Merge pull request #26 from r-hyperspec/feature/move-remaining

Update count_lines.R, read_asc_Andor, & Perkin from `hyperSpec`

DESCRIPTION

@@ -4,10 +4,12 @@ Title: File Import Functions for Spectra in Various ASCII or Text File Formats
 Version: 0.0.0.9001
 Maintainer: Erick Oduniyi <eeoduniyi@gmail.com>
 Authors@R: c(
-    person("Claudia",   "Beleites",  role = c("aut"), email = "Claudia.Beleites@chemometrix.gmbh"),
-    person("Erick",     "Oduniyi", role = c("aut","cre"), email = "eeoduniyi@gmail.com"),
+    person("Claudia", "Beleites", role = c("aut"), email = "Claudia.Beleites@chemometrix.gmbh"),
+    person("Erick", "Oduniyi", role = c("aut","cre"), email = "eeoduniyi@gmail.com"),
     person("Vilmantas", "Gegzna", role = c("aut")),
-    person("Bryan",     "Hanson", role = c("aut")))
+    person("Bryan", "Hanson", role = c("aut")),
+    person("Marcel", "Dahms", role = c("aut")),
+    person("Bjoern", "Egert", role = c("aut")))
 Description: File import filters for a number of file formats produced by Witec instruments.
     The imported data are returned as hyperSpec objects.
 License: MIT + file LICENSE
@@ -32,3 +34,21 @@ Suggests:
 VignetteBuilder: knitr
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
+Collate: 
+    '0temp_fileio_optional.R'
+    'count_lines.R'
+    'helpers.R'
+    'microbenchmark.R'
+    'read_txt_Witec.R'
+    'read_asc_Andor.R'
+    'read_asc_PerkinElmer.R'
+    'read_dat_Witec.R'
+    'read_ini.R'
+    'read_mat_Witec.R'
+    'read_txt_Graph_Witec.R'
+    'read_txt_Horiba.R'
+    'read_txt_Renishaw.R'
+    'read_txt_Shimadzu.R'
+    'read_txt_Witec_TrueMatch.R'
+    'read_txt_long.R'
+    'read_txt_wide.R'

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(count_lines)
+export(read_asc_Andor)
+export(read_asc_PerkinElmer)
 export(read_dat_Witec)
 export(read_ini)
 export(read_mat_Witec)

R/count_lines.R

@@ -0,0 +1,41 @@
+#' Count Lines (of an ASCII File)
+#'
+#' @param file the file name or connection
+#' @param chunksize `file` is read in chunks of `chunksize` lines.
+#' @return number of lines in file
+#' @export
+#'
+#' @concept io
+#'
+#' @author C. Beleites
+count_lines <- function(file, chunksize = 1e4) {
+  nlines <- 0
+
+  con <- file(file, open = "r")
+  on.exit(close(con))
+
+  while ((n <- length(readLines(con, n = chunksize))) > 0L) {
+    nlines <- nlines + n
+  }
+
+  nlines
+}
+
+hySpc.testthat::test(count_lines) <- function() {
+  context("count_lines")
+
+  tmpfile <- tempfile()
+  on.exit(unlink(tmpfile))
+
+  writeLines("blabla\nblubb", con = tmpfile)
+
+  test_that(
+    "file read in one chunk",
+    expect_equal(count_lines(tmpfile), 2)
+  )
+
+  test_that(
+    "file read in more chunks",
+    expect_equal(count_lines(tmpfile, chunksize = 1L), 2)
+  )
+}

R/read_asc_Andor.R

@@ -0,0 +1,46 @@
+#' Import Raman Spectra/Maps from Andor Cameras/Solis ASCII files.
+#'
+#' `read_asc_Andor()` reads Andor Solis ASCII (`.asc`) files where the first column gives the wavelength
+#' axes and the other columns the spectra.
+#'
+#' @param file filename or connection to ASCII file
+#' @param ...,quiet,dec,sep handed to [base::scan()]
+#' @return a hyperSpec object
+#' @author Claudia Beleites
+#' @seealso `vignette ("fileio")` for more information on file import and
+#'
+#' @concept io
+#'
+#' @export
+read_asc_Andor <- function(file = stop("filename or connection needed"),
+                           ..., quiet = TRUE, dec = ".", sep = ",") {
+
+  ## check for valid data connection
+  check_con(file = file)
+
+  ## read spectra
+  tmp <- readLines(file)
+  nwl <- length(tmp)
+  txt <- scan(text = tmp, dec = dec, sep = sep, quiet = quiet, ...)
+
+  dim(txt) <- c(length(txt) / nwl, nwl)
+
+  ## fix: Andor Solis may have final comma without values
+  if (all(is.na(txt [nrow(txt), ]))) {
+    txt <- txt [-nrow(txt), ]
+  }
+
+  spc <- new("hyperSpec", wavelength = txt [1, ], spc = txt [-1, ])
+
+  ## consistent file import behaviour across import functions
+  .fileio.optional(spc, file)
+}
+
+hySpc.testthat::test(read_asc_Andor) <- function() {
+  skip("Need to adapt to new package")
+  context("read_asc_Andor")
+  test_that("Andor Solis .asc text files", {
+    skip_if_not_fileio_available()
+    expect_known_hash(read_asc_Andor("fileio/asc.Andor/ASCII-Andor-Solis.asc"), "9ead937f51")
+  })
+}

R/read_asc_PerkinElmer.R

@@ -0,0 +1,43 @@
+#' File import filter PerkinElmer ASCII spectra.
+#'
+#' Imports a single spectrum in PerkinElmer's ASCII format. This function is experimental.
+#'
+#' @param file filename (or connection)
+#' @param ... further parameters are handed to [hySpc.read.txt::read_txt_long()]
+#'
+#' @return hyperSpec object
+#' @importFrom utils packageDescription
+#' @export
+#'
+#' @concept io
+#'
+read_asc_PerkinElmer <- function(file = stop("filename or connection needed"), ...) {
+  content <- readLines(con = file)
+
+  message(
+    "read_asc_PerkinElmer is experimental, hyperSpec so far has no test data for PE .asc files.",
+    " Please consider submitting your spectrum in an enhancement request to ", packageDescription("hyperSpec")$BugReports,
+    " in order to help the development of hyperSpec."
+  )
+
+  ## find beginning of DATA section
+  startDATA <- grep("DATA", content)
+
+  if (length(startDATA) != 1L) {
+    stop(
+      "read_asc_PerkinElmer so far can deal with single spectra files only.",
+      " Please file an enhancement request at", packageDescription("hyperSpec")$BugReports,
+      " with your file as an example or contact the maintainer (",
+      maintainer("hyperSpec"), ")."
+    )
+  }
+
+  ## Spectra values are stored
+  content <- content[-seq_len(startDATA)]
+
+  spc <- read_txt_long(textConnection(content), header = FALSE, sep = "\t", ...)
+  spc$filename <- NULL # not meaningful due to textConnection use
+
+  ## consistent file import behaviour across import functions
+  .fileio.optional(spc, file)
+}