),
expression (`/` (E, eV)),
NA, # old version file uses label in gcatxt
'Diode No',
'Channel',
expression (`/` (x, degree)),
expression (`/` (T, degree*F)),
expression (`/` (T, degree*C)), # 20
expression (`/` (T, K)),
'Data Point',
expression (`/` (t, ms)),
expression (`/` (t, micro*s)),
expression (`/` (t, ns)),
expression (`/` (f, GHz)),
expression (`/` (lambda, cm)),
expression (`/` (lambda, m)),
expression (`/` (lambda, mm)),
expression (`/` (t, h)) # 30
)
.spc.xlab <- function (x) {
## x = 255 is for double interferogram and supposed not to have a label.
## Thus, returning NA is appropriate
if (x <= length (.spc.FXTYPE) + 1)
.spc.FXTYPE [x + 1]
else
NA
}
## y-axis units .....................................................................................
.spc.FYTYPE <- c (expression (`/` (I[Ref], "a. u.")), # -1
expression (`/` (I, "a. u.")),
expression (`/` (I[IGRM], "a. u.")),
'A',
expression (frac ((1 - R)^2, 2 * R)),
'Counts',
expression (`/` (U, V)),
expression (`/` (y, degree)),
expression (`/` (I, mA)),
expression (`/` (l, mm)),
expression (`/` (U, mV)),
expression (-log (R)), # 10
expression (`/` (y, '%')),
expression (`/` (I, 'a. u.')),
expression (I / I[0]),
expression (`/` (E, J)),
NA, # old version file uses label in gcatxt
expression (`/` (G, dB)),
NA, # old version file uses label in gcatxt
NA, # old version file uses label in gcatxt
expression (`/` (T, degree*F)),
expression (`/` (T, degree*C)), # 20
expression (`/` (T, K)),
'n',
'K', # extinction coeaffictient
expression (Re (y)),
expression (Im (y)),
'y (complex)', # complex
'T',
'R',
expression (`/` (I, 'a. u.')),
expression (`/` (I[Emission], 'a. u.'))
)
.spc.ylab <- function(x){
if (x <= 26)
.spc.FYTYPE [x + 2]
else if (x %in% 128 : 131)
.spc.FYTYPE [x - 99]
else
NA
}
## helper functions ---------------------------------------------------------------------------------
### raw.split.nul - rawToChar conversion, splitting at \0
raw.split.nul <- function (raw, trunc = c (TRUE, TRUE), firstonly = FALSE) {
# todo make better truncation
trunc <- rep (trunc, length.out = 2)
if (trunc [1] && raw [1] == .nul)
raw <- raw [-1]
if (trunc [2]) {
tmp <- which (raw > .nul)
if (length (tmp) == 0)
return ("")
raw <- raw [1 : tail (tmp, 1)]
}
if (raw [length (raw)] != .nul)
raw <- c (raw , .nul)
tmp <- c (0, which (raw == .nul))
out <- character (length (tmp) - 1)
for (i in 1 : (length (tmp) - 1))
if (tmp [i] + 1 < tmp [i + 1] - 1)
out [i] <- rawToChar (raw [(tmp [i] + 1) : (tmp [i + 1] - 1)])
if (length (out) > 1L & firstonly){
warning ("multiple strings encountered: ", paste (out, collapse = ", "), " but using only the first one.")
out <- out [1]
}
out
}
## file part reading functions ----------------------------------------------------------------------
## read file header .................................................................................
##
##
.spc.filehdr <- function (raw.data) {
## check file format
## NEW.LSB = 75 supported,
## NEW.MSB = 76 not supported (neither by many Grams software according to spc doc)
## OLD = 77 not supported (replaced by new format in 1996)
if (raw.data [2] != 75)
stop ("Wrong spc file format version.\n",
"Only 'new' spc files (1996 file format) with LSB word order are supported.")
