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705 lines
30 KiB
705 lines
30 KiB
#' @title Read a Bruker OPUS spectrum binary file
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#' @description
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#' Read single binary file acquired with an
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#' Bruker Vertex FTIR Instrument
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#' @param file_path Character vector with path to file
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#' @param extract Character vector of spectra types to extract from OPUS binary
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#' file. Default is \code{c("spc")}, which will extract the final spectra, e.g.
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#' expressed in absorbance (named \code{AB} in Bruker OPUS programs). Possible
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#' additional values for the character vector supplied to extract are
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#' \code{"ScSm"} (single channel spectrum of the sample measurement), \
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#' code{"ScRf"} (single channel spectrum of the reference measurment),
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#' \code{"IgSm"} (interferogram of the sample measurment) and \code{"IgRf"}
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#' (interferogram of the reference measurement).
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#' @param print_progress Logical (default \code{TRUE}) whether a message is
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#' printed when an OPUS binary file is parsed into an R list entry.
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#' @param atm_comp_minus4offset Logical whether spectra after atmospheric
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#' compensation are read with an offset of \code{-4} bites from Bruker OPUS
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#' files. Default is \code{FALSE}.
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#' @usage read_opus_bin_univ(file_path, extract = c("spc"),
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#' print_progress = TRUE, atm_comp_minus4offset = FALSE)
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# Importing functions `%do%` and foreach::`%dopar%` does not work, see
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# http://stackoverflow.com/questions/30216613/how-to-use-dopar-when-only-import-foreach-in-description-of-a-package
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# Got the following error:
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# "Error : object '`%do%`' is not exported by 'namespace:foreach'"
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#' @importFrom foreach %dopar% %do%
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#' @export
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read_opus_bin_univ <- function(file_path, extract = c("spc"),
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print_progress = TRUE,
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atm_comp_minus4offset = FALSE) {
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# Avoid `R CMD check` NOTE: no visible binding for global variable ...
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x <- y <- i <- npt <- NULL
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if (!file.exists(file_path)) {
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stop(paste0("File does not exist"))
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}
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try({
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# file_path <- "data/soilspec_background/yamsys_bg_gold/BF_lo_15_soil_cal.0"
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# Read entire content of file as bytes
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pa <- hexView::readRaw(file_path, offset = 0,
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nbytes = file.info(file_path)$size, human = "char",
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size = 1, endian = "little")
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# Get raw vector
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pr <- pa$fileRaw
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# Read byte positions for selected 3 letter strings that flag important
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# spectral information -----------------------------------------------------
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# Get positions of "END" strings
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end <- grepRaw("END", pr, all = TRUE) + 11
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# Get all positions of "NPT" (number of points) string
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npt_all <- grepRaw("NPT", pr, all = TRUE) + 3
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# Get frequency of first (FXV) and last point (LXV) positions
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fxv_all <- grepRaw("FXV", pr, all = TRUE) + 7
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lxv_all <- grepRaw("LXV", pr, all = TRUE) + 7
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# For some files, the number of positions where "FXV" and "LXV" occur
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# are not equal, e.g. for the file in
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# data/soilspec_esal_bin/BF_mo_01_soil_cal.0 ; As a consequence, the
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# fist and last point numbers (e.g. wavenumber or points for interferograms)
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# are not correctly read. This results in an error when trying to calculate
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# the wavenumbers; The below code is a quick and dirty fix to remove
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# FXV values that don't have LXV values and vice versa
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# (difference between "LXV" and "FXV" for a spectral data block
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# should be 16) ------------------------------------------------------------
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if (length(fxv_all) > length(lxv_all)) {
