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read_chemstation_ch.R
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#' Read 'ChemStation' CH files
#'
#' Agilent \code{.ch} files come in several different varieties. This parser
#' can automatically detect and read several versions of these files from
#' 'Agilent ChemStation' and 'OpenLab', including versions \code{30} and \code{130},
#' which are generally produced by ultraviolet detectors, as well as \code{81},
#' \code{179}, and \code{181} which are generally produced by flame ionization
#' detectors.
#'
#' @importFrom bitops bitAnd bitShiftL
#' @param path Path to \code{.ch} file
#' @param format_out Matrix or data.frame.
#' @param data_format Whether to return data in \code{wide} or \code{long} format.
#' @param read_metadata Logical. Whether to attach metadata.
#' @param metadata_format Format to output metadata. Either \code{chromconverter}
#' or \code{raw}.
#' @author Ethan Bass
#' @return A 2D chromatogram in the format specified by \code{data_format} and
#' \code{format_out}. If \code{data_format} is \code{wide}, the chromatogram will
#' be returned with retention times as rows and a single column for the intensity.
#' If \code{long} format is requested, two columns will be returned: one for the
#' retention time and one for the intensity. The \code{format_out} argument
#' determines whether the chromatogram is returned as a \code{matrix} or
#' \code{data.frame}. Metadata can be attached to the chromatogram as
#' \code{\link{attributes}} if \code{read_metadata} is {TRUE}.
#' @note This function was adapted from the
#' \href{https://github.com/chemplexity/chromatography}{Chromatography Toolbox}
#' ((c) James Dillon 2014).
#' @export
read_chemstation_ch <- function(path, format_out = c("matrix", "data.frame"),
data_format = c("wide", "long"),
read_metadata = TRUE,
metadata_format = c("chromconverter", "raw")){
format_out <- match.arg(format_out, c("matrix", "data.frame"))
data_format <- match.arg(data_format, c("wide", "long"))
metadata_format <- match.arg(metadata_format, c("chromconverter", "raw"))
metadata_format <- switch(metadata_format, chromconverter = "chemstation",
raw = "raw")
f <- file(path, "rb")
on.exit(close(f))
# HEADER
seek(f, 1, "start")
version <- readBin(f, "character", n = 1)
version <- match.arg(version,
choices = c("8", "81", "30", "130", "179", "181"))
offsets <- get_agilent_offsets(version)
if (version == "179"){
seek(f, 348)
filetype <- paste(readBin(f, "character", n = 2), collapse = "")
if (filetype == "OL"){
bytes = "8b"
} else if (filetype == "GC"){
seek(f, offsets$software)
n <- get_nchar(f)
soft <- cc_collapse(readBin(f, "character", n = n))
chemstation_version <- strsplit(soft, " ")[[1]][1]
bytes <- ifelse(chemstation_version == "Mustang", "8b", "4b")
}
version <- paste(version, bytes, sep = "_")
}
decoder <- switch(version,
"8" = decode_delta,
"81" = decode_double_delta,
"30" = decode_delta,
"130" = decode_delta,
"181" = decode_double_delta,
"179_4b" = decode_double_array_4byte,
"179_8b" = decode_double_array_8byte)
# Sample Info
# offsets <- list(sample = 858, description = 1369, method = 2574,
# operator = 1880, date = 2391, instrument = 2533,
# inlet = 2492, units = 4172)
seek(f, 264, "start")
offset <- (readBin(f, "integer", n = 1, endian = "big", size = 4) - 1) * 512
data <- decoder(f, offset)
seek(f, where = 282, origin = "start")
seek(f, where = 282, origin = "start")
if (version %in% c("8", "30", "130")){
xmin <- as.double(readBin(f, "integer", n = 1, size = 4, signed = TRUE,
endian = "big")) / 60000
xmax <- as.double(readBin(f, "integer", n = 1, size = 4, signed = TRUE,
endian = "big")) / 60000
} else {
xmin <- readBin(f, "numeric", n = 1, endian = "big", size = 4) / 60000
xmax <- readBin(f, "numeric", n = 1, endian = "big", size = 4) / 60000
}
times <- seq(xmin, xmax, length.out = length(data))
seek(f, offsets$intercept, "start")
intercept <- readBin(f, "double", n = 1, endian = "big", size = 8)
if (is.na(intercept)){
intercept <- 0
}
seek(f, offsets$scaling_factor, "start")
scaling_factor <- readBin(f, "double", n = 1, endian = "big", size = 8)
data <- data * scaling_factor + intercept
if (data_format == "wide"){
data <- data.frame(Intensity = data, row.names = times)
} else if (data_format == "long"){
data <- data.frame(RT = times, Intensity = data)
}
if (format_out == "matrix"){
data <- as.matrix(data)
}
if (read_metadata){
meta_slots <- switch(version, "8" = 10,
"81" = 10,
"30" = 13,
"130" = 14,
"179_4b" = 10,
"179_8b" = 10,
"181" = 10)
meta <- lapply(offsets[seq_len(meta_slots)], function(offset){
seek(f, where = offset, origin = "start")
n <- get_nchar(f)
if (version == "30"){
readBin(f, what = "character")
} else{
cc_collapse(readBin(f, "character", n = n))
}
})
metadata_from_file <- try(read_chemstation_metadata(path), silent = TRUE)
if (!inherits(metadata_from_file, "try-error")){
meta <- c(meta, metadata_from_file)
}
datetime_regex <- "(\\d{2}-[A-Za-z]{3}-\\d{2}, \\d{2}:\\d{2}:\\d{2})|(\\d{2}/\\d{2}/\\d{4} \\d{1,2}:\\d{2}:\\d{2} (?:AM|PM)?)"