hdr <- list (ftflgs = readBin (raw.data [ 1], "integer", 1, 1, signed = FALSE),
## byte 2 is already interpreted
fexper = readBin (raw.data [ 3], "integer", 1, 1, signed = TRUE ),
fexp = readBin (raw.data [ 4], "integer", 1, 1, signed = TRUE ),
fnpts = readBin (raw.data [ 5 : 8], "integer", 1, 4 ),
ffirst = readBin (raw.data [ 9 : 16], "double", 1, 8 ),
flast = readBin (raw.data [ 17 : 24], "double", 1, 8 ),
fnsub = readBin (raw.data [ 25 : 28], "integer", 1, 4 ),
fxtype = readBin (raw.data [ 29], "integer", 1, 1, signed = FALSE),
fytype = readBin (raw.data [ 30], "integer", 1, 1, signed = FALSE),
fztype = readBin (raw.data [ 31], "integer", 1, 1, signed = FALSE),
fpost = readBin (raw.data [ 32], "integer", 1, 1, signed = TRUE ),
fdate = readBin (raw.data [ 33 : 36], "integer", 1, 4 ),
fres = raw.split.nul (raw.data [ 37 : 45], firstonly = TRUE),
fsource = raw.split.nul (raw.data [ 46 : 54], firstonly = TRUE),
fpeakpt = readBin (raw.data [ 55 : 56], "integer", 1, 2, signed = FALSE),
fspare = readBin (raw.data [ 57 : 88], "numeric", 8, 4 ),
fcmnt = raw.split.nul (raw.data [ 89 : 218], firstonly = TRUE),
fcatxt = raw.split.nul (raw.data [219 : 248], trunc = c (FALSE, TRUE) ),
flogoff = readBin (raw.data [249 : 252], "integer", 1, 4), #, signed = FALSE),
fmods = readBin (raw.data [253 : 256], "integer", 1, 4), #, signed = FALSE),
fprocs = readBin (raw.data [ 257], "integer", 1, 1, signed = TRUE ),
flevel = readBin (raw.data [ 258], "integer", 1, 1, signed = TRUE ),
fsampin = readBin (raw.data [259 : 260], "integer", 1, 2, signed = FALSE),
ffactor = readBin (raw.data [261 : 264], "numeric", 1, 4 ),
fmethod = raw.split.nul (raw.data [265 : 312]),
fzinc = readBin (raw.data [313 : 316], "numeric", 1, 4), #, signed = FALSE),
fwplanes = readBin (raw.data [317 : 320], "integer", 1, 4), #, signed = FALSE),
fwinc = readBin (raw.data [321 : 324], "numeric", 1, 4 ),
fwtype = readBin (raw.data [ 325], "integer", 1, 1, signed = TRUE ),
## 187 bytes reserved
.last.read = .spc.size ['hdr']
)
## R doesn't have unsigned long int .................................
if (any (unlist (hdr [c ("flogoff", "fmods", "fzinc", "fwplanes")]) < 0))
stop ("error reading header: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
## do some post processing ..........................................
experiments <- c ("General", "Gas Chromatogram", "General Chromatogram", "HPLC Chromatogram",
"NIR Spectrum", "UV-VIS Spectrum", "* reserved *", "X-ray diffraction spectrum",
"Mass Spectrum", "NMR Spectrum", "Raman Spectrum", "Fluorescence Spectrum",
"Atomic Spectrum", "Chroatography Diode Array Data")
hdr$fexper <- factor (hdr$fexper + 1, levels = seq_along (experiments))
levels (hdr$fexper) <- experiments
hdr$ftflgs <- .spc.ftflags (hdr$ftflgs)
hdr$fdate <- ISOdate (year = hdr$fdate %/% 1048560,
month = hdr$fdate %/% 65536 %% 16,
day = hdr$fdate %/% 2048 %% 32,
hour = hdr$fdate %/% 64 %% 32,
min = hdr$fdate %% 64)
## interferogram ?
## if not, hdr$fpeakpt is set to NULL
if (hdr$fytype == 1){
if (hdr$fpeakpt != 0)
hdr$fpeakpt <- hdr$fpeakpt + 1
} else {
hdr$fpeakpt <- NULL
}
## set the axis labels
if (hdr$ftflgs ['TALABS']) {
# TODO: find test data
tmp <- rep (0, 4)
tmp [seq_along (hdr$fcatxt)] <- nchar (hdr$fcatxt)
if (tmp [1] > 0) hdr$fxtype <- hdr$fcatxt[1]
if (tmp [2] > 0) hdr$fytype <- hdr$fcatxt[2]
if (tmp [3] > 0) hdr$fztype <- hdr$fcatxt[3]
if (tmp [4] > 0) hdr$fwtype <- hdr$fcatxt[4]
}
hdr$fxtype <- .spc.xlab (hdr$fxtype)
hdr$fytype <- .spc.ylab (hdr$fytype)
hdr$fztype <- .spc.xlab (hdr$fztype)
hdr$fwtype <- .spc.xlab (hdr$fwtype)