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diff_lxv_fxv <- lapply(lxv_all, function(x) x - fxv_all)
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# Return list of logical vectors indicating whether difference of fxv
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# and lxv is 16 (distance of 16 bytes)
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lxv_fxv_min <- lapply(diff_lxv_fxv, function(x) x == 16)
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fxv_list <- rep(list(fxv_all), length(fxv_all))
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fxv_all <- foreach::foreach(
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x = 1:length(fxv_list), y = 1:length(lxv_fxv_min),
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.combine = 'c') %do% {
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fxv_list[[x]][lxv_fxv_min[[y]]]
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}
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}
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if (length(lxv_all) > length(fxv_all)) {
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diff_fxv_lxv <- lapply(fxv_all, function(x) x - lxv_all)
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# Return list of logical vectors indicating whether difference of fxv
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# and lxv is 16 (distance of 16 bytes)
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fxv_lxv_min <- lapply(diff_fxv_lxv, function(x) x == -16)
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lxv_list <- rep(list(lxv_all), length(lxv_all))
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lxv_all <- foreach::foreach(
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x = 1:length(lxv_list), y = 1:length(fxv_lxv_min),
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.combine = 'c') %do% {
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lxv_list[[x]][fxv_lxv_min[[y]]]
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}
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}
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# Reduce size of npt_all -----------------------------------------------------
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# Some files have an extra "NPT" string without FXV, LXV, and spectral block
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if (length(npt_all) != length(fxv_all)) {
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diff_npt_fxv <- lapply(npt_all, function(x) fxv_all - x)
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min_bigger0_smallerequal40 <- lapply(diff_npt_fxv, function(x) {
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which_min_bigger0 <- x == min(x[x > 0])
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which_smallerequal40 <- x <= 40
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which_min_bigger0 & which_smallerequal40
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}
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)
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which_npt_valid <- sapply(min_bigger0_smallerequal40,
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function(x) any(x == TRUE))
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npt_all <- npt_all[which_npt_valid]
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}
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# --------------------------------------------------------------------------
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## Read basic spectral information =========================================
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# Read all number of points (NPT) at once
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NPT <- foreach::foreach(npt = npt_all, .combine = 'c') %do% {
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hexView::readRaw(
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file_path, offset = npt, nbytes = 12, human = "int", size = 4)[[5]][2]
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}
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# Specific error for file: <"data/soilspec_eth_bin/CI_tb_05_soil_cal.2">
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# "Invalid number of bytes" when trying to read spectra
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# -> Reason: NPT at position 1 is 995236000 !!!
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# Omit this entry in NPT and corresponding byte position in npt_all
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# Quick fix ----------------------------------------------------------------
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npt_all <- npt_all[NPT < 40000]
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NPT <- NPT[NPT < 40000]
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# --------------------------------------------------------------------------
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# Figure out how many spectral blocks exist and select final spectra
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# positions; end_spc is vector of offsets where spectra start
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if (length(end) == 1) {
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end_spc <- end
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} else {
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end_spc <- end[diff(end) > 4 * min(NPT)]
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}
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## Find final spectra information block positions
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## that belong to spectra data =============================================
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# Save positions that contain possible spectra data block
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# standard parameters
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spc_param_list <- list(
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'npt' = npt_all,
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'fxv' = fxv_all,
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'lxv' = lxv_all
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)
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## Return list of final parameters corresponding to data blocks that contain
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## spectra, elements are npt (number of points),