meta$date <- regmatches(meta$date, gregexpr(datetime_regex, meta$date))[[1]]
data <- attach_metadata(data, meta, format_in = metadata_format,
data_format = data_format, format_out = format_out,
parser = "chromconverter", source_file = path)
}
data
}
#' @noRd
cc_collapse <- function(x){
paste(x, collapse="")
}
#' @noRd
cc_trim_str <- function(x, len=2){
substr(x, len, nchar(x))
}
#' Find .D folder
#' @noRd
get_chemstation_dir_name <- function(path){
dir <- gsub(basename(path), "", path)
sp <- str_split_fixed(dir, "/", stringr::str_count(dir,"/")+1)[1,]
grep("\\.D|\\.d$", sp, ignore.case = TRUE, value = TRUE)
}
#' @noRd
get_nchar <- function(f){
as.numeric(readBin(f, what = "raw", n = 1))
}
#' Decode double delta array
#' @noRd
#' @note This function was adapted from the
#' \href{https://github.com/chemplexity/chromatography}{Chromatography Toolbox}
#' ((c) James Dillon 2014).
decode_double_delta <- function(file, offset) {
seek(file, 0, 'end')
fsize <- seek(file, NA, "current")
# Read data
seek(file, offset, "start")
seek(file, offset, "start")
signal <- numeric(fsize/2)
count <- 1
buffer <- numeric(3)
while (seek(file, NA, "current") < fsize) {
buffer[3] <- readBin(file, "integer", n = 1, endian = "big", size = 2)
if (buffer[3] != 32767) {
buffer[2] <- buffer[2] + buffer[3]
buffer[1] <- buffer[1] + buffer[2]
} else {
buffer[1] <- readBin(file, "integer", n=1, endian = "big", size = 2) * 4294967296
buffer[1] <- readBin(file, "integer", n=1, endian = "big", size = 4) + buffer[1]
buffer[2] <- 0
}
signal[count] <- buffer[1]
count <- count + 1
}
signal <- signal[1:(count - 1)]
return(signal)
}
#' Decode double array
#' @noRd
#' @note This function was adapted from the
#' \href{https://github.com/chemplexity/chromatography}{Chromatography Toolbox}
#' ((c) James Dillon 2014).
decode_double_array_4byte <- function(file, offset) {
seek(file, 0, 'end')
fsize <- seek(file, NA, "current")
offset <- 6144
# Read data
seek(file, offset, "start")
signal <- readBin(file, what = "double", size = 4, endian = "little",
n = (fsize - offset))
signal <- signal[seq(2, length(signal), 2)]
return(signal)
}
#' Decode double array
#' @noRd
decode_double_array_8byte <- function(file, offset) {
seek(file, 0, 'end')
fsize <- seek(file, NA, "current")
offset <- 6144
# Read data
seek(file, offset, "start")
signal <- readBin(file, what = "double", size = 8, endian = "little",
n = (fsize - offset))
return(signal)
}
#' Decode delta array
#' @noRd
#' @note This function was adapted from the
#' \href{https://github.com/chemplexity/chromatography}{Chromatography Toolbox}
#' ((c) James Dillon 2014).