## File with subfiles with individual x axes?
## Then there should be a subfile directory:
if (hdr$ftflgs ['TXYXYS'] && hdr$ftflgs ['TMULTI']){
## try to reject impossible values for the subfiledir offset
if (hdr$fnpts > length (raw.data) ||
(hdr$fnpts > hdr$flogoff && hdr$flogoff > 0) ||
hdr$fnpts < 512)
.spc.error (".spc.read.hdr", list (hdr = hdr),
"file header flags specify TXYXYS and TMULTI, ",
"but fnpts does not give a valid offset for the subfile directory.\n hdr$ftflgs = ",
paste (names (hdr$ftflgs)[hdr$ftflgs], collapse = " | "),
" (", sum (2^(0:7) [hdr$ftflgs]) , ")\n",
"You can try to read the file using hdr$ftflgs & ! TXYXYS (",
sum (2^(0 : 7) [hdr$ftflgs & c (TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)]),
"). This assumes that all subfiles do have the same x axis.\n\n")
hdr$subfiledir <- hdr$fnpts
hdr$fnpts <- 0
} else {
hdr$subfiledir <- 0
}
## some checks ......................................................
if (hdr$ftflgs ['TMULTI']){
## multiple spectra in file
if (hdr$fnsub <= 1)
warning ("spc file header specifies multiple spectra but only zero or one subfile.")
} else {
## single spectrum file
if (hdr$fnsub == 0)
hdr$fnsub <- 1
if (hdr$fnsub > 1) {
warning ("spc file header specifies single spectrum file but", hdr$fnsub,
"subfiles (spectra).\nOnly first subfile will be read.")
hdr$fnsub <- 1
}
if (hdr$ftflgs ['TRANDM'])
warning ("spc file header: file type flag TRANDM does not make sense without TMULTI.")
if (hdr$ftflgs ['TORDRD'])
warning ("spc file header: file type flag TORDRD does not make sense without TMULTI.")
if ((hdr$ftflgs ['TRANDM'] || hdr$ftflgs ['TORDRD']) && hdr$fnsub > 1)
hdr$ftflgs ['TMULTI'] <- TRUE
}
if (hdr$ftflgs ['TXYXYS'] && ! hdr$ftflgs ['TXVALS']) {
warning ("spc file header: file type flag TXYXYS does not make sense without TXVALS.")
hdr$ftflgs ['TXVALS'] <- TRUE
}
if (hdr$fwplanes > 0)
warning ("w planes found! This is not yet tested as the developer didn't have access to such files.\n",
"Please contact the package maintainer (cbeleites@units.it)",
"stating whether the file was imported successfully or not.")
hdr
}
## read sub file header .............................................................................
##
## needs header for consistency checks
##
.spc.subhdr <- function (raw.data, pos, hdr) {
subhdr <- list (subflgs = raw.data [pos + ( 1)],
subexp = readBin (raw.data [pos + ( 2)], "integer", 1, 1, signed = FALSE),
subindx = readBin (raw.data [pos + ( 3 : 4)], "integer", 1, 2, signed = FALSE),
subtime = readBin (raw.data [pos + ( 5 : 8)], "numeric", 1, 4),
subnext = readBin (raw.data [pos + ( 9 : 12)], "numeric", 1, 4),
subnois = readBin (raw.data [pos + (13 : 16)], "numeric", 1, 4),
subnpts = readBin (raw.data [pos + (17 : 20)], "integer", 1, 4), #, signed = FALSE),
subscan = readBin (raw.data [pos + (21 : 24)], "integer", 1, 4), #, signed = FALSE),
subwlevel = readBin (raw.data [pos + (25 : 28)], "numeric", 1, 4))
## 4 bytes reserved
## R doesn't have unsigned long int .................................
if (any (unlist (subhdr [c ("subnpts", "subscan")]) < 0))
stop ("error reading subheader: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
hdr$.last.read <- pos + .spc.size ['subhdr']
## checking
if (subhdr$subexp == -128 && hdr$fexp != -128)
warning ("subfile ", subhdr$subindx, " specifies data type float, but file header doesn't.",
"\nData will be interpreted as float.")
