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v 0.6.2, additional shimadzu support
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| Package: chromConverter | ||
| Title: Chromatographic File Converter | ||
| Version: 0.6.1 | ||
| Version: 0.6.2 | ||
| Authors@R: c( | ||
| person(given = "Ethan", family = "Bass", email = "[email protected]", | ||
| role = c("aut", "cre"), | ||
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| #' Shimadzu GCD parser | ||
| #' | ||
| #' Read 2D PDA data stream from 'Shimadzu' GCD files. | ||
| #' | ||
| #' A parser to read chromatogram data streams from 'Shimadzu' \code{.gcd} files. | ||
| #' GCD files are encoded as 'Microsoft' OLE documents. The parser relies on the | ||
| #' [olefile](https://pypi.org/project/olefile/) package in Python to unpack the | ||
| #' files. The PDA data is encoded in a stream called \code{PDA 3D Raw Data:3D Raw Data}. | ||
| #' The GCD data stream contains a segment for each retention time, beginning | ||
| #' with a 24-byte header. | ||
| #' | ||
| #' The 24 byte header consists of the following fields: | ||
| #' * 4 bytes: segment label (\code{17234}). | ||
| #' * 4 bytes: Little-endian integer specifying the sampling interval in milliseconds. | ||
| #' * 4 bytes: Little-endian integer specifying the number of values in the file. | ||
| #' * 4 bytes: Little-endian integer specifying the total number of bytes in the file | ||
| #' (However, this seems to be off by a few bytes?). | ||
| #' * 8 bytes of \code{00}s | ||
| #' | ||
| #' After the header, the data are simply encoded as 64-bit (little-endian) | ||
| #' floating-point numbers. The retention times can be (approximately?) derived | ||
| #' from the number of values and the sampling interval encoded in the header. | ||
| #' @param path Path to GCD file. | ||
| #' @param format_out Matrix or data.frame. | ||
| #' @param data_format Either \code{wide} (default) or \code{long}. | ||
| #' @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 from the chromatogram stream in \code{matrix} or | ||
| #' \code{data.frame} format, according to the value of \code{format_out}. | ||
| #' The chromatograms will be returned in \code{wide} or \code{long} format | ||
| #' according to the value of \code{data_format}. | ||
| #' @note This parser is experimental and may still need some work. It is not | ||
| #' yet able to interpret much metadata from the files. | ||
| #' @export | ||
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| read_shimadzu_gcd <- 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")) | ||
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| olefile_installed <- reticulate::py_module_available("olefile") | ||
| if (!olefile_installed){ | ||
| configure_python_environment(parser = "olefile") | ||
| } | ||
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| existing_streams <- check_streams(path, what = "chromatogram") | ||
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| dat <- lapply(existing_streams, function(stream){ | ||
| decode_shimadzu_gcd(path, stream = stream) | