417 lines
18 KiB
R
417 lines
18 KiB
R
#Code adapted from github.com/philipp-baumann/simplerspec
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read_opus_univ <- function(file_path, limit){
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`%do%` <- foreach::`%do%`
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extract <- 'spc'
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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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# 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 code (spc_code)
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# in character vector
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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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## Get additional parameters from OPUS binary file =========================
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# Optics parameters --------------------------------------------------------
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csf_all <- grepRaw("CSF", pr, all = TRUE) + 7 # y-scaling factor
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# Read only CSF byte positions that correspond to final spectra
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CSF <- lapply(csf_all[npt_all %in% npt_spc],
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function(csf) hexView::readRaw(
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file_path, offset = csf, nbytes = 8, human = "real", size = 8)[[5]][1])
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# Scale all spectra with y-scaling factor if any of spectra types present
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# in file are not 1 --------------------------------------------------------
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# Set names of CSF elements equal to spectra list element names
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names(CSF) <- names(spc)
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if (any(unlist(CSF) != 1)) {
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# Return all elements in CSF that have scaling value not equal to 1
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CSF_toscale <- Filter(function(x) x != 1, CSF)
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# Apply scaling for spectra with CSF value not equal to 1;
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# Map() returns list
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spc_scaled <- Map(function(CSF, spc) CSF * spc,
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unlist(CSF_toscale), spc[names(CSF_toscale)])
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# Replace all spc list elements that have CSF not equal 1 with
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# scaled values
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spc <- replace(x = spc, list = names(CSF_toscale), values = spc_scaled)
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}
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## Allocate and return data from spectra in output list (out) ==============
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out <- data.frame(round(wavenumbers[['spc']], limit), round(spc[['spc']], limit), row.names = NULL)
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# Return spectra data and metadata contained as elements in list out
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out
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}) # closes try() function
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}
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