if (subhdr$subnpts > 0 && subhdr$subnpts != hdr$fnpts && ! hdr$ftflgs ['TXYXYS'])
warning ('subfile ', subhdr$subindx, ": number of points in subfile should be 0 if file",
" header flags do not specify TXYXYS.")
if (subhdr$subnpts == 0){
if (hdr$ftflgs ['TXYXYS'])
warning ('subfile ', subhdr$subindx, ': number of data points per spectrum not specified. ',
'Using fnpts (', hdr$fnpts, ').')
subhdr$subnpts <- hdr$fnpts
}
if (! hdr$ftflgs ['TXYXYS'])
if (hdr$fnpts != subhdr$subnpts) {
.spc.error (".spc.read.subhdr", list (hdr = hdr, subhdr = subhdr),
"hdr and subhdr differ in number of points per spectrum, ",
"but TXYXYS is not specified.\n hdr$ftflgs = ",
paste (names (hdr$ftflgs)[hdr$ftflgs], collapse = " | "),
" (", sum (2^(0:7) [hdr$ftflgs]) , ")\n",
"You can try to read the file using hdr$ftflgs | TMULTI | TXYXYS (",
sum (2^(0 : 7) [hdr$ftflgs |
c (FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE)]),
").\n\n")
}
# str (subhdr)
## according to .spc file documentation:
if (! hdr$ftflgs ['TMULTI'])
subhdr$subexp <- hdr$fexp
else if (hdr$fexp == -128 && subhdr$subexp != -128) {
warning ("Header file specifies float data format, but subfile uses integer exponent.",
" Subfile settings are overwritten.")
subhdr$subexp <- -128
}
## the z values
if (hdr$fzinc == 0) # should only happen for the first subfile...
hdr$fzinc = subhdr$subnext - subhdr$subtime
if (subhdr$subindx == 0)
hdr$firstz <- subhdr$subtime
if (subhdr$subtime == 0)
subhdr$subtime = subhdr$subindx * hdr$fzinc + hdr$firstz
## the w values
if (hdr$fwplanes > 0) {
if (subhdr$subwlevel != 0) {
subhdr$w <- subhdr$subwlevel
} else if (subhdr$subindx %% hdr$fwplanes == 1)
subhdr$w <- hdr$subhdr$w + hdr$fwinc
else
subhdr$w <- hdr$subhdr$w
}
hdr$subhdr <- subhdr
hdr
}
## read subfile directory ...........................................................................
##
.spc.subfiledir <- function (raw.data, pos, nsub) {
dir <- data.frame (ssfposn = rep (NA, nsub),
ssfsize = rep (NA, nsub),
ssftime = rep (NA, nsub))
for (s in seq_len (nsub)){
dir [s,] <- c (readBin (raw.data [pos + ( 1 : 4)], "integer", 1, 4), # , signed = FALSE),
readBin (raw.data [pos + ( 5 : 8)], "integer", 1, 4), # , signed = FALSE),
readBin (raw.data [pos + ( 9 : 12)], "numeric", 1, 4))
pos <- pos + .spc.size ['subfiledir']
}
## R doesn't have unsigned long int .................................
if (any (dir [, 1:2] < 0))
stop ("error reading subfiledir: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
# dir$ssfposn <- dir$ssfposn
dir
}
## read log block header ............................................................................
##
.spc.log <- function (raw.data, pos, log.bin, log.disk, log.txt, keys.log2data, keys.log2log,
replace.nul = as.raw (255), iconv.from = "latin1", iconv.to = "utf8") {
if (pos == 0) # no log block exists
return (list (data = list (),
log = list ()))
loghdr <- list (logsizd = readBin (raw.data [pos + ( 1 : 4)], "integer", 1, 4), # , signed = FALSE),
logsizm = readBin (raw.data [pos + ( 5 : 8)], "integer", 1, 4), # , signed = FALSE),
logtxto = readBin (raw.data [pos + ( 9 : 12)], "integer", 1, 4), # , signed = FALSE),
logbins = readBin (raw.data [pos + (13 : 16)], "integer", 1, 4), # , signed = FALSE),
logdsks = readBin (raw.data [pos + (17 : 20)], "integer", 1, 4), # , signed = FALSE),
## 44 bytes reserved
.last.read = pos + .spc.size ['loghdr']
)
## R doesn't have unsigned long int .................................
if (any (unlist (loghdr) < 0))
stop ("error reading log: R does not support unsigned long integers.",
"Please contact the maintainer of the package.")
