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r-hyperspec / hySpc.read.txt

Import ASCII formatted data into hyperSpec
https://r-hyperspec.github.io/hySpc.read.txt/
MIT License
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Code from `fileio.Rmd` vignette for unit tests #79

Open GegznaV opened 2 years ago

GegznaV commented 2 years ago

This issue is to continue discussion that started as:

The original message:

This is the code from fileio.Rmd which could be used to create unit tests: fileio-for-unit-tests.zip as stated in

untangle historic mix with unit tests into vignette and unit tests

The contents of 'fileio-for-unit-tests.zip': ```r # ============================================================================ # =========== R code extracted from fileio.Rmd vignette ====================== # ============================================================================ ## ----setup-io, include=FALSE--------------------------------------------------------- # Packages ------------------------------------------------------------------- library(hyperSpec) library(R.matlab) ## ----array--------------------------------------------------------------------------- data <- array(1:24, 4:2) wl <- c(550, 630) x <- c(1000, 1200, 1400) y <- c(1800, 1600, 1400, 1200) data ## ----array-import-------------------------------------------------------------------- d <- dim(data) dim(data) <- c(d[1] * d[2], d[3]) x <- rep(x, each = d[1]) y <- rep(y, d[2]) spectra <- new("hyperSpec", spc = data, data = data.frame(x, y), wavelength = wl ) ## ------------------------------------------------------------------------------------ y <- seq_len(d[1]) x <- seq_len(d[2]) ## ----readcollapse-------------------------------------------------------------------- files <- Sys.glob("fileio/spc.Kaisermap/*.spc") files <- files[seq(1, length(files), by = 2)] # import low wavenumber region only spc <- lapply(files, read.spc) length(spc) spc[[1]] spc <- collapse(spc) spc ## ----read.txt.t---------------------------------------------------------------------- file <- read.table("fileio/txt.t/Triazine 5_31.txt", header = TRUE, dec = ",", sep = "\t") triazine <- new("hyperSpec", wavelength = file[, 1], spc = t(file[, -1]), data = data.frame(sample = colnames(file[, -1])), labels = list( .wavelength = expression(2 * theta / degree), spc = "I / a.u." ) ) triazine ## ----plot-triazine, fig.cap=CAPTION-------------------------------------------------- plot(triazine[1]) ## ------------------------------------------------------------------------------------ read.jdx("fileio/jcamp-dx/shimadzu.jdx", encoding = "latin1", keys.hdr2data = TRUE) read.jdx("fileio/jcamp-dx/virgilio.jdx") ## ------------------------------------------------------------------------------------ read.jdx("fileio/jcamp-dx/virgilio.jdx", ytol = 1e-9) ## ----nist-aes------------------------------------------------------------------------ file <- readLines("fileio/NIST/mercurytable2.htm") # file <- readLines("http://physics.nist.gov/PhysRefData/Handbook/Tables/mercurytable2.htm") file <- file[-(1:grep("Intensity.*Wavelength", file) - 1)] file <- file[1:(grep("", file) [1] - 1)] file <- gsub("<[^>]*>", "", file) file <- file[!grepl("^[[:space:]]+$", file)] colnames <- file[1] colnames <- gsub("[[:space:]][[:space:]]+", "\t", file[1]) colnames <- strsplit(colnames, "\t")[[1]] if (!all(colnames == c("Intensity", "Wavelength (Å)", "Spectrum", "Ref. "))) { stop("file format changed!") } tablestart <- grep("^[[:blank:]]*[[:alpha:]]+$", file) + 1 tableend <- c(tablestart[-1] - 2, length(file)) tables <- list() for (t in seq_along(tablestart)) { tmp <- file[tablestart[t]:tableend[t]] tables[[t]] <- read.fwf(textConnection(tmp), c(5, 8, 12, 15, 9)) colnames(tables[[t]]) <- c("Intensity", "persistent", "Wavelength", "Spectrum", "Ref. ") tables[[t]]$type <- gsub("[[:space:]]", "", file[tablestart[t] - 1]) } tables <- do.call(rbind, tables) levels(tables$Spectrum) <- gsub(" ", "", levels(tables$Spectrum)) Hg.AES <- list() for (s in levels(as.factor(tables$Spectrum))) { Hg.AES[[s]] <- new("hyperSpec", wavelength = tables$Wavelength[tables$Spectrum == s], spc = tables$Intensity[tables$Spectrum == s], data = data.frame(Spectrum = s), label = list( .wavelength = expression(lambda / ring(A)), spc = "I" ) ) } ## ----plot-hg-aes, fig.cap=CAPTION---------------------------------------------------- plot(collapse(Hg.AES), lines.args = list(type = "h"), col = 1:2) ## ------------------------------------------------------------------------------------ library(R.matlab) ## ----eval=FALSE---------------------------------------------------------------------- ## **V. Gegznas's notes**: ## FIXME:`file `spectra.mat` is not present. spc.mat <- readMat("fileio/spectra.mat") ## ----eval=FALSE---------------------------------------------------------------------- ## **V. Gegznas's notes**: ## FIXME: there are issues in downloading `Rcompression` package as omegahat.org ## does not update as quickly as a new version of R is released. install.packages("Rcompression", repos = "http://www.omegahat.org/R") ## ----read.mat.Cytospec-blocks-------------------------------------------------------- read.mat.Cytospec("fileio/mat.cytospec/cytospec.mat", blocks = TRUE) ## ----read.mat.Cytospec--------------------------------------------------------------- read.mat.Cytospec("fileio/mat.cytospec/cytospec.mat", blocks = 1) ## ----read.ENVI----------------------------------------------------------------------- spc <- read.ENVI("fileio/ENVI/example2.img") spc ## ------------------------------------------------------------------------------------ read.spc("fileio/spc.Kaisermap/ebroAVII.spc", keys.hdr2data = TRUE) ## ------------------------------------------------------------------------------------ read.spc("fileio/spc.Kaisermap/ebroAVII.spc", keys.log2data = TRUE) ## ----read.spc.list-old--------------------------------------------------------------- barbiturates <- read.spc("fileio/spc/BARBITUATES.SPC") ## ------------------------------------------------------------------------------------ class(barbiturates) ## ------------------------------------------------------------------------------------ length(barbiturates) ## ------------------------------------------------------------------------------------ barbiturates <- collapse(barbiturates, collapse.equal = FALSE) barbiturates ## ------------------------------------------------------------------------------------ barbiturates[[1:10, , 25 ~ 30]] ## ----eval=FALSE---------------------------------------------------------------------- header <- list( samples = 64 * no.images.in.row, lines = 64 * no.images.in.column, bands = no.data.points.per.spectrum, `data type` = 4, interleave = "bip" ) ## ----readENVINicolet----------------------------------------------------------------- spc <- read.ENVI.Nicolet("fileio/ENVI/example2.img", nicolet.correction = TRUE) spc ## dummy sample with all intensities zero ## ----Kaiser.txt.comma---------------------------------------------------------------- ## 1. import as character tmp <- scan("fileio/txt.Kaiser/test-lo-4.txt", what = rep("character", 4), sep = ",") tmp <- matrix(tmp, nrow = 4) ## 2. concatenate every two columns by a dot wl <- apply(tmp[1:2, ], 2, paste, collapse = ".") spc <- apply(tmp[3:4, ], 2, paste, collapse = ".") ## 3. convert to numeric and create hyperSpec objectne, though). spc <- new("hyperSpec", spc = as.numeric(spc), wavelength = as.numeric(wl)) spc ## ----readspcKaiserMap---------------------------------------------------------------- files <- Sys.glob("fileio/spc.Kaisermap/*.spc") spc.low <- read.spc.KaiserMap(files[seq(1, length(files), by = 2)]) spc.high <- read.spc.KaiserMap(files[seq(2, length(files), by = 2)]) wl(spc.high) <- wl(spc.high) + 1340 spc ## ----read.txt.Renishaw--------------------------------------------------------------- paracetamol <- read.txt.Renishaw("fileio/txt.Renishaw/paracetamol.txt", "spc") paracetamol ## ------------------------------------------------------------------------------------ read.txt.Renishaw("fileio/txt.Renishaw/laser.txt.gz", data = "ts") ## ----read.txt.Renishaw-file---------------------------------------------------------- read.txt.Renishaw("fileio/txt.Renishaw/chondro.txt", nlines = 1e5, nspc = 875) ## ----read.txt.Renishaw-compressed, results='hide'------------------------------------ read.txt.Renishaw("fileio/txt.Renishaw/chondro.gz") read.txt.Renishaw("fileio/txt.Renishaw/chondro.xz") read.txt.Renishaw("fileio/txt.Renishaw/chondro.lzma") read.txt.Renishaw("fileio/txt.Renishaw/chondro.gz") read.txt.Renishaw("fileio/txt.Renishaw/chondro.bz2") read.zip.Renishaw("fileio/txt.Renishaw/chondro.zip") ## ----Horiba-------------------------------------------------------------------------- spc <- read.txt.Horiba("fileio/txt.HoribaJobinYvon/ts.txt", cols = list( t = "t / s", spc = "I / a.u.", .wavelength = expression(Delta * tilde(nu) / cm^-1) ) ) spc ## ----testHoriba-1-------------------------------------------------------------------- spc <- read.txt.Horiba.xy("fileio/txt.HoribaJobinYvon/map.txt") if (any(dim(spc) != c(141, 4, 616)) || any(abs(spc) < .Machine$double.eps^.5) || is.null(spc$x) || any(is.na(spc$x)) || is.null(spc$y) || any(is.na(spc$y)) || length(setdiff(wl(spc), 1:616)) == 0L) { stop("error in testing read.txt.Horiba.xy. Please contact ", maintainer("hyperSpec")) } spc ## ----testHoriba-2-------------------------------------------------------------------- spc <- read.txt.Horiba.t("fileio/txt.HoribaJobinYvon/ts.txt") if (any(dim(spc) != c(100, 3, 1024)) || is.null(spc$t) || any(is.na(spc$t)) || length(setdiff(wl(spc), 1:1024)) == 0L) { stop("error in testing read.txt.Horiba.xy. Please contact ", maintainer("hyperSpec")) } spc rm(spc) ## ------------------------------------------------------------------------------------ read.asc.Andor("fileio/asc.Andor/ASCII-Andor-Solis.asc") ## ----witec-spc, results='hide'------------------------------------------------------- read.spc("fileio/spc.Witec/Witec-timeseries.spc") read.spc("fileio/spc.Witec/Witec-Map.spc") ## ----witec-dat, results='hide'------------------------------------------------------- read.dat.Witec("fileio/txt.Witec/Witec-timeseries-x.dat") read.dat.Witec( filex = "fileio/txt.Witec/Witec-Map-x.dat", points.per.line = 5, lines.per.image = 5, type = "map" ) ## ----witec-txt, include=FALSE-------------------------------------------------------- read.txt.Witec("fileio/txt.Witec/Witec-timeseries_no.txt") ## ----witec-txt-textfiles, include=FALSE---------------------------------------------- headline <- c( "with exported labels and units headerlines:", "\nwith exported labels headerline:", "\nwith exported units headerline:", "\nwithout headerline:" ) files <- c( "fileio/txt.Witec/Witec-timeseries_full.txt", "fileio/txt.Witec/Witec-timeseries_label.txt", "fileio/txt.Witec/Witec-timeseries_unit.txt", "fileio/txt.Witec/Witec-timeseries_no.txt" ) for (f in seq_along(files)) { cat(headline[f], "\n") tmp <- format(as.matrix(read.table(files[f], sep = "\t")[1:4, 1:3])) apply(tmp, 1, function(l) cat(l, "\n")) } ## ----witec-txt-map, include=FALSE---------------------------------------------------- read.txt.Witec("fileio/txt.Witec/Witec-Map_full.txt", type = "map", hdr.label = TRUE, hdr.units = TRUE) read.txt.Witec("fileio/txt.Witec/Witec-Map_label.txt", type = "map", hdr.label = TRUE, hdr.units = FALSE) read.txt.Witec("fileio/txt.Witec/Witec-Map_unit.txt", type = "map", hdr.label = FALSE, hdr.units = TRUE) read.txt.Witec("fileio/txt.Witec/Witec-Map_unit.txt", type = "map", hdr.label = FALSE, hdr.units = TRUE, points.per.line = 5 ) read.txt.Witec("fileio/txt.Witec/Witec-Map_no.txt", type = "map", hdr.label = FALSE, hdr.units = FALSE) read.txt.Witec("fileio/txt.Witec/Witec-Map_no.txt", type = "map", hdr.label = FALSE, hdr.units = FALSE, lines.per.image = 5 ) read.txt.Witec("fileio/txt.Witec/Witec-Map_no.txt", type = "map", hdr.label = FALSE, hdr.units = FALSE, points.per.line = 5, lines.per.image = 5 ) ## ----witec-txt-Graph, results='hide'------------------------------------------------- read.txt.Witec.Graph("fileio/txt.Witec/Witec-timeseries (Header).txt") read.txt.Witec.Graph("fileio/txt.Witec/Witec-Map (Header).txt", type = "map") read.txt.Witec.Graph("fileio/txt.Witec/nofilename (Header).txt", encoding = "latin1") ## ----comment="", eval=TRUE, echo=FALSE, class.output="add-border sourceCode r"------- writeLines(readLines("read.txt.PerkinElmer.R")) ## ----read.txt.PerkinElmer, message=FALSE--------------------------------------------- source("read.txt.PerkinElmer.R") read.txt.PerkinElmer(Sys.glob("fileio/txt.PerkinElmer/flu?.txt"), skip = 54) ``` *** Please, close tis issue when it gets not relevant.