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## fxv (frequency of first point) and lxv (frequency of last point);
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## returned values represent byte positions in the file where spectra
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## parameters are stored. --------------------------------------------------
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return_spc_param <- function(end_spc, spc_param_list) {
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# Difference between any NPT position vector elements end_spc element
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# (end_spc[i] is a scalar, constant value at iteration i)
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diff_l <- lapply(end_spc, function(x) npt_all - x)
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# Test of any vector in list contains -164 (returns list of vectors
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# TRUE or FALSE)
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isminus164 <- lapply(diff_l, function(x) x == -164)
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# Find minimum positive difference within each list
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if (length(diff_l) == 1) {sel_min <- list(TRUE)} else {
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sel_min <- lapply(diff_l,
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function(x) {if (any(x > 0)) {x == min(x[x > 0])} else {x == -164}})
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}
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# Set FALSE repeated vector in sel_min element where TRUE positions are
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# duplicated
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which_elem_dupl <- which(duplicated(sapply(sel_min, which)))
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if (length(which_elem_dupl) > 1) {
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sel_min[which_elem_dupl] <- NULL
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# Reduce end_spc with duplicated elements
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end_spc <- end_spc[- which_elem_dupl]
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}
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# Select minimum difference NPT position for each END position
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npt_min <- Map(function(x, y) x[y],
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rep(list(npt_all), length(end_spc)), sel_min)
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npt_min <- Filter(length, npt_min)
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# Select spectra parameters that immediately follow END positions before
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# corresponding spectra
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param_min <- foreach::foreach(i = 1:length(spc_param_list),
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.final = function(i) setNames(i, names(spc_param_list))) %do% {
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Map(function(x, y) x[y],
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rep(list(spc_param_list[[i]]), length(end_spc)), sel_min)
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}
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# Test if any difference in list is -164
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if (any(unlist(isminus164) == TRUE)) {
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# Find all list element that contain TRUE in logical vector
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minus164 <- lapply(isminus164, function(x) Find(isTRUE, x))
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# Return element position of last TRUE in list
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where <- function(f, x) {
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vapply(x, f, logical(1))
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}
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last_minus164 <- Position(isTRUE, where(isTRUE, minus164),
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right = TRUE)
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# Replace positions in parameter list are at positions of last
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# -164 difference between end_spc element and NPT position
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param_min <- foreach::foreach(i = 1:length(spc_param_list),
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.final = function(i) setNames(i, names(spc_param_list))) %do% {
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param_min[[i]][[last_minus164]] <-
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spc_param_list[[i]][isminus164[[last_minus164]]]
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param_min[[i]]
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}
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}
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# Return list of final parameters corresponding to data blocks that
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# contain spectra
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param_spc <- lapply(param_min, unlist)
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param_spc$end_spc <- end_spc
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param_spc
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}
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# Save spectra parameter list
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param_spc <- return_spc_param(end_spc, spc_param_list)
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# Create individual vectors containing spectra parameters
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npt_spc <- param_spc[["npt"]]
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fxv_spc <- param_spc[["fxv"]]
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lxv_spc <- param_spc[["lxv"]]
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end_spc <- param_spc[["end_spc"]]
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# Read number of points corresponding to spectra in file -------------------
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NPT_spc <- foreach::foreach(i = 1:length(npt_spc), .combine = 'c') %do% {
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hexView::readRaw(
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file_path, offset = npt_spc[i],
