R/read.spc.R

In soil.spec: Soil Spectroscopy Tools and Reference Models

#' Function for reading SPC files
#'
#' @author Andrew Sila \email{asila@cgiar.org}
#' Note:

read.spc<-function (loa = "", path = "", sav = "F", out = "Sm", save.as = "workspace", 
    wn = "first") 
    {#Declare global variable
   #blockString<-NULL
tmp<-c()
    if (loa != "") {
        setwd(loa)
    }
    tmp<-list.files()
    a<-nchar(tmp)
    a<-substr(tmp, a - 2, a)
    a<-which(a != "spc" & a != "SPC")
    if (length(a) > 0) {
        tmp<-tmp[-a]
    }
    rm(a)
    if (length(tmp) == 0) 
        stop("Invalid argument: the path is either incorrect or the folder empty.")
    if (is.na(match(sav, c("F", "T")))) {
        stop("Invalid argument: 'sav' has to either 'F' or 'T'.")
    }
    if (class(out) != "character") {
        stop("Invalid argument: 'out' has to be of class 'character'.")
    }
    if (is.na(match(save.as, c("workspace", "csv.file")))) {
        stop("invalid argument: 'save.as' has to be either 'workspace' or 'csv.file'.")
    }
    if (is.na(match(wn, c("first", "ICRAF")))) {
        stop("Invalid argument: 'wn' has to be either 'first' or 'ICRAF'.")
    }
    if (wn == "ICRAF") {
        n.mpa<-2307
        Flast.mpa<-12493.2
        Ffirst.mpa<-3598.69
        bla<-c(rep(NA, n.mpa - 2))
        for (k in 1:(n.mpa - 2)) {
            bla[k]<-k * (Flast.mpa - Ffirst.mpa)/(n.mpa - 1)
        }
        w<-Ffirst.mpa + bla
        waveb.mpa<-round(c(Ffirst.mpa, w, Flast.mpa), 6)
        n.hts<-3578
        Flast.hts<-7497.964
        Ffirst.hts<-599.76
        bla<-c(rep(NA, n.hts - 2))
        for (k in 1:(n.hts - 2)) {
            bla[k]<-k * (Flast.hts - Ffirst.hts)/(n.hts - 1)
        }
        w<-Ffirst.hts + bla
        waveb.hts<-round(c(Ffirst.hts, w, Flast.hts), 6)
    }
    rang<-c()
    for (i in 1:length(tmp)) {
       #library(hexView, quietly = T)
        bla<-readRaw(tmp[i], offset = 4, nbytes = 4, human = "int", 
            size = 4, endian = "little")[[5]]
        test<-readRaw(tmp[i], offset = (bla * 4 + 544 + 64), nbytes = 428, human = "char", endian = "little")
        test<-blockString(test)
        test<-strsplit(test, "..", fixed = T)
        model<-test[[1]][1]
        test<-substr(test[[1]][17], nchar(test[[1]][17]) - 
            2, nchar(test[[1]][17]))
        ifelse(test == c("NIR") & nchar(test) == 3, rang[i]<-test, 
            rang[i]<-c("MIR"))
    }
    rm(test, i)
    mir<-which(rang == "MIR")
    nir<-which(rang == "NIR")
    if (length(mir) > 0) {
        test<-c()
        for (i in 1:length(tmp[mir])) {
            test[i]<-nchar(tmp[mir][i], type = "chars")
        }
        test.1<-c(rep(NA, length(tmp[mir])))
        for (i in 1:length(tmp[mir])) {
            test.1[i]<-substr(tmp[mir][i], 1, (test[i] - 4))
        }
        test.2<-c(rep(NA, length(tmp[mir])))
        for (i in 1:length(tmp[mir])) {
            test.2[i]<-substr(tmp[mir][i], 1, (test[i] - 4))
              #test.2[i]<-substr(tmp[mir][i], 1, (test[i][[1]] - 4))
               }
        a<-unique(test.1)
        b<-list()
        for (i in 1:length(a)) {
            b[[i]]<-which(test.1 == a[i])
        }
        mir.ad.tmp<-as.data.frame(matrix(nrow = length(mir), 
            ncol = 7, dimnames = list(c(1:length(tmp[mir])), 
                c("SSN", "Wavebands", "Material", "Spectral_range", 
                  "Scan_date", "Resolution", "Zero_filling"))))
        mir.ad.tmp[, "SSN"]<-test.1
        mir.ad.tmp[, "Spectral_range"]<-c("MIR")
        for (i in 1:length(tmp[mir])) {
            n<-readRaw(tmp[mir][i], offset = 4, nbytes = 4, 
                human = "int", size = 4, endian = "little")[[5]]
            mir.ad.tmp[i, "Wavebands"]<-n
            Ffirst<-readRaw(tmp[mir][1], offset = 8, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            Flast<-readRaw(tmp[mir][1], offset = 16, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            if (Ffirst > Flast) {
                c<-Ffirst
                Ffirst<-Flast
                Flast<-c
            }
            bla<-c(rep(NA, n - 2))
            for (k in 1:(n - 2)) {
                bla[k]<-k * (Flast - Ffirst)/(n - 1)
            }
            w<-Ffirst + bla
            waveb.hts<-round(c(Ffirst, w, Flast), 6)
            test<-as.character(readRaw(tmp[mir][i], offset = 32, 
                nbytes = 4, human = "int", size = 1.5, machine = "binary", 
                signed = F, endian = "little"))
            test.a<-paste(substr(test, 35, 42), substr(test, 
