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read_spc.R
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read_spc.R
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############################################################################## ~
# read_spc: Import Thermo Galactic's .spc file format into a 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_log2data <- FALSE
## 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) {
if (is.character(x)) {
x
} else if (x <= length(.spc_FXTYPE) + 1) {
.spc_FXTYPE[x + 1]
} else {
## x = 255 is for double interferogram and supposed not to have a label.
## Thus, returning NA is appropriate
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 (is.character(x)) {
x
} else 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
#' @importFrom utils tail
.raw_split_nul <- function(raw, trunc = c(TRUE, TRUE), firstonly = FALSE,
paste.collapse = NULL) {
# 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) {
if (firstonly) {
message("multiple strings encountered in spc file ", paste(out, collapse = ", "), ": using only the first one.")
out <- out[1]
} else if (!is.null(paste.collapse)) {
if (hy_get_option("debuglevel") > 2L) {
message("multiple strings encountered in spc file ", paste(out, collapse = ", "), " => pasting.")
}
out <- paste(out, collapse = paste.collapse)
}
}
out
}
## file part reading functions ----------------------------------------------------------------------
## read file header ..........................................................
##
##
#' @importFrom utils maintainer
.spc_file_hdr <- function(raw_data) {
## check file format
## Detect Shimadzu SPC (which is effectively a variant of OLE CF format)
if (isTRUE(all.equal(
raw_data[1:4],
as.raw(c("0xD0", "0xCF", "0x11", "0xE0"))
))) {
stop("Support for Shimadzu SPC file format (OLE CF) is not yet implemented")
}
## 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 (or no spc file at all).\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], paste.collapse = "\r\n"),
fsource = .raw_split_nul(raw_data[46:54], paste.collapse = "\r\n"),
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], paste.collapse = "\r\n"),
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", "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$fnsub <= 1) {
if (hy_get_option("debuglevel") >= 2L) {
message("spc file header specifies multiple spectra but only zero or one subfile.")
}
}
} else {
## single spectrum file
if (hdr$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$ftflgs["TRANDM"]) {
message("spc file header: file type flag TRANDM encountered => Enforcing TMULTI.")
}
if (hdr$ftflgs["TORDRD"]) {
message("spc file header: file type flag TORDRD encountered => Enforcing 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 encountered => Enforcing 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 ", maintainer("hyperSpec"),
" 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 = TRUE),
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$fexp != -128) {
message(
"subfile ", subhdr$subindx, " specifies data type float, but file header doesn't.",
"\n=> Data will be interpreted as float unless TMULTI is set."
)
}
if (subhdr$subnpts > 0 && subhdr$subnpts != hdr$fnpts && !hdr$ftflgs["TXYXYS"]) {
message(
"subfile ", subhdr$subindx, ": number of points in file header and subfile header ",
"inconsistent. => Going to use subheader."
)
}
if (subhdr$subnpts == 0) {
if (hdr$ftflgs["TXYXYS"]) {
message(
"subfile ", subhdr$subindx, ": number of data points per spectrum not specified. ",
"=> Using file header information (", 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$subexp != -128) {
message(
"Header file specifies float data format, but subfile uses integer exponent. ",
"=> Using file header settings."
)
subhdr$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$fwplanes > 0) {
if (hdr$fwinc == 0) { ## unevenly spaced w planes
}
# 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$subhdr <- subhdr
hdr
}
## read subfile directory ...........................................................................
##
.spc_subfile_dir <- function(raw_data, pos, nsub) {
dir <- data.frame(
ssfposn = rep(NA, nsub),
ssfsize = rep(NA, nsub),
ssftime = rep(NA, nsub)
)
for (s in seq_len(nsub)) {
dir[s, ] <- c(
readBin(raw_data[pos + (1:4)], "integer", 1, 4), # , signed = FALSE),
readBin(raw_data[pos + (5:8)], "integer", 1, 4), # , signed = FALSE),
readBin(raw_data[pos + (9:12)], "numeric", 1, 4)
)
pos <- pos + .spc_size["subfiledir"]
}
## R doesn't have unsigned long int .................................
if (any(dir[, 1:2] < 0)) {
stop(
"error reading subfiledir: R does not support unsigned long integers.",
"Please contact the maintainer of the package."