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nbytes = 12, human = "int", size = 4)[[5]][2]
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}
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# Delete NPT with negative signs
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NPT_spc <- NPT_spc[NPT_spc > 0]
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## Read all spectra ========================================================
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spc <- Map(function(end, NPT) hexView::readRaw(file_path, width = NULL,
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offset = end - 4, nbytes = NPT * 4,
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human = "real", size = 4, endian = "little")[[5]], end_spc, NPT_spc)
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# Read FXV and LXV and calculate wavenumbers ------------------------------
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FXV_spc <- foreach::foreach(i = 1:length(fxv_spc), .combine = 'c') %do% {
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hexView::readRaw(file_path,
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offset = fxv_spc[i], nbytes = 16, human = "real", size = 8)[[5]][1]
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}
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LXV_spc <- foreach::foreach(i = 1:length(lxv_spc), .combine = 'c') %do% {
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hexView::readRaw(file_path,
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offset = lxv_spc[i], nbytes = 16, human = "real", size = 8)[[5]][1]
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}
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# Calculate wavenumbers
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wavenumbers <- foreach::foreach(i = 1:length(FXV_spc)) %do% {
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rev(seq(LXV_spc[i], FXV_spc[i],
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(FXV_spc[i] - LXV_spc[i]) / (NPT_spc[i] - 1)))
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}
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## Assigning list of intially read spectra depending on block type =========
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# Assign an index name to the spectra and parameters for reading
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names(end_spc) <- paste0("idx", 1:length(end_spc))
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names(spc) <- paste0("idx", 1:length(spc))
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names(NPT_spc) <- paste0("idx", 1:length(NPT_spc))
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names(FXV_spc) <- paste0("idx", 1:length(FXV_spc))
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names(wavenumbers) <- paste0("idx", 1:length(wavenumbers))
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# Check if elements in FXV_spc (frequency of first point) are equal to 0;
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# these are interferogram spectra ------------------------------------------
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which_Ig <- FXV_spc[which(FXV_spc == 0)]
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Ig_assigned <- if (length(which_Ig) == 0) {
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NULL
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} else if (length(which_Ig) == 1) {
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list(
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spc_idx = names(which_Ig),
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spc_code = "IgSm"
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)
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} else if (length(which_Ig) == 3) {
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list(
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spc_idx = names(which_Ig)[c(1, 3)],
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spc_code = c("IgSm", "IgRf")
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)
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} else {
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list(
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spc_idx = names(which_Ig),
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spc_code = c("IgSm", "IgRf")
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)
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}
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na_assigned <- list(
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spc_idx = NULL,
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spc_code = NULL
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)
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if (length(which_Ig) == 3) {
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# Assign duplicated interferogram spectrum to 'not available' assigned
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na_assigned <- list(
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spc_idx = names(which_Ig)[2],
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spc_code = NA
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)
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}
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# Remove NA assigned spectra in spc list -------------------------------------
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if (!is.null(na_assigned$spc_idx)) {
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spc[na_assigned$spc_idx] <- NULL
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# Remove wavenumbers with NA assigned spectra in spc list
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wavenumbers[na_assigned$spc_idx] <- NULL
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}
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# Assign single channel spectra if present in file -------------------------
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# Return idx (index names) of all remaining spectra that are not
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# interferograms
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notIg <- names(spc)[!names(spc) %in%
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c(Ig_assigned$spc_idx, na_assigned$spc_idx)]
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# Check if the MIR range was measured