log <- list ()
data <- list ()
## read binary part of log
if (log.bin)
log$.log.bin <- raw.data [loghdr$.last.read + seq_len (loghdr$logbins)]
## read binary on-disk-only part of log
if (log.disk)
log$.log.disk <- raw.data [loghdr$.last.read + loghdr$logbins + seq_len (loghdr$logdsks)]
## read text part of log
if (log.txt) {
log.txt <- raw.data [pos + loghdr$logtxto + seq_len (loghdr$logsizd - loghdr$logtxto)]
if (tail (log.txt, 1) == .nul) # throw away nul at the end
log.txt <- head (log.txt, -1)
log.txt [log.txt == .nul] <- replace.nul
log.txt <- readChar (log.txt, length (log.txt), useBytes=T)
log.txt <- gsub (rawToChar (replace.nul), '\r\n', log.txt)
log.txt <- iconv (log.txt, iconv.from, iconv.to)
# log.txt <- paste (rawToChar (log.txt, multiple = TRUE), collapse = "")
log.txt <- split.string (log.txt, "\r\n") ## spc file spec says \r\n regardless of OS
log.txt <- split.line (log.txt, "=")
data <- getbynames (log.txt, keys.log2data)
log <- c (log, getbynames (log.txt, keys.log2log))
}
list (log.long = log, extra.data = data)
}
## read y data ......................................................................................
##
.spc.read.y <- function (raw.data, pos, npts, exponent, word) {
if (exponent == -128) { # 4 byte float
list (y = readBin (raw.data [pos + seq_len (npts * 4)], "numeric", npts, 4),
.last.read = pos + npts * 4)
} else if (word) { # 2 byte fixed point integer = word
list (y = readBin (raw.data [pos + seq_len (npts * 2)], "integer", npts, 2, signed = TRUE) *
2 ^ (exponent - 16),
.last.read = pos + npts * 2)
} else { # 4 byte fixed point integer = dword
list (y = readBin (raw.data [pos + seq_len (npts * 4)], "integer", npts, 4) *
2 ^ (exponent - 32),
.last.read = pos + npts * 4)
}
}
## read x data ......................................................................................
##
.spc.read.x <- function (raw.data, pos, npts) {
list (x = readBin (raw.data [pos + seq_len (npts * 4)], "numeric", npts, 4),
.last.read = pos + 4 * npts)
}
## error .............................................................................................
.spc.error <- function (fname, objects, ...) {
cat ('ERROR in read.spc function ', fname, '\n\n')
for (i in seq_along (objects)) {
cat (names (objects) [i], ":\n")
str (objects [[i]], vec.len = 20)
}
stop (...)
}
.spc.ftflags <- function (x) {
ftflgs <- as.logical (x %/% 2^(0 : 7) %% 2)
names (ftflgs) <- c ('TSPREC', 'TCGRAM', 'TMULTI', 'TRANDM',
'TORDRD', 'TALABS', 'TXYXYS', 'TXVALS')
ftflgs
}
#####################################################################################################
##' Import for Thermo Galactic's spc file format
##' These functions allow to import .spc files.
##' A detailed description of the .spc file format is available at
##' \url{https://ftirsearch.com/features/converters/SPCFileFormat.htm}.
##'
##' @param filename The complete file name of the .spc file.
##' @param files If \code{glob = TRUE}, \code{filename} can contain wildcards.
##' Thus all files matching the name pattern in \code{filename} can be
##' specified.
##' @param keys.hdr2data,keys.hdr2log,keys.log2data,keys.log2log character
##' vectors with the names of parameters in the .spc file's log block
##' (log2xxx) or header (hdr2xxx) that should go into the extra data
##' (yyy2data) or into the \code{long.description} field of the returned
##' hyperSpec object's log (yyy2log).
##'
##' All header fields specified in the .spc file format specification (see
##' below) are imported and can be referred to by their de-capitalized names.
##' @param log.txt Should the text part of the .spc file's log block be read?
##' @param log.bin,log.disk Should the normal and on-disk binary parts of the
##' .spc file's log block be read? If so, they will be put as raw vectors
##' into the hyperSpec object's log.
##' @param hdr A list with fileheader fields that overwrite the settings of
##' actual file's header.