)
}
# dir$ssfposn <- dir$ssfposn
dir
}
## read log block header ......................................................
##
.spc_log <- function(raw_data, pos, log_bin, log_disk, log_txt, keys_log2data,
replace.nul = as.raw(255), iconv.from = "latin1",
iconv.to = "utf8") {
if (pos == 0) { # no log block exists
return(list(
data = list(),
log = list()
))
}
loghdr <- list(
logsizd = readBin(raw_data[pos + (1:4)], "integer", 1, 4), # , signed = FALSE),
logsizm = readBin(raw_data[pos + (5:8)], "integer", 1, 4), # , signed = FALSE),
logtxto = readBin(raw_data[pos + (9:12)], "integer", 1, 4), # , signed = FALSE),
logbins = readBin(raw_data[pos + (13:16)], "integer", 1, 4), # , signed = FALSE),
logdsks = readBin(raw_data[pos + (17:20)], "integer", 1, 4), # , signed = FALSE),
## 44 bytes reserved
.last.read = pos + .spc_size["loghdr"]
)
## R doesn't have unsigned long int .................................
if (any(unlist(loghdr) < 0)) {
stop(
"error reading log: R does not support unsigned long integers.",
"Please contact the maintainer of the package."
)
}
log <- list()
data <- list()
## read binary part of log
if (log_bin) {
log$.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 & loghdr$logsizd > loghdr$logtxto) {
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, useBytes = TRUE)
log_txt <- iconv(log_txt, iconv.from, iconv.to)
log_txt <- split_string(log_txt, "\r\n") ## spc file spec says \r\n regardless of OS
log_txt <- split_line(log_txt, "=")
data <- get_by_names(log_txt, keys_log2data)
}
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
}
# Main function ###############################################################
#' Import for Thermo Galactic's `spc` file format
#'
#' These functions allow to import Thermo Galactic/Grams `.spc` files.
#'
#' @param filename The complete file name of the `.spc` file.
#' @param keys_hdr2data,keys_log2data 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) of the returned hyperSpec object.
#'
#' 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.
#'
#' Use with care, and look into the source code for detailed insight on the
#' elements of this list.
#' @param no_object If `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, `read_spc()` returns a list of hyperSpec objects. Otherwise the
#' result is a hyperSpec object.
#'
#' `read_spc_Kaiser_map()` 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
#' @references Source development kit and file format specification of `.spc`
#' files.
#' @export
#'
#' @keywords IO file
#' @concept io
#'
#' @examples
#'
#' ## get the sample .spc files from ftirsearch.com (see above)
#' \dontrun{
#' # 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"))
#' }
#'
#' @importFrom utils modifyList
read_spc <- function(filename,
keys_hdr2data = FALSE, keys_log2data = FALSE,
log_txt = TRUE, log_bin = FALSE, log_disk = FALSE,
hdr = list(),
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_file_hdr(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$ftflgs ['TMULTI']) { # also for multifile with common
# wavelength axis
tmp <- .spc_read_x(f, fpos, hdr$fnpts)
wavelength <- tmp$x
fpos <- tmp$.last.read
}
# }
}
## otherwise (TXYXYS set) hdr$fnpts gives offset to subfile directory if
## that exists
## obtain labels from file hdr or from parameter
label <- list(
.wavelength = hdr$fxtype, spc = hdr$fytype,
z = hdr$fztype, z.end = hdr$fztype
)
if (hdr$fwplanes > 0) {
label$w <- hdr$fwtype
}
## 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
)
## TODO: remove data2log
data <- c(data, tmp$extra.data, get_by_names(hdr, keys_hdr2data))
## preallocate spectra matrix or list for multispectra file with separate
## wavelength axes
## populate extra data
if (hdr$ftflgs["TXYXYS"] && hdr$ftflgs["TMULTI"]) {
spc <- list()
data <- .prepare_hdr_df(data, n_subfiles = 1L)
} else {
spc <- matrix(NA, nrow = hdr$fnsub, ncol = hdr$fnpts)
data <- .prepare_hdr_df(data, n_subfiles = hdr$fnsub)
}
## read subfiles
if (hdr$subfiledir) { ## TXYXYS
hdr$subfiledir <- .spc_subfile_dir(f, hdr$subfiledir, hdr$fnsub)
for (s in seq_len(hdr$fnsub)) {
hdr <- .spc_subhdr(f, hdr$subfiledir$ssfposn[s], hdr)
fpos <- hdr$.last.read
wavelength <- .spc_read_x(f, fpos, hdr$subhdr$subnpts)
fpos <- wavelength$.last.read
y <- .spc_read_y(f, fpos,
npts = hdr$subhdr$subnpts, exponent = hdr$subhdr$subexp,
word = hdr$ftflgs["TSPREC"]
)
fpos <- y$.last.read
data$z <- hdr$subhdr$subtime
data$z.end <- hdr$subhdr$subnext
if (hdr$fwplanes > 0) {
data$w <- hdr$subhdr$w
}
if (!exists("wavelength")) {
.spc_error(
"read_spc", list(hdr = hdr),
"wavelength not read. This may be caused by wrong header information."