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wavenumbers_mir <- lapply(names(wavenumbers[notIg]),
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function(i) spc[[i]][wavenumbers[notIg][[i]] < 2392 &
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wavenumbers[notIg][[i]] > 2358])
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is_mir <- any(sapply(wavenumbers_mir, function(x) length(x) != 0))
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if (isTRUE(is_mir)) {
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# Calculate peak ratio for absorbance at around 2392 cm^(-1)
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# and 2358 cm^(-1)
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peak_ratio <- lapply(
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lapply(names(wavenumbers[notIg]),
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function(i) spc[[i]][wavenumbers[notIg][[i]] < 2392 &
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wavenumbers[notIg][[i]] > 2358]),
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function(j) j[[1]] / j[[length(j)]]
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)
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names(peak_ratio) <- names(spc[notIg])
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# Single channel (Sc) assignment list
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which_Sc <- names(which(peak_ratio > 2))
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} else {
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peak_ratio <- lapply(
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lapply(names(wavenumbers[notIg]),
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function(i) spc[[i]][wavenumbers[notIg][[i]] < 5340 &
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wavenumbers[notIg][[i]] > 5318]),
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function(j) j[[1]] / j[[length(j)]]
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)
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names(peak_ratio) <- names(spc[notIg])
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# Single channel (Sc) assignment list
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which_Sc <- names(which(peak_ratio < 0.9))
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}
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# Check for single channel, exclude spectral blocks already assigned to
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# interferograms
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Sc_assigned <- if (length(which_Sc) == 0) {
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NULL
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} else if (length(which_Sc) == 1) {
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list(
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spc_idx = which_Sc,
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spc_code = "ScSm"
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)
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} else {
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list(
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spc_idx = which_Sc,
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spc_code = c("ScSm", "ScRf")
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)
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}
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# Assign corrected and uncorrected (if present) ----------------------------
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# AB spectra list
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which_AB <- names(spc)[!names(spc) %in%
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c(Ig_assigned[["spc_idx"]], na_assigned[["spc_idx"]],
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Sc_assigned[["spc_idx"]])]
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AB_assigned <- if (length(which_AB) == 1) {
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list(
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spc_idx = which_AB,
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spc_code = "spc"
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)
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} else {
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list(
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spc_idx = which_AB,
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spc_code = c("spc_nocomp", "spc")
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)
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}
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# Read result spectrum with new offset (no `-4`) when atmospheric
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# compensation was done by the OPUS software; replace the spectrum position
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# with index name idx that corresponds to final spectrum after atmospheric
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# compensation; OPUS files from particular spectrometers/OPUS software
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# versions do still need the same offset end_spc[[spc_idx]] - 4 as the other
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# spectra types; new argument atm_comp_minus4offset (default FALSE) is a
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# quick fix to read files with different offsets after atmospheric
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# compensation -------------------------------------------------------------
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if (length(which_AB) == 2 && !atm_comp_minus4offset) {
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spc[[which_AB[length(which_AB)]]] <-
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hexView::readRaw(file_path, width = NULL,
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offset = end_spc[which_AB[length(which_AB)]],
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nbytes = NPT_spc[which_AB[length(which_AB)]] * 4,
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human = "real", size = 4, endian = "little")[[5]]
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}
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# Assign spectra type for final spectra in element names of spc list -------
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# Combine spectral assignments lists
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list_assigned <- list(