decode_delta <- function(file, offset) {
seek(file, 0, 'end')
fsize <- seek(file, NA, "current")
seek(file, offset, "start")
start <- seek(file, NA, "current")
signal <- rep(NA, round((fsize - start)/2))
buffer <- rep(0, 4)
index <- 1
while (TRUE) {
head <- readBin(file, "integer", n = 1, size = 1, endian = "big")
if (head != 0x10) {
break
}
buffer[2] <- buffer[4]
segment_length <- readBin(file, "integer", n = 1, size = 1, endian = "big")
for (i in seq_len(segment_length)){
buffer[3] <- readBin(file, "integer", n = 1, size = 2, endian = "big")
if (buffer[3] != -32768L) {
buffer[2] <- buffer[2] + buffer[3]
} else {
buffer[2] <- readBin(file, "integer", n = 1, size = 4 ,endian = "big")
}
signal[index] <- buffer[2]
index <- index + 1
}
buffer[4] <- buffer[2]
}
signal <- signal[!is.na(signal)]
return(signal)
}
#' Get Agilent offsets
#' @noRd
get_agilent_offsets <- function(version){
if (version == "131_LC"){
offsets <- list(version = 326,
file_type = 347,
sample_name = 858,
operator = 1880,
date = 2391,
detector = 2492,
method = 2574,
software = 3089,
units = 3093,
sample_id = 4055,
num_times = 278, #big-endian
rt_first = 282,
rt_last = 286,
scaling_factor = 3085,
data_start = 4096
)
} else if (version == "131_OL"){
offsets <- list(version = 326,
file_type = 347,
sample_name = 858,
operator = 1880,
date = 2391,
# detector = 2492,
method = 2574,
# software = 3089,
units = 3093,
sample_id = 4055,
num_times = 278, #big-endian
rt_first = 282,
rt_last = 286,
scaling_factor = 3085,
data_start = 4096
)
} else if (version == "31"){
offsets <- list(version = 0,
file_type = 4,
sample_name = 24,
operator = 148,
date = 178,
detector = 208,
instrument = 218,
method = 228,
# unknown = 260,
num_times = 278, # big-endian
scaling_factor = 318,
units = 326,
data_start = 512
)
} else if (version %in% c("179","179_4b", "179_8b", "181")){
offsets <- list(
version = 326,
file_type = 347, #0x15B
sample_name = 858, #0x35A
operator = 1880, #0x758
date = 2391, # 0x957
instrument = 2492, # 0x9BC
method = 2574, # 0xA0E
software = 3089, # 0xC11
unit = 4172, # 0x104C
signal = 4213, # 0x1075
num_times = 278, # 0x116
rt_first = 282, # 0x11A
rt_last = 286, # 0x11E
scaling_factor = 4732, # 0x127C
intercept = 4724,
data_start = 4096 # 0x1000
)
} else if (version == "130"){
offsets <- list(
# sequence_line_or_injection = 252, #UINT16
# injection_or_sequence_line = 256, #UINT16
# data_offset = 264, # UINT32
# start_time = 282,
# end_time = 286,
version = 326, # utf16
file_type = 347, # utf16
sample_name = 858, # utf16
operator = 1880, # utf16
date = 2391, # utf16
inlet = 2492, # utf16
instrument = 2533, # utf16'
method = 2574, # utf16
software = 3089, # 'utf16'
software_version = 3601, #utf16'
software_revision = 3802, #'utf16'
sample_id = 4054,
units = 4172, # 'utf16'
signal = 4213, # 'utf16'
intercept = 4110, # INT32
scaling_factor = 4732) #ENDIAN + 'd'
} else if (version == 30){
offsets <- list(
version = 0,
file_type = 4, # utf16
sample_name = 24, # utf16
operator = 148, # utf16
date = 178, # utf16
detector = 208, # utf16'
instrument = 218,
method = 228, # utf16
software = 322, # 'utf16'
software_version = 355, #utf16'
software_revision = 405, #'utf16'
units = 580, # 'utf16'
signal = 596, # 'utf16'
intercept = 636, # INT32
scaling_factor = 644,
data_start = 1024 #ENDIAN + 'd'
)
} else if (version %in% c("8","81")){
offsets <- list(version = 0,
file_type = 4,
sample_name = 24,
description = 86,
operator = 148,
date = 178,
detector = 208,
instrument = 218,
method = 228,
unit = 580,
num_times = 0x116,
rt_first = 0x11A,
rt_last = 0x11E,
scaling_factor = 644,
intercept = 636,
data_start = 4096)
}
offsets
}
#' Parser for reading Agilent ('.dx') files into R
#' @importFrom utils unzip
#' @param path Path to \code{.dx} file.
#' @param path_out Path to directory to export unzipped files.
#' @param format_out Matrix or data.frame.
#' @param data_format Whether to return data in \code{wide} or \code{long} format.
#' @param read_metadata Logical. Whether to attach metadata.
#' @author Ethan Bass
#' @return A chromatogram in the format specified by \code{format_out}
#' (retention time x wavelength).
#' @author Ethan Bass
#' @export
read_agilent_dx <- function(path, path_out = NULL, format_out = c("matrix","data.frame"),
data_format = c("wide","long"),
read_metadata = TRUE){
format_out <- match.arg(format_out, c("matrix","data.frame"))
data_format <- match.arg(data_format, c("wide","long"))
files <- unzip(path, list = TRUE)
files.idx <- grep(".ch$", files$Name, ignore.case = TRUE)
# make temp directory
if (is.null(path_out)){
path_out <- tempdir()
on.exit(unlink(path_out), add = TRUE)
}
# copy .dx file to directory
file.copy(path, path_out)
path <- fs::path(path_out, basename(path))
# unzip .dx file
unzip(path, files = files$Name[files.idx], exdir = path_out)
# read in `.ch` files
read_chemstation_ch(fs::path(path_out, files$Name[files.idx]), format_out = format_out,
data_format = data_format, read_metadata = read_metadata)
}