                26, 33), substr(test, 17, 21), sep = "")
            year<-substr(test.a, 1, 12)
            c<-nchar(year)
            d<-c(rep(NA, c))
            k<-0
            for (j in c:1) {
                d[j]<-as.numeric(substr(year, j, j)) * 2^k
                k<-k + 1
            }
            year<-sum(d)
            month<-substr(test.a, 13, 16)
            c<-nchar(month)
            d<-c(rep(NA, c))
            k<-0
            for (j in c:1) {
                d[j]<-as.numeric(substr(month, j, j)) * 2^k
                k<-k + 1
            }
            month<-sum(d)
            day<-substr(test.a, 17, 21)
            c<-nchar(day)
            d<-c(rep(NA, c))
            k<-0
            for (j in c:1) {
                d[j]<-as.numeric(substr(day, j, j)) * 2^k
                k<-k + 1
            }
            day<-sum(d)
            mir.ad.tmp[i, "Scan_date"]<-paste(month, "/", day, 
                "/", year, sep = "")
            test<-readRaw(tmp[mir][i], offset = (length(waveb.hts) * 
                4 + 544 + 64), nbytes = 428, human = "char", 
                endian = "little")
            test<-blockString(test)
            test<-strsplit(test, "..", fixed = T)
            if (grepl("Plant", test[[1]][8])) {
                mir.ad.tmp[i, "Material"]<-"Plant"
            }
            if (grepl("Soil", test[[1]][8])) {
                mir.ad.tmp[i, "Material"]<-"Soil"
            }
            mir.ad.tmp[i, "Resolution"]<-as.integer(substr(test[[1]][7], 
                nchar(test[[1]])[7], nchar(test[[1]])[7]))
            mir.ad.tmp[i, "Zero_filling"]<-as.integer(substr(test[[1]][20], 
                nchar(test[[1]])[20], nchar(test[[1]])[20]))
        }
        if (length(summary(as.factor(mir.ad.tmp[, "Material"]))) != 
            1 | length(summary(as.factor(mir.ad.tmp[, "Resolution"]))) != 
            1 | length(summary(as.factor(mir.ad.tmp[, "Zero_filling"]))) != 
            1 | length(summary(as.factor(mir.ad.tmp[, "Wavebands"]))) != 
            1) {
            test<-menu("Scan settings for mir-spectra not uniform. Find a txt-file with detailed scaning information named 'mir.ad.tmp.txt' in 'loa'.", 
                graphics = T)
            if (test == 1) {
                write.table(mir.ad.tmp, file = "mir.ad.tmp.txt", 
                  sep = ",", dec = ".", row.names = F)
            }
        }
        if (length(summary(as.factor(mir.ad.tmp[, "Material"]))) != 
            1) {
            ma<-names(summary(as.factor(mir.ad.tmp[, "Material"])))
            mat<-c()
            mat[1]<-paste("Different materials for mir-spectra. Shall only ", 
                ma[1], " be saved?", sep = "")
            for (i in 2:length(ma)) {
                mat[i]<-paste("Different materials for mir-spectra. Shall only ", 
                  ma[i], " be saved?", sep = "")
            }
            test<-menu(mat, graphics = T)
            for (i in 1:length(ma)) {
                if (test == i) {
                  bla<-which(mir.ad.tmp[, "Material"] == ma[i])
                  mir.ad.tmp<-mir.ad.tmp[bla, ]
                }
            }
        }
        if (length(summary(as.factor(mir.ad.tmp[, "Resolution"]))) != 
            1) {
            re<-as.integer(names(summary(as.factor(mir.ad.tmp[, 
                "Resolution"]))))
            res<-c()
            res[1]<-paste("Different resolutions for 'mir' spectra. Shall only ", 
                re[1], " be saved?", sep = "")
            for (i in 2:length(re)) {
                res[i]<-paste("Different resolutions for 'mir' spectra. Shall only ", 
                  re[i], " be saved?", sep = "")
            }
            test<-menu(res, graphics = T)
            for (i in 1:length(re)) {
                if (test == i) {
                  bla<-which(mir.ad.tmp[, "Resolution"] == 
                    re[i])
                  mir.ad.tmp<-mir.ad.tmp[bla, ]
                }
            }
        }
        if (length(summary(as.factor(mir.ad.tmp[, "Zero_filling"]))) != 
            1) {
            ze<-as.integer(names(summary(as.factor(mir.ad.tmp[, 
                "Zero_filling"]))))
            zer<-c()
            zer[1]<-paste("Different Zero_fillings for 'mir' spectra. Shall only ", 
                ze[1], " be saved?", sep = "")
            for (i in 2:length(ze)) {
                zer[i]<-paste("Different Zero_fillings. Shall only ", 
                  ze[i], " be saved?", sep = "")
            }