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'Ig' = Ig_assigned,
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'Sc' = Sc_assigned,
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'AB' = AB_assigned
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)
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# Transpose spectra assignment list, first remove NULL elements in list
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list_assigned_t <- purrr::transpose(
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Filter(Negate(function(x) is.null(unlist(x))), list_assigned)
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)
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# Save spectra index (spc_idx) and spectra code (spc_code)
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# in character vector
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spc_idx <- unlist(list_assigned_t[["spc_idx"]])
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spc_code <- unlist(list_assigned_t[["spc_code"]])
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# Order spc_idx from 1 to n spectra (n = length of end_spc)
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order_spc <- as.numeric(
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sub(".*idx", "", unlist(list_assigned_t[["spc_idx"]])))
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spc_type <- spc_code[order(order_spc)]
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# Set spectrum type as element names of spectra list (spc)
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names(spc) <- spc_type
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# Set spectrum type in wavenumbers list
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names(wavenumbers) <- spc_type
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# Read with new offset when first value of
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# ScSm single channel sample spectrumspectrum is 0 and replace previous ---
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if (any(names(spc) %in% "ScSm" & spc[["ScSm"]][1] == 0)) {
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spc[["ScSm"]] <-
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hexView::readRaw(file_path, width = NULL,
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offset = end_spc[Sc_assigned$spc_idx[Sc_assigned$spc_code == "ScSm"]],
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nbytes = NPT_spc[Sc_assigned$spc_idx[Sc_assigned$spc_code == "ScSm"]]
|
|
* 4,
|
|
human = "real", size = 4, endian = "little")[[5]]
|
|
}
|
|
|
|
## Get additional parameters from OPUS binary file =========================
|
|
|
|
# Instrument parameters ----------------------------------------------------
|
|
ins <- grepRaw("INS", pr, all = TRUE) # Instrument type
|
|
INS <- hexView::blockString(
|
|
hexView::readRaw(
|
|
file_path, offset = ins[length(ins)] + 7,
|
|
nbytes = 10, human = "char", size = 1, endian = "little"))
|
|
lwn <- grepRaw("LWN", pr, all = TRUE)[1] + 7 # Laser wavenumber
|
|
LWN <- hexView::readRaw(file_path, offset = lwn,
|
|
nbytes = 8, human = "real", size=8)[[5]][1]
|
|
tsc <- grepRaw("TSC", pr, all = TRUE) + 7 # Scanner temperature
|
|
TSC_all <- lapply(tsc, function(tsc)
|
|
hexView::readRaw(file_path, offset = tsc,
|
|
nbytes = 16, human = "real", size = 8)[[5]][[1]] # can include sample
|
|
# and background temperature
|
|
)
|
|
# Read relative humidity of the interferometer during measurement
|
|
hum_rel <- grepRaw("HUM", pr, all = TRUE) + 7
|
|
HUM_rel <- lapply(hum_rel, function(hum_rel)
|
|
hexView::readRaw(
|
|
file_path, offset = hum_rel, nbytes = 16,
|
|
human = "int", size = 8)[[5]][[1]] # can include sample and background
|
|
# humidity
|
|
)
|
|
# Read absolute humidity of the interferometer during measurement
|
|
hum_abs <- grepRaw("HUA", pr, all = TRUE) + 7
|
|
HUM_abs <- lapply(hum_abs, function(hum_abs)
|
|
hexView::readRaw(
|
|
file_path, offset = hum_abs, nbytes = 16,
|
|
human = "real", size = 8)[[5]][[1]] # can include sample and background
|
|
# humidity
|
|
)
|
|
|
|
# Optics parameters --------------------------------------------------------
|
|
src <- grepRaw("SRC", pr, all = TRUE) # Source: MIR or NIR
|
|
SRC <- hexView::blockString(
|
|
hexView::readRaw(
|
|
file_path, offset = src[length(src)] + 4,
|
|
nbytes = 3, human = "char", size = 1, endian = "little"))
|
|
instr_range <- tolower(paste(INS, SRC, sep = "-")) # instrument range
|
|
bms <- grepRaw("BMS", pr, all = TRUE) # Beamsplitter
|
|
BMS <- hexView::blockString(
|
|
hexView::readRaw(file_path, offset = bms[length(bms)] + 4,
|
|
nbytes = 3, human = "char", size = 1, endian = "little"))
|
|
|
|
# Fourier transform parameters ---------------------------------------------
|
|
zff <- grepRaw("ZFF", pr, all = TRUE)[1] + 5 # Zero filling factor (numeric)
|
|
ZFF <- hexView::readRaw(file_path, offset = zff,
|
|
nbytes = 4, human = "int", size=2)[[5]][1]
|
|
|
|
# (Additional) Standard parameters -----------------------------------------
|
|
csf_all <- grepRaw("CSF", pr, all = TRUE) + 7 # y-scaling factor
|
|
# Read only CSF byte positions that correspond to final spectra
|
|
CSF <- lapply(csf_all[npt_all %in% npt_spc],
|
|
function(csf) hexView::readRaw(
|
|
file_path, offset = csf, nbytes = 8, human = "real", size = 8)[[5]][1])
|
|
mxy_all <- grepRaw("MXY", pr, all = TRUE) + 7 # Y-maximum
|
|
MXY <- unlist(lapply(mxy_all[npt_all %in% npt_spc],
|
|
function(mxy) hexView::readRaw(
|
|
file_path, offset = mxy, nbytes = 8, human = "real", size = 8)[[5]][1]))
|
|
mny <- grepRaw("MNY", pr, all = TRUE) + 7 # Y-minimum
|
|
dxu_all <- grepRaw("DXU", pr, all = TRUE) + 7 # X units
|
|
DXU <- lapply(dxu_all, function(dxu)
|
|
hexView::blockString(
|
|
hexView::readRaw(file_path, offset = dxu,
|
|
nbytes = 3, human = "char", size = 1, endian = "little")
|
|
)
|
|
)
|
|
# Y units -> there is no DYU present in file
|
|
dyu_all <- grepRaw("DYU", pr, all = TRUE) + 7
|
|
dat <- grepRaw("DAT", pr, all = TRUE) + 7 # Date
|
|
tim <- grepRaw("TIM", pr, all = TRUE) + 7 # Time
|
|
time <- unlist(lapply(tim, function(tim)
|
|
hexView::blockString(
|
|
hexView::readRaw(file_path, offset = tim,
|
|
nbytes = 22, human = "char",
|
|
size = 1, endian = "little")))
|
|
)
|
|
# Only select "DAT" string positions that are immediately before time
|
|
dat_sel <- foreach::foreach(i = 1:length(tim), .combine = 'c') %do% {
|
|
diff_sel <- dat - tim[i]
|
|
dat[which(diff_sel <= 32 & diff_sel >= -20)]