##' @param nosubhdr Boolean value to decide if the header should be read or not.
##' Default to TRUE.
##'
##' Use with care, and look into the source code for detailed insight on the
##' elements of this list.
##' @param no.object If \code{TRUE}, a list with wavelengths, spectra, labels,
##' log and data are returned instead of a hyperSpec object.
##'
##' This parameter will likely be subject to change in future - use with care.
##' @return If the file contains multiple spectra with individual wavelength
##' axes, \code{read.spc} returns a list of hyperSpec objects. Otherwise the
##' result is a hyperSpec object.
##'
##' \code{read.spc.KaiserMap} returns a hyperSpec object with data columns x,
##' y, and z containing the stage position as recorded in the .spc files'
##' log.
##' @note Only a restricted set of test files was available for development.
##' Particularly, the w-planes feature could not be tested.
##'
##' If you have .spc files that cannot be read with these function, don't
##' hesitate to contact the package maintainer with your code patch or asking
##' advice.
##' @author C. Beleites
##' @rdname read-spc
##' @seealso \code{\link[hyperSpec]{textio}}
##' @references Source development kit and file format specification of .spc
##' files:
##' \url{https://ftirsearch.com/features/converters/SPCFileFormat.htm}.
##' @export
##' @keywords IO file
##' @examples
##'
##' ## get the sample .spc files from ftirsearch.com (see above)
##' \donttest{
##' # single spectrum
##' spc <- read.spc ("BENZENE.SPC")
##' plot (spc)
##'
##' # multi-spectra .spc file with common wavelength axis
##' spc <- read.spc ('IG_MULTI.SPC')
##' spc
##'
##' # multi-spectra .spc file with individual wavelength axes
##' spc <- read.spc ("BARBITUATES.SPC")
##' plot (spc [[1]], lines.args = list (type = "h"))
##' }
##'
read_spc_nosubhdr <- function (filename,
keys.hdr2data = c('fexper', 'fres', 'fsource'), keys.hdr2log = c('fdate', 'fpeakpt'),
keys.log2data = FALSE, keys.log2log = TRUE,
log.txt = TRUE, log.bin = FALSE, log.disk = FALSE,
hdr = list (), nosubhdr = TRUE,
no.object = FALSE){
## f contains the raw bytes of the file
## fpos marks the position of the last read byte
## this is the same as the offset from beginning of the file (count 0) in the .spc definition
f <- readBin (filename, "raw", file.info (filename)$size, 1)
hdr <- modifyList (.spc.filehdr (f), hdr)
fpos <- hdr$.last.read
if (! hdr$ftflgs ['TXYXYS']) {
if (! hdr$ftflgs ['TXVALS']) {
## spectra with common evenly spaced wavelength axis
wavelength <- seq (hdr$ffirst, hdr$flast, length.out = hdr$fnpts)
} else {
## spectra with common unevenly spaced wavelength axis
if (! hdr$ftflgs ['TMULTI']) {
tmp <- .spc.read.x (f, fpos, hdr$fnpts)
wavelength <- tmp$x
fpos <- tmp$.last.read
}
}
}
## otherwise (TXYXYS set) hdr$fnpts gives offset to subfile directory if that exists
## obtain labels from file hdr or from parameter
if (hdr$fwplanes > 0)
label <- modifyList (list (w = hdr$fwtype), label)
label <- list (.wavelength = hdr$fxtype, spc = hdr$fytype,
z = hdr$fztype, z.end = hdr$fztype)
## prepare list for hyperSpec log and data.frame for extra data
data <- list (z = NA, z.end = NA)
if (hdr$fwplanes > 0)
data <- c (data, w = NA)
## process the log block
tmp <- .spc.log (f, hdr$flogoff,
log.bin, log.disk, log.txt,
keys.log2data, keys.log2log)
log <- list (short = "read.spc",
long = list (call = match.call (),
log = tmp$log.long,
header = getbynames (hdr, keys.hdr2log)))
data <- c (data, tmp$extra.data, getbynames (hdr, keys.hdr2data))
## try to preallocate spectra matrix and extra data data.frame
## if multispectra file with separate wavelength axes, prepare a list
if (hdr$ftflgs ['TXYXYS'] && hdr$ftflgs ['TMULTI']) {
spc <- list ()
data <- as.data.frame (data)
} else {
spc <- matrix (NA, nrow = hdr$fnsub, ncol = hdr$fnpts)
data <- as.data.frame (lapply (data, rep, hdr$fnsub))
}
## read subfiles
if (hdr$subfiledir){ ## TXYXYS
hdr$subfiledir <- .spc.subfiledir (f, hdr$subfiledir, hdr$fnsub)
for (s in seq_len (hdr$fnsub)) {
if (!nosubhdr){
hdr <- .spc.subhdr (f, hdr$subfiledir$ssfposn [s], hdr)
}
#hdr <- .spc.subhdr (f, hdr$subfiledir$ssfposn [s], hdr)
fpos <- hdr$.last.read
wavelength <- .spc.read.x (f, fpos, hdr$fnpts)
fpos <- wavelength$.last.read
y <- .spc.read.y (f, fpos, npts = hdr$fnpts, exponent = hdr$fexp,
word = hdr$ftflgs ['TSPREC'])
fpos <- y$.last.read
if (!nosubhdr) {
data$z <- hdr$subhdr$subtime
data$z.end <- hdr$subhdr$subnext
if (hdr$fwplanes > 0)
data$w <- hdr$subhdr$w
}
if (! exists ('wavelength'))
.spc.error ("read.spc", list (hdr = hdr),
"wavelength not read. This may be caused by wrong header information.")