            test<-menu(zer, graphics = T)
            for (i in 1:length(ze)) {
                if (test == i) {
                  bla<-which(mir.ad.tmp[, "Zero_filling"] == 
                    ze[i])
                  mir.ad.tmp<-mir.ad.tmp[bla, ]
                }
            }
        }
        if (length(summary(as.factor(mir.ad.tmp[, "Wavebands"]))) != 
            1) {
            test<-menu(c("Differing number of wavebands  for 'mir' spectra - continue according to function argument 'wn'.", 
                "Differing number of wavebands  for 'mir' spectra - stop."), 
                graphics = T)
            if (test == 2) {
                stop("You stopped reading spc-files.")
            }
        }
        a<-unique(mir.ad.tmp[, "SSN"])
        b<-list()
        for (i in 1:length(a)) {
            b[[i]]<-which(mir.ad.tmp[, "SSN"] == a[i])
        }
        mir.ad<-as.data.frame(matrix(nrow = length(a), ncol = 7, 
            dimnames = list(a, c("SSN", "Wavebands", 
                "Material", "Spectral_range", "Scan_date", "Resolution", 
                "Zero_filling"))))
        mir.ad[, "SSN"]<-unique(mir.ad.tmp[, "SSN"])
        mir.ad[, "Wavebands"]<-mir.ad.tmp[1, "Wavebands"]
        mir.ad[, "Material"]<-mir.ad.tmp[1, "Material"]
        mir.ad[, "Spectral_range"]<-mir.ad.tmp[1, "Spectral_range"]
        mir.ad[, "Resolution"]<-mir.ad.tmp[1, "Resolution"]
        mir.ad[, "Zero_filling"]<-mir.ad.tmp[1, "Zero_filling"]
        for (i in 1:length(a)) {
            if (length(which(mir.ad.tmp[b[[i]], "Scan_date"] == 
                mir.ad.tmp[b[[i]][1], "Scan_date"])) == length(b[[i]])) {
                mir.ad[i, "Scan_date"]<-mir.ad.tmp[b[[i]][1], 
                  "Scan_date"]
            }
        }
        #mir<-mir[as.integer(rownames(mir.ad.tmp))]
        #test.2<-c(rep(NA, length(tmp[mir])))
       # for (i in 1:length(tmp[mir])) {
           # test.2[i]<-substr(tmp[mir][i], 1, (test[i][[1]] - 4))
       # }
    }
    if (length(nir) > 0) {
        test<-c()
        for (i in 1:length(tmp[nir])) {
            test[i]<-nchar(tmp[nir][i], type = "chars")
        }
        test.1<-c(rep(NA, length(tmp[nir])))
        for (i in 1:length(tmp[nir])) {
            test.1[i]<-substr(tmp[nir][i], 1, (test[i] - 6))
        }
        nir.ad<-as.data.frame(matrix(nrow = length(test.1), 
            ncol = 7, dimnames = list(test.1, c("SSN", 
                "Wavebands", "Material", "Spectral_range", "Scan_date", 
                "Resolution", "Zero_filling"))))
        nir.ad[, "SSN"]<-test.1
        nir.ad[, "Spectral_range"]<-c("NIR")
        for (i in 1:length(tmp[nir])) {
            n<-readRaw(tmp[nir][i], offset = 4, nbytes = 4, 
                human = "int", size = 4, endian = "little")[[5]]
            nir.ad[i, "Wavebands"]<-n
            Ffirst<-readRaw(tmp[nir][1], offset = 8, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            Flast<-readRaw(tmp[nir][1], offset = 16, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            if (Ffirst > Flast) {
                c<-Ffirst
                Ffirst<-Flast
                Flast<-c
            }
            bla<-c(rep(NA, n - 2))
            for (k in 1:(n - 2)) {
                bla[k]<-k * (Flast - Ffirst)/(n - 1)
            }
            w<-Ffirst + bla
            waveb.mpa<-round(c(Ffirst, w, Flast), 6)
            test<-as.character(readRaw(tmp[nir][i], offset = 32, 
                nbytes = 4, human = "int", size = 1.5, machine = "binary", 
                signed = F, endian = "little"))
            test.a<-paste(substr(test, 35, 42), substr(test, 
                26, 33), substr(test, 17, 21), sep = "")
            year<-substr(test.a, 1, 12)
            c<-nchar(year)
            d<-c(rep(NA, c))
            k<-0
            for (j in c:1) {
                d[j]<-as.numeric(substr(year, j, j)) * 2^k
                k<-k + 1
            }
            year<-sum(d)
            month<-substr(test.a, 13, 16)
            c<-nchar(month)
            d<-c(rep(NA, c))
            k<-0
            for (j in c:1) {
                d[j]<-as.numeric(substr(month, j, j)) * 2^k
                k<-k + 1
            }
            month<-sum(d)
            day<-substr(test.a, 17, 21)
            c<-nchar(day)
            d<-c(rep(NA, c))
            k<-0
            for (j in c:1) {
                d[j]<-as.numeric(substr(day, j, j)) * 2^k
                k<-k + 1
            }
            day<-sum(d)
            nir.ad[i, "Scan_date"]<-paste(month, "/", day, 