)
}
spc[[s]] <- new("hyperSpec",
spc = y$y,
wavelength = wavelength$x,
data = data,
labels = label
)
}
} else { ## multiple y data blocks behind each other
for (s in seq_len(hdr$fnsub)) {
hdr <- .spc_subhdr(f, fpos, hdr)
fpos <- hdr$.last.read
tmp <- .spc_read_y(f, fpos,
npts = hdr$subhdr$subnpts, exponent = hdr$subhdr$subexp,
word = hdr$ftflgs["TSPREC"]
)
fpos <- tmp$.last.read
spc[s, ] <- tmp$y
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"]) {
## list of hyperSpec objects
## consistent file import behaviour across import functions
lapply(spc, .spc_io_postprocess_optional, filename = filename)
} else if (no_object) {
list(spc = spc, wavelength = wavelength, data = data, labels = label)
} else {
if (hdr$fnsub > 1L && nrow(data) == 1L) {
data <- data[rep(1L, hdr$fnsub), ]
}
spc <- new("hyperSpec",
spc = spc, wavelength = wavelength,
data = data, labels = label
)
## consistent file import behaviour across import functions
.spc_io_postprocess_optional(spc, filename)
}
}
# Unit tests -----------------------------------------------------------------
hySpc.testthat::test(read_spc) <- function() {
context("read_spc()")
spc_path <- system.file("extdata/spc", package = "hySpc.read.spc")
shimadzu_path <- system.file("extdata/spc.Shimadzu", package = "hySpc.read.spc")
kaisermap_path <- system.file("extdata/spc.Kaisermap", package = "hySpc.read.spc")
witec_path <- system.file("extdata/spc.Witec", package = "hySpc.read.spc")
labram_path <- system.file("extdata/spc.LabRam", package = "hySpc.read.spc")
old_spc <- paste0(spc_path, c("/CONTOUR.SPC", "/DEMO_3D.SPC", "/LC_DIODE_ARRAY.SPC"))
test_that("old file format -> error", {
for (f in old_spc) {
expect_error(read_spc(f))
}
})
test_that("SPC SDK example files", {
checksums <- c(
`fileio/spc/BARBITUATES.SPC` = "f49bbc854c",
`fileio/spc/barbsvd.spc` = "8a4d30672c",
`fileio/spc/BENZENE.SPC` = "6fc7901d15",
`fileio/spc/DRUG SAMPLE_PEAKS.SPC` = "a600cd05e2",
`fileio/spc/DRUG SAMPLE.SPC` = "981e42bfb8",
`fileio/spc/FID.SPC` = "ab65b6bb23",
`fileio/spc/HCL.SPC` = "c657dd8279",
`fileio/spc/HOLMIUM.SPC` = "18dc3b1ca3",
`fileio/spc/IG_BKGND.SPC` = "0b083dab3a",
`fileio/spc/IG_MULTI.SPC` = "fed652db3b",
`fileio/spc/IG_SAMP.SPC` = "c72dd5fc70",
`fileio/spc/KKSAM.SPC` = "8e905a5500",
`fileio/spc/POLYR.SPC` = "78b5987d93",
`fileio/spc/POLYS.SPC` = "608c01f69b",
`fileio/spc/SINGLE POLYMER FILM.SPC` = "0e13423de4",
`fileio/spc/SPECTRUM WITH BAD BASELINE.SPC` = "a05b77fada",
`fileio/spc/time.spc` = "98eabdd347",
`fileio/spc/TOLUENE.SPC` = "eb08948be8",
`fileio/spc/TriVista-linear.spc` = "31b30dac34",
`fileio/spc/TriVista-normal.spc` = "15d5d219b0",
`fileio/spc/TUMIX.SPC` = "7f8db885fb",
`fileio/spc/TWO POLYMER FILMS.SPC` = "173a0bb6d3",
`fileio/spc/Witec-timeseries.spc` = "65f84533d8",
`fileio/spc/XYTRACE.SPC` = "28594b6078"
)
# FIXME: unit test is missing
})
