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feat: add support for openlab 179 files, refactored read_chemstation_ch
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added UV offsets to get_agilent_offsets

Update read_chemstation_ch.Rd
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@ethanbass
ethanbass committed Sep 24, 2023
1 parent 8e50ab9 commit 411a50e
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Showing 2 changed files with 128 additions and 51 deletions.
173 changes: 123 additions & 50 deletions R/read_chemstation_ch.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
#' @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 chromatogram in the format specified by \code{format_out}
#' (retention time x wavelength).
Expand All @@ -12,27 +14,37 @@
#' ((c) James Dillon 2014).
#' @export

read_chemstation_ch <- function(path, format_out = c("matrix","data.frame"),
read_chemstation_ch <- function(path, 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"))
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"))
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 = "")
version <- paste(version, filetype, sep = "_")
}
decoder <- switch(version,
"8" = decode_delta,
"81" = decode_double_delta,
"30" = decode_delta,
"130" = decode_delta,
"181" = decode_double_delta,
"179" = decode_double_array)
"179_GC" = decode_double_array_gc,
"179_OL" = decode_double_array_ol)

# Sample Info
# offsets <- list(sample = 858, description = 1369, method = 2574,
Expand Down Expand Up @@ -78,37 +90,33 @@ read_chemstation_ch <- function(path, format_out = c("matrix","data.frame"),
data <- as.matrix(data)
}
if (read_metadata){
meta_slots <- switch(version, "8" = 9,
"81" = 9,
"30" = 11,
"130" = 12,
"181" = 9,
"179" = 9)

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))
}
})
if (read_metadata){
meta_slots <- switch(version, "8" = 10,
"81" = 10,
"30" = 13,
"130" = 14,
"179_GC" = 10,
"179_OL" = 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)?)"
datetime <- regmatches(meta$date, gregexpr(datetime_regex, meta$date))[[1]]
datetime_formats <- c("%d-%b-%y, %H:%M:%S", "%m/%d/%Y %I:%M:%S %p", "%d/%m/%Y %I:%M:%S %p")
datetime <- as.POSIXct(datetime, tz = "UTC", tryFormats = datetime_formats)
data <- structure(data, file_version = version, sample_name = meta$sample_name,
run_date = datetime,
instrument = meta$instrument,
method = meta$method, software_version = meta$software_version,
software = meta$software, software_rev = meta$software_revision,
signal = meta$signal, detector_unit = meta$unit,
time_range = c(xmin, xmax), time_interval = mean(diff(times)),
time_unit = "Minutes", source_file = path,
data_format = data_format, parser = "chromConverter")
}
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
}
Expand Down Expand Up @@ -180,10 +188,10 @@ decode_double_delta <- function(file, offset) {
#' @note This function was adapted from the
#' \href{https://github.com/chemplexity/chromatography}{Chromatography Toolbox}
#' ((c) James Dillon 2014).
decode_double_array <- function(file, offset) {
decode_double_array_gc <- function(file, offset) {
seek(file, 0, 'end')
fsize <- seek(file, NA, "current")
offset <- 0x1800
offset <- 6144
# Read data
seek(file, offset, "start")
signal <- readBin(file, what = "double", size = 4, endian = "little",
Expand All @@ -192,6 +200,19 @@ decode_double_array <- function(file, offset) {
return(signal)
}

#' Decode double array
#' @noRd
decode_double_array_ol <- 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
Expand All @@ -217,12 +238,11 @@ decode_delta <- function(file, offset) {

segment_length <- readBin(file, "integer", n = 1, size = 1, endian = "big")
for (i in seq_len(segment_length)){
# for (i in (1:bitwAnd(buffer[1], 4095L))) {
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")
buffer[2] <- readBin(file, "integer", n = 1, size = 4 ,endian = "big")
}

signal[index] <- buffer[2]
Expand All @@ -237,8 +257,58 @@ decode_delta <- function(file, offset) {
#' Get Agilent offsets
#' @noRd
get_agilent_offsets <- function(version){
if (version %in% c("179","181")){
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_GC", "179_OL", "181")){
offsets <- list(
version = 326,
file_type = 347, #0x15B
sample_name = 858, #0x35A
operator = 1880, #0x758
Expand All @@ -260,34 +330,36 @@ get_agilent_offsets <- function(version){
# sequence_line_or_injection = 252, #UINT16
# injection_or_sequence_line = 256, #UINT16
# data_offset = 264, # UINT32
start_time = 282,
# start_time = 282,
# end_time = 286,
# version_string = 326, # utf16
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_version = 3601, #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
# inlet = 2492, # utf16
instrument = 208, # utf16'
detector = 208, # utf16'
instrument = 218,
method = 228, # utf16
software_version = 355, #utf16'
software = 322, # 'utf16'
software_version = 355, #utf16'
software_revision = 405, #'utf16'
units = 580, # 'utf16'
signal = 596, # 'utf16'
Expand All @@ -296,14 +368,15 @@ get_agilent_offsets <- function(version){
data_start = 1024 #ENDIAN + 'd'
)
} else if (version %in% c("8","81")){
offsets <- list(sample_name = 24,
offsets <- list(version = 0,
file_type = 4,
sample_name = 24,
description = 86,
operator = 148,
date = 178,
detector = 208,
instrument = 218,
inlet = 208,
method = 228,
# software = 0xC11,
unit = 580,
num_times = 0x116,
rt_first = 0x11A,
Expand Down
6 changes: 5 additions & 1 deletion man/read_chemstation_ch.Rd
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