                "/", year, sep = "")
            test<-readRaw(tmp[nir][i], offset = (length(waveb.mpa) * 
                4 + 544 + 64), nbytes = 431, human = "char", 
                endian = "little")
            test<-blockString(test)
            test<-strsplit(test, "..", fixed = T)
            if (grepl("Plant", test[[1]][8])) {
                nir.ad[i, "Material"]<-"Plant"
            }
            if (grepl("Soil", test[[1]][8])) {
                nir.ad[i, "Material"]<-"Soil"
            }
            nir.ad[i, "Resolution"]<-as.integer(substr(test[[1]][7], 
                nchar(test[[1]])[7], nchar(test[[1]])[7]))
            nir.ad[i, "Zero_filling"]<-as.integer(substr(test[[1]][20], 
                nchar(test[[1]])[20], nchar(test[[1]])[20]))
        }
        if (length(summary(as.factor(nir.ad[, "Material"]))) != 
            1 | length(summary(as.factor(nir.ad[, "Resolution"]))) != 
            1 | length(summary(as.factor(nir.ad[, "Zero_filling"]))) != 
            1 | length(summary(as.factor(nir.ad[, "Wavebands"]))) != 
            1) {
            test<-menu("Scan settings for nir-spectra not uniform. Find a txt-file with detailed scaning information named 'nir.ad.txt' in 'loa'.", 
                graphics = T)
            if (test == 1) {
                write.table(nir.ad, file = "nir.ad.txt", sep = ",", 
                  dec = ".", row.names = F)
            }
        }
        if (length(summary(as.factor(nir.ad[, "Material"]))) != 
            1) {
            ma<-names(summary(as.factor(nir.ad[, "Material"])))
            mat<-c()
            mat[1]<-paste("Different materials for nir-spectra. Shall only ", 
                ma[1], " be saved?", sep = "")
            for (i in 2:length(ma)) {
                mat[i]<-paste("Different materials for nir-spectra. Shall only ", 
                  ma[i], " be saved?", sep = "")
            }
            test<-menu(mat, graphics = T)
            for (i in 1:length(ma)) {
                if (test == i) {
                  bla<-which(nir.ad[, "Material"] == ma[i])
                  nir.ad<-nir.ad[bla, ]
                }
            }
        }
        if (length(summary(as.factor(nir.ad[, "Resolution"]))) != 
            1) {
            re<-as.integer(names(summary(as.factor(nir.ad[, 
                "Resolution"]))))
            res<-c()
            res[1]<-paste("Different resolutions for nir-spectra. Shall only ", 
                re[1], " be saved?", sep = "")
            for (i in 2:length(re)) {
                res[i]<-paste("Different resolutions. Shall only ", 
                  re[i], " be saved?", sep = "")
            }
            test<-menu(res, graphics = T)
            for (i in 1:length(re)) {
                if (test == i) {
                  bla<-which(nir.ad[, "Resolution"] == re[i])
                  nir.ad<-nir.ad[bla, ]
                }
            }
        }
        if (length(summary(as.factor(nir.ad[, "Zero_filling"]))) != 
            1) {
            ze<-as.integer(names(summary(as.factor(nir.ad[, 
                "Zero_filling"]))))
            zer<-c()
            zer[1]<-paste("Different Zero_fillings for nir-spectra. Shall only ", 
                ze[1], " be saved?", sep = "")
            for (i in 2:length(ze)) {
                zer[i]<-paste("Different Zero_fillings. Shall only ", 
                  ze[i], " be saved?", sep = "")
            }
            test<-menu(zer, graphics = T)
            for (i in 1:length(ze)) {
                if (test == i) {
                  bla<-which(nir.ad[, "Zero_filling"] == ze[i])
                  nir.ad<-nir.ad[bla, ]
                }
            }
        }
        if (length(summary(as.factor(nir.ad[, "Wavebands"]))) != 
            1) {
            test<-menu(c("Differing number of wavebands  for nir-spectra - continue according to function argument 'wn'.", 
                "Differing number of wavebands  for nir-spectra - stop."), 
                graphics = T)
            if (test == 2) {
                stop("You stopped reading spc-files.")
            }
        }
        nir<-nir[match(rownames(nir.ad), test.1)]
    }
    if (wn == "first") {
        if (length(mir) > 0) {
            n<-readRaw(tmp[mir][1], offset = 4, nbytes = 4, 
                human = "int", size = 4, endian = "little")[[5]]
            Ffirst<-readRaw(tmp[mir][1], offset = 8, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            Flast<-readRaw(tmp[mir][1], offset = 16, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            if (Ffirst > Flast) {