|
|
}
|
|
date <- lapply(dat_sel, function(dat) hexView::blockString(
|
|
hexView::readRaw(file_path, offset = dat,
|
|
nbytes = 10, human = "char", size = 1,
|
|
endian = "little"))
|
|
)
|
|
|
|
date_time <- unique(paste(date, time))
|
|
# Convert date_time from character to class POSIXct (calendar date and time)
|
|
date_time <- as.POSIXct(date_time, format = "%d/%m/%Y %H:%M:%S")
|
|
# , tz = "GMT+1") # tz is argument for time zone
|
|
|
|
# Scale all spectra with y-scaling factor if any of spectra types present
|
|
# in file are not 1 --------------------------------------------------------
|
|
# Set names of CSF elements equal to spectra list element names
|
|
names(CSF) <- names(spc)
|
|
if (any(unlist(CSF) != 1)) {
|
|
# Return all elements in CSF that have scaling value not equal to 1
|
|
CSF_toscale <- Filter(function(x) x != 1, CSF)
|
|
# Apply scaling for spectra with CSF value not equal to 1;
|
|
# Map() returns list
|
|
spc_scaled <- Map(function(CSF, spc) CSF * spc,
|
|
unlist(CSF_toscale), spc[names(CSF_toscale)])
|
|
# Replace all spc list elements that have CSF not equal 1 with
|
|
# scaled values
|
|
spc <- replace(x = spc, list = names(CSF_toscale), values = spc_scaled)
|
|
}
|
|
|
|
# Data aquisition parameters -----------------------------------------------
|
|
|
|
plf <- grepRaw("PLF", pr, all = TRUE) + 4 # Result spectrum
|
|
PLF_all <- lapply(plf, function(plf) hexView::blockString(
|
|
hexView::readRaw(file_path, offset = plf,
|
|
nbytes = 2, human = "char", size = 1,
|
|
endian = "little"))
|
|
)
|
|
# Select only result spectra abbreviations that are more than 0 characters
|
|
# long
|
|
PLF <- unlist(PLF_all[lapply(PLF_all, nchar) > 0])
|
|
res <- grepRaw("RES", pr, all = TRUE)[1] + 5 # Resolution (wavenumber)
|
|
RES <- hexView::readRaw(
|
|
file_path, offset = res, nbytes = 4, human = "int", size = 2)[[5]][1]
|
|
|
|
## Create sample metadata objects ==========================================
|
|
# File name
|
|
file_name_nopath <- sub(".+/(.+)", "\\1", file_path)
|
|
# Create sample id from file name;
|
|
# remove extension .0, .1 etc. from OPUS files
|
|
sample_id <- sub("(.+)\\.[[:digit:]]+$", "\\1", file_name_nopath)
|
|
# Extract sample repetition number (rep_no) from file name
|
|
rep_no <- sub(".+\\.([[:digit:]])+$", "\\1", file_path)
|
|
snm <- grepRaw("SNM", pr, all = TRUE)[1] + 7
|
|
SNM <- hexView::blockString(
|
|
hexView::readRaw(file_path, offset = snm,
|
|
nbytes = 30, human = "char", size = 1, endian = "little")
|
|
)
|
|
# Create unique_id using file_name and time
|
|
# ymd_id <- format(max(date_time), "%Y%m%d")
|
|
ymdhms_id <- max(date_time)
|
|
unique_id <- paste0(file_name_nopath, "_", ymdhms_id)
|
|
|
|
## Convert all spectra in list spc into a matrix of 1 row ==================
|
|
spc_m <- lapply(spc,
|
|
function(x) matrix(x, ncol = length(x), byrow = FALSE))
|
|
# Add dimnames (wavenumbers for columns and unique_id for rows
|
|
spc_m <- foreach::foreach(i = 1:length(spc_m),
|
|
.final = function(i) setNames(i, names(spc_m))) %do% {
|
|
colnames(spc_m[[i]]) <- round(wavenumbers[[i]], 1)
|
|
rownames(spc_m[[i]]) <- unique_id
|
|
data.table::as.data.table(spc_m[[i]])
|
|
}
|
|
|
|
# Save all relevant data parameters (metadata)
|
|
# in tibble data frame (class "data.frame" and "tbl_diff" ==================
|
|
metadata <- tibble::tibble(
|
|
unique_id = unique_id,
|
|
file_id = file_name_nopath, # pb (20170514): changed `scan_id` to `file_id`
|
|
sample_id = sample_id,
|
|
rep_no = as.numeric(rep_no),
|
|
date_time_sm = max(date_time),
|
|
date_time_rf = min(date_time),
|
|
sample_name = SNM,
|
|
instr_name_range = instr_range,
|
|
resolution_wn = RES,
|
|
# Result spectrum; e.g. "AB" = Absorbance
|
|
# result_spc = ifelse(length(unique(PLF)) == 1, unique(PLF), unique(PLF)[2]),
|
|
# // pb: 2019-11-19: allow NULL value for PLF
|
|
result_spc <- if (length(unique(PLF)) == 1) {
|
|
unique(PLF)} else if (length(unique(PLF)) > 1) {
|
|
unique(PLF)[2]} else { NA },
|
|
beamspl = BMS,
|
|
laser_wn = LWN,
|
|
# `spc_in_file`: character vector of spectra found in OPUS file
|
|
spc_in_file = paste(unlist(list_assigned_t[["spc_code"]]),
|
|
collapse = ";", sep = ";"),
|
|
zero_filling = ZFF, # Zero filling factor for fourier transformation
|
|
# Temperature of scanner during sample measurement
|
|
temp_scanner_sm = TSC_all[[length(TSC_all)]], # select last element
|
|
# Temperature of scanner during reference measurement;
|
|
# if there is only one element in TSC_all, temperature during reference
|
|
# mesurement is not saved
|
|
temp_scanner_rf = ifelse(length(TSC_all) == 1, NA, TSC_all[[1]]),
|
|
# Relative humidity
|
|
hum_rel_sm = HUM_rel[[length(HUM_rel)]], # sample measurement
|
|
hum_rel_rf = ifelse(length(HUM_rel) == 1, NA, HUM_rel[[1]]), # reference
|
|
# measurement
|
|
# Absolute humidity; sample measurement (sm); reference measurment (rf);
|
|
# note: for Vertex 70 instrument HUA is not present, in this case,
|
|
# HUM_abs is a list without elements
|
|
hum_abs_sm = ifelse(length(HUM_abs) != 0, HUM_abs[[length(HUM_abs)]], NA),
|
|
hum_abs_rf = ifelse(length(HUM_abs) == 1 | length(HUM_abs) == 0, NA,
|
|
HUM_abs[[1]]) # reference measurement
|
|
)
|
|
|
|
## Allocate and return data from spectra in output list (out) ==============
|
|
out <- list(
|
|
'metadata' = metadata,
|
|
'spc' = spc_m[["spc"]],
|
|
'spc_nocomp' = if ("spc_nocomp" %in% extract &&
|
|
"spc_nocomp" %in% names(spc_m)) {
|
|
spc_m[["spc_nocomp"]]} else {NULL},
|
|
'sc_sm' = if ("ScSm" %in% extract && "ScSm" %in% names(spc_m)) {
|
|
spc_m[["ScSm"]]} else {NULL},
|
|
'sc_rf' = if ("ScRf" %in% extract && "ScRf" %in% names(spc_m)) {
|
|
spc_m[["ScRf"]]} else {NULL},
|
|
'ig_sm' = if ("IgSm" %in% extract && "IgSm" %in% names(spc_m)) {
|
|
spc_m[["IgSm"]]} else {NULL},
|
|
'ig_rf' = if ("IgRf" %in% extract && "IgRf" %in% names(spc_m)) {
|
|
spc_m[["IgRf"]]} else {NULL},
|
|
# Wavenumbers of final AB spectra
|
|
wavenumbers = wavenumbers[["spc"]],
|
|
wavenumbers_sc_sm = if ("ScSm" %in% extract) {
|
|
wavenumbers[["ScSm"]]} else {NULL},
|
|
wavenumbers_sc_rf = if ("ScRf" %in% extract) {
|
|
wavenumbers[["ScRf"]]} else {NULL}
|
|
)
|
|
|
|
# Print message that file was read if option is set
|
|
if (print_progress == TRUE) {
|
|
message(
|
|
paste0("Extracted spectra data from file: <", file_name_nopath, ">")
|
|
)
|
|
}
|
|
# Return spectra data and metadata contained as elements in list out
|
|
out
|
|
}) # closes try() function
|
|
|
|
}
|
|
|
|
#' @title Read a list of Bruker OPUS spectrum binary files.