spc [[s]] <- list (spc = y$y,
wavelength = wavelength$x,
data = data,
log = log,
labels = label)
}
} else { ## multiple y data blocks behind each other
for (s in seq_len (hdr$fnsub)) {
if (!nosubhdr) {
hdr <- .spc.subhdr (f, fpos, hdr)
}
fpos <- hdr$.last.read
tmp <- .spc.read.y (f, fpos, npts = hdr$fnpts, exponent = hdr$fexp,
word = hdr$ftflgs ['TSPREC'])
fpos <- tmp$.last.read
spc [s, ] <- tmp$y
if (!nosubhdr) {
data [s, c('z', 'z.end')] <- unlist (hdr$subhdr [c('subtime', 'subnext')])
if (hdr$fwplanes > 0)
data [s, "w"] <- hdr$subhdr$w
}
}
}
if (hdr$ftflgs ['TXYXYS'] && hdr$ftflgs ['TMULTI'])
spc
else if (no.object)
list (spc = spc, wavelength = wavelength, data = data, log = log, labels = label)
else
list (spc = spc, wavelength = wavelength,
data = data [rep (1, hdr$fnsub), ], log = log, labels = label)
}
getbynames = function (x, e) {
x <- x [e]
if (length (x) > 0) {
if (is.character (e))
names (x) <- e
x [sapply (x, is.null)] <- NA
x
} else {
list ()
}
}
###-----------------------------------------------------------------------------
###
### split.line - split line into list of key-value pairs
###
###
split.line <- function (x, separator, trim.blank = TRUE) {
tmp <- regexpr (separator, x)
#if (length (tmp) == 1 && tmp [[1]] == -1)
# warning ("line without separator", separator)
key <- substr (x, 1, tmp - 1)
value <- substr (x, tmp + 1, nchar (x))
if (trim.blank){
blank.pattern <- "^[[:blank:]]*([^[:blank:]]+.*[^[:blank:]]+)[[:blank:]]*$"
key <- sub (blank.pattern, "\\1", key)
value <- sub (blank.pattern, "\\1", value)
}
value <- as.list (value)
names (value) <- key
value
}
###-----------------------------------------------------------------------------
###
### split.string - split string at pattern
###
###
split.string <- function (x, separator, trim.blank = TRUE, remove.empty = TRUE) {
pos <- gregexpr (separator, x)
if (length (pos) == 1 && pos [[1]] == -1)
return (x)
pos <- pos [[1]]
pos <- matrix (c (1, pos + attr (pos, "match.length"),
pos - 1, nchar (x)),
ncol = 2)
if (pos [nrow (pos), 1] > nchar (x))
pos <- pos [- nrow (pos), ]
x <- apply (pos, 1, function (p, x) substr (x, p [1], p [2]), x)
if (trim.blank){
blank.pattern <- "^[[:blank:]]*([^[:blank:]]+.*[^[:blank:]]+)[[:blank:]]*$"
x <- sub (blank.pattern, "\\1", x)
}
if (remove.empty){
x <- x [sapply (x, nchar) > 0]
}
x
}
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