                c<-Ffirst
                Ffirst<-Flast
                Flast<-c
            }
            bla<-c(rep(NA, n - 2))
            for (k in 1:(n - 2)) {
                bla[k]<-k * (Flast - Ffirst)/(n - 1)
            }
            w<-Ffirst + bla
            waveb.hts<-round(c(Ffirst, w, Flast), 6)
        }
        if (length(nir) > 0) {
            n<-readRaw(tmp[nir][1], offset = 4, nbytes = 4, 
                human = "int", size = 4, endian = "little")[[5]]
            Ffirst<-readRaw(tmp[nir][1], offset = 8, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            Flast<-readRaw(tmp[nir][1], offset = 16, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            if (Ffirst > Flast) {
                c<-Ffirst
                Ffirst<-Flast
                Flast<-c
            }
            bla<-c(rep(NA, n - 2))
            for (k in 1:(n - 2)) {
                bla[k]<-k * (Flast - Ffirst)/(n - 1)
            }
            w<-Ffirst + bla
            waveb.mpa<-round(c(Ffirst, w, Flast), 6)
        }
    }
    if (length(mir) > 0) {
        mir.spec<-matrix(nrow = nrow(mir.ad), ncol = length(waveb.hts), 
            dimnames = list(rownames(mir.ad), waveb.hts))
        mir.spec.tmp<-matrix(nrow = length(mir), ncol = length(waveb.hts), 
            dimnames = list(test.2, waveb.hts))
        for (i in 1:length(tmp[mir])) {
            n<-readRaw(tmp[mir][i], offset = 4, nbytes = 4, 
                human = "int", size = 4, endian = "little")[[5]]
            Ffirst<-readRaw(tmp[mir][i], offset = 8, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            Flast<-readRaw(tmp[mir][i], offset = 16, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            spec<-readRaw(tmp[mir][i], offset = 544, nbytes = (4 * 
                n), human = "real", size = 4, endian = "little")[[5]]
            if (Ffirst > Flast) {
                c<-Ffirst
                Ffirst<-Flast
                Flast<-c
                spec<-rev(spec)
            }
            if (round(Ffirst, 6) == waveb.hts[1] & n == length(waveb.hts)) {
                mir.spec.tmp[i, ]<-spec
            }
            else {
                bla<-c(rep(NA, n - 2))
                for (k in 1:(n - 2)) {
                  bla[k]<-k * (Flast - Ffirst)/(n - 1)
                }
                w<-Ffirst + bla
                wa<-round(c(Ffirst, w, Flast), 6)
                mir.spec.tmp[i, ]<-round(spline(wa, spec, method = "natural", 
                  xout = waveb.hts)[[2]], 6)
                for (l in 1:length(wa)) {
                  if ((waveb.hts[l] > wa[1]) == T) 
                    break
                  if (waveb.hts[l] < wa[1]) {
                    mir.spec.tmp[i, l]<-NA
                  }
                }
                for (m in (length(waveb.hts)):(length(waveb.hts) - 
                  length(wa))) {
                  if ((waveb.hts[m] < wa[length(wa)]) == T) 
                    break
                  if (waveb.hts[m] > wa[length(wa)]) {
                    mir.spec.tmp[i, m]<-NA
                  }
                }
            }
        }
        for (i in 1:length(a)) {
            if (length(mir.spec.tmp[b[[i]]]) > 1) {
                mir.spec[i, ]<-colMeans(mir.spec.tmp[b[[i]], 
                  ])
            }
            if (length(mir.spec.tmp[b[[i]]]) == 1) {
                mir.spec[i, ]<-mir.spec.tmp[b[[i]], ]
            }
        }
        if (dim(mir.spec)[1] < 1000) {
            f<-1
        }
        else {
            f<-round(dim(mir.spec)[1]/1000, 0) + 1
        }
        g<-1
        for (i in 1:f) {
            plot(mir.spec[g, ] ~ waveb.hts, type = "l", ylim = c(min(mir.spec, 
                na.rm = T), max(mir.spec, na.rm = T)), xlab = "Wavebands (cm^-1)", 
                ylab = "Absorption")
            if (dim(mir.spec)[1] > 1) {
                for (j in (g + 1):(if ((dim(mir.spec)[1] - g) < 
                  1000) {
                  g + dim(mir.spec)[1] - g
                }
                else {
                  (g + 999)
                })) {
                  lines(mir.spec[j, ] ~ waveb.hts)
                }
            }
            test<-menu(c("Spectra ok - please continue", "Spectra not ok - please stop"), 
                graphics = T)
            graphics.off()
            if (test == 2) 
                stop("You stopped importing those spectra")
            g<-g + 1000
        }
    }
    