|
|
#' @description
|
|
#' Read multiple spectral files measured with a Bruker FTIR Instrument. Files
|
|
#' containing spectra are in OPUS binary format.
|
|
#' \code{read_opus_univ} is a wrapper for \code{read_opus_bin_univ()})
|
|
#' @param fnames List of character vectors containing full path names of spectra
|
|
#' @param extract Character vector of spectra types to extract from file.
|
|
#' Possible values are: "spc" (AB block in Bruker Opus software), "spc_nocomp"
|
|
#' (Spectra before final atmospheric compensation; only present if background
|
|
#' correction has been set in Opus), "ScSm" (Single channel spectrum of the
|
|
#' sample), "ScRf" (Single channel spectrum of the sample), "IgSm" (Interferogram
|
|
#' of the sample), "IgRf" (Interferogram of the reference). Default is
|
|
#' \code{extract = c("spc")}.
|
|
#' @param parallel Logical (\code{TRUE} or \code{FALSE} indicating whether
|
|
#' files are read in parallel (multiple processors or multiple cores)).
|
|
#' Default is \code{parallel = FALSE}. If \code{TRUE} a parallel backend needs
|
|
#' to be registered, e.g. by using the \code{doParallel} package.
|
|
#' @param atm_comp_minus4offset Logical whether spectra after atmospheric
|
|
#' compensation are read with an offset of \code{-4} bites from Bruker OPUS
|
|
#' files. Default is \code{FALSE}.
|
|
#' @usage read_opus_univ(fnames, extract = c("spc"), parallel = FALSE,
|
|
#' atm_comp_minus4offset = FALSE)
|
|
#' @return out List spectra and metadata (parameters) extracted from
|
|
#' Bruker OPUS spectrometer files. List names are the names of the OPUS
|
|
#' files whose spectral data were extracted.
|
|
#' @export
|
|
read_opus_univ <- function(fnames, extract = c("spc"), parallel = FALSE,
|
|
atm_comp_minus4offset = FALSE) {
|
|
|
|
# Avoid `R CMD check` NOTE: ``no visible binding for variable ...
|
|
i <- NULL
|
|
|
|
if (parallel == TRUE) {
|
|
foreach::foreach(i = 1:length(fnames),
|
|
.export = "read_opus_bin_univ",
|
|
.errorhandling = "pass", # error object generated by task evaluation will
|
|
# be included with the rest of the results
|
|
# export the foreach package to the individual workers
|
|
.packages = c("foreach", "simplerspec"),
|
|
.final = function(i) setNames(i, sub(".+/(.+)", "\\1", fnames))) %dopar% {
|
|
try(
|
|
read_opus_bin_univ(file_path = fnames[[i]], extract = extract,
|
|
atm_comp_minus4offset = atm_comp_minus4offset)
|
|
)
|
|
}
|
|
} else if (parallel == FALSE) {
|
|
spc_list <- lapply(fnames,
|
|
function(x) try(read_opus_bin_univ(file_path = x, extract = extract,
|
|
atm_comp_minus4offset = atm_comp_minus4offset)))
|
|
names(spc_list) <- sub(".+/(.+)", "\\1", fnames)
|
|
spc_list
|
|
}
|
|
}
|
|
|