test_that("LabRam spc files", {
labram1 <- read_spc(paste0(labram_path, "/LabRam-1.spc"))
labram2 <- read_spc(paste0(labram_path, "/LabRam-2.spc"))
expect_equal(labram1[[2]][[1]], 785)
expect_equal(labram1[[1]][[4]], 678)
expect_equal(labram2[[1]][[69]], 1849)
expect_equal(labram2[[1]][[253]], 2563)
})
test_that("Shimadzu spc files do not yet work", {
expect_error(read_spc(paste0(shimadzu_path, "/F80A20-1.SPC")))
fname <- paste0(shimadzu_path, "/UV-2600_labeled_DNA.spc")
# TODO #102 - implement support for Shimadzu files
SHIMADZU_SPC_IMPLEMENTED <- F
if (SHIMADZU_SPC_IMPLEMENTED) {
# Compare data from SPC file and from CSV file. They should be equal
spc <- read_spc(fname)
expected <- read.txt.long(paste0(fname, ".csv"), sep = ",")
expect_true(all.equal(spc$spc, expected$spc))
} else {
# IF NOT IMPLEMENTED
# expect_error(
# read_spc("fileio/spc.Shimadzu/F80A20-1.SPC"),
# regexp = 'Shimadzu SPC'
# )
expect_error(read_spc(fname),
regexp = "Support for Shimadzu SPC file format (OLE CF) is not yet implemented",
fixed = T
)
}
})
test_that("Witec: some files supported", {
expect_error(read_spc(paste0(witec_path, "/P_A32_006_Spec_Data_1.spc")))
expect_error(read_spc(paste0(witec_path, "/P_A32_007_Spec_Data_1.spc")))
tmp <- read_spc(paste0(witec_path, "/Witec-Map.spc"))
expect_equal(tmp[[4]][[179]], 1138)
expect_equal(tmp[[5]][[347]], 1019)
## no spatial information
expect_null(tmp$x)
expect_null(tmp$y)
## spectra numbered in z
tmp <- read_spc(paste0(witec_path, "/Witec-timeseries.spc"))
expect_equal(tmp[[53]][[231]], 1100)
expect_equal(tmp[[71]][[739]], 981)
})
## Kaiser spc files tested mostly in Kaiser-specific read_spc_Kaiser*
## unit tests
# test_that("wplanes", {
#
# skip("wplanes do not yet work")
# # wplanes
# })
test_that("option file.keep.name", {
file.keep.name <- hy_get_option("file.keep.name")
hy_set_options(file.keep.name = FALSE)
expect_null(read_spc(paste0(labram_path, "/LabRam-2.spc"))$filename)
hy_set_options(file.keep.name = TRUE)
expect_equal(
read_spc(paste0(labram_path, "/LabRam-2.spc"))$filename,
paste0(labram_path, "/LabRam-2.spc")
)
hy_set_options(file.keep.name = file.keep.name)
})
test_that("hdr2data", {
expect_equal(
colnames(
read_spc(paste0(labram_path, "/LabRam-2.spc"), keys_hdr2data = TRUE)
),
c(
"z", "z.end", "ftflgs", "fexper", "fexp", "fnpts", "ffirst",
"flast", "fnsub", "fxtype", "fytype", "fztype", "fpost", "fdate",
"fres", "fsource", "fspare", "fcmnt", "fcatxt", "flogoff", "fmods",
"fprocs", "flevel", "fsampin", "ffactor", "fmethod", "fzinc",
"fwplanes", "fwinc", "fwtype", ".last.read", "subfiledir", "spc",
"filename"
)
)
})
}
.prepare_hdr_df <- function(data, n_subfiles) {
## the *type header elements are expressions. They need to be converted
## to character.
data <- lapply(data, function(x) {
if (mode(x) == "expression") {
as.character(x)
} else {