    if (length(mir) > 0) {  
     #Get laser wavenumber
laser.all<-c()
Laser_Wavelength<-c()
for (i in 1:length(tmp)) {
	 bla<-readRaw(tmp[i], offset = 4, nbytes = 4, human = "int", 
            size = 4, endian = "little")[[5]]
test<-readRaw(tmp[i],offset = (bla * 4 + 544 + 64), nbytes = 428,human="char",endian="little");

test<-blockString(test);test
test<-strsplit(test,"..",fixed=T);
lwn<-as.vector(substr(test[[1]],1,3))
y<-which(lwn=="LWN")
Laser_Wavelength[i]<-as.numeric(substr(test[[1]][y],6,nchar(test[[1]][y])))
laser.all<-c(laser.all,Laser_Wavelength[i])
	}
 #Get limits for plotting  the laser wavelength
   icraf<- ifelse(model=="MODEL = Alpha", 11602.1,15798.4)

#daw<-Laser_Wavelength[1]

#mn<-min(icraf,daw)
#mx<-max(icraf,daw)
#Scaling for the laserwavelegth plot
#a<-mn-5
#b<-mx+5

#Check the Laserwavenumber
plot(laser.all,pch=19,cex=0.5,col="red",xlab="Samples scanned",ylab="Laser-Wavelength",main="Laser-wavelength trend", sub=paste("Continous blue line=ICRAF ", paste(substr(model,9,29),sep=""),sep=""),ylim=c(0.999*(icraf),(icraf+10.3)))
abline(h=icraf,col="blue",lty=1,lwd=2)


# Check the trend of the wavenumbers and decide:
test<-menu(c("Spectral Laser-Wavelength ok - please continue","Spectral Laser-Wavelength off - please tune up the instrument"),graphics=T)
graphics.off();
if(test==2)stop("Decide which spectra were completely off");
}


    if (length(nir) > 0) {
        nir.spec<-matrix(nrow = nrow(nir.ad), ncol = length(waveb.mpa), 
            dimnames = list(rownames(nir.ad), waveb.mpa))
        for (i in 1:length(tmp[nir])) {
            n<-readRaw(tmp[nir][i], offset = 4, nbytes = 4, 
                human = "int", size = 4, endian = "little")[[5]]
            Ffirst<-readRaw(tmp[nir][i], offset = 8, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            Flast<-readRaw(tmp[nir][i], offset = 16, nbytes = 8, 
                human = "real", size = 8, endian = "little")[[5]]
            spec<-readRaw(tmp[nir][i], offset = 544, nbytes = (4 * 
                n), human = "real", size = 4, endian = "little")[[5]]
            if (Ffirst > Flast) {
                c<-Ffirst
                Ffirst<-Flast
                Flast<-c
                spec<-rev(spec)
            }
            if (round(Ffirst, 6) == waveb.mpa[1] & n == length(waveb.mpa)) {
                nir.spec[i, ]<-spec
            }
            else {
                bla<-c(rep(NA, n - 2))
                for (k in 1:(n - 2)) {
                  bla[k]<-k * (Flast - Ffirst)/(n - 1)
                }
                w<-Ffirst + bla
                wa<-round(c(Ffirst, w, Flast), 6)
                nir.spec[i, ]<-round(spline(wa, spec, method = "natural", 
                  xout = waveb.mpa)[[2]], 6)
                for (l in 1:length(wa)) {
                  if ((waveb.mpa[l] > wa[1]) == T) 
                    break
                  if (waveb.mpa[l] < wa[1]) {
                    nir.spec[i, l]<-NA
                  }
                }
                for (m in (length(waveb.mpa)):(length(waveb.mpa) - 
                  length(wa))) {
                  if ((waveb.mpa[m] < wa[length(wa)]) == T) 
                    break
                  if (waveb.mpa[m] > wa[length(wa)]) {
                    nir.spec[i, m]<-NA
                  }
                }
            }
        }
        if (dim(nir.spec)[1] < 1000) {
            f<-1
        }
        else {
            f<-round(dim(nir.spec)[1]/1000, 0) + 1
        }
        g<-1
        for (i in 1:f) {
            plot(nir.spec[g, ] ~ waveb.mpa, type = "l", ylim = c(min(nir.spec, 
                na.rm = T), max(nir.spec, na.rm = T)), xlab = "Wavebands (cm^-1)", 
                ylab = "Absorption")
            if (dim(nir.spec)[1] > 1) {
                for (j in (g + 1):(if ((dim(nir.spec)[1] - g) < 
                  1000) {
                  g + dim(nir.spec)[1] - g
                }
                else {
                  (g + 999)
                })) {
                  lines(nir.spec[j, ] ~ waveb.mpa)
                }
            }
            test<-menu(c("Spectra ok - please continue", "Spectra not ok - please stop"), 
                graphics = T)
            graphics.off()
            if (test == 2) 
                stop("You stopped importing those spectra")
            g<-g + 1000
        }
    }
       
  if (length(nir) > 0) {  
     #Get laser wavenumber
laser.all<-c()
Laser_Wavelength<-c()
for (i in 1:length(tmp)) {
	 bla<-readRaw(tmp[i], offset = 4, nbytes = 4, human = "int", 
            size = 4, endian = "little")[[5]]
test<-readRaw(tmp[i],offset = (bla * 4 + 544 + 64), nbytes = 428,human="char",endian="little");

test<-blockString(test);test
test<-strsplit(test,"..",fixed=T);
lwn<-as.vector(substr(test[[1]],1,3))
y<-which(lwn=="LWN")
Laser_Wavelength[i]<-as.numeric(substr(test[[1]][y],6,nchar(test[[1]][y])))
laser.all<-c(laser.all,Laser_Wavelength[i])
	}
 #Get limits for plotting  the laser wavelength
   icraf<- ifelse(model=="MODEL = MPA", 15798.4,15798.4)

#Check the Laserwavenumber
plot(laser.all,pch=19,cex=0.5,col="red",xlab="Samples scanned",ylab="Laser-Wavelength",main="Laser-wavelength trend", sub=paste("Continous blue line=ICRAF ", paste(substr(model,9,29),sep=""),sep=""),ylim=c(0.999*(icraf),(icraf+10.3)))
abline(h=icraf,col="blue",lty=1,lwd=2)


# Check the trend of the wavenumbers and decide:
test<-menu(c("Spectral Laser-Wavelength ok - please continue","Spectral Laser-Wavelength off - please tune up the instrument"),graphics=T)
graphics.off();
if(test==2)stop("Decide which spectra were completely off");
}

    if (length(mir) > 0 & length(nir) > 0) {
        round(nir.spec, 6)
        round(mir.spec, 6)
        output<-list(mir.spectra = mir.spec, mir.additional.information = mir.ad, 
            nir.spectra = nir.spec, nir.additional.information = nir.ad,output)
        class(output)<-"read.spc"
        if (sav == "T") {
            if (path != "") {
                setwd(path)
            }
            if (save.as == "workspace") {
                save(output, file = out)
            }
            if (save.as == "csv.file") {
                write.table(mir.spec, file = paste("Mir.", out, 
                  ".csv", sep = ""), dec = ".", sep = ",")
                write.table(nir.spec, file = paste("Nir.", out, 
                  ".csv", sep = ""), dec = ".", sep = ",")
            }
        }
       return(output)
    }
    if (length(mir) > 0 & length(nir) == 0) {
        round(mir.spec, 6)
        
        resu<-cbind(mir.ad,mir.spec)[,-c(2:4)]
        if(model=="MODEL = Alpha"){
ssn<-strsplit(resu$SSN,"_",fixed=FALSE)
snll<-c()
snij.all<-c()
for (i in 1:length(ssn))
{
	snl<-length(ssn[[i]])
	snij<-c()
	for (j in 1:(snl)){
	sni<-ssn[[i]][j]
		snij<-paste(snij,sni,sep="")}
snij.all<-c(snij.all,snij)
}
resu$SSN<-substr(snij.all,1,9)
}
  output<-list(spectra = mir.spec, additional.information = mir.ad,raw.spectra=resu)

        if(model!="MODEL = Alpha"){
ssn<-strsplit(resu$SSN,"_",fixed=FALSE)
snll<-c()
snij.all<-c()
for (i in 1:length(ssn))
{
	snl<-length(ssn[[i]])
	snij<-c()
	for (j in 1:(snl)){
	sni<-ssn[[i]][j]
		snij<-paste(snij,sni,sep="")}
snij.all<-c(snij.all,snij)
}
resu$SSN<-paste(substr(snij.all,1,9),substr(snij.all,10,10),sep="_")
}
 output<-list(spectra = mir.spec, additional.information = mir.ad,raw.spectra=resu)
 
        class(output)<-"read.spc"
        if (sav == "T") {
            if (path != "") {
                setwd(path)
            }
            if (save.as == "workspace") {
                save(output, file = out)
            }
            if (save.as == "csv.file") {
                write.table(mir.spec, file = paste(out, ".csv", 
                  sep = ""), dec = ".", sep = ",")
            }
        }
        return(output)
    }
    if (length(nir) > 0 & length(mir) == 0) {
        round(nir.spec, )
        resu<-cbind(nir.ad,nir.spec)[,-c(2:4)]
        ssn<-strsplit(resu$SSN,"_",fixed=FALSE)
snll<-c()
snij.all<-c()
for (i in 1:length(ssn))
{
	snl<-length(ssn[[i]])
	snij<-c()
	for (j in 1:(snl)){
	sni<-ssn[[i]][j]
		snij<-paste(snij,sni,sep="")}
snij.all<-c(snij.all,snij)
}
resu$SSN<-substr(snij.all,1,9)


        output<-list(spectra = nir.spec, additional.information = nir.ad,raw.spectra=resu)
        class(output)<-"read.spc"
        if (sav == "T") {
            if (path != "") {
                setwd(path)
            }
            if (save.as == "workspace") {
                save(output, file = out)
            }
            if (save.as == "csv.file") {
                write.table(nir.spec, file = paste(out, ".csv", 
                  sep = ""), dec = ".", sep = ",")
            }
        }
        
        return(output)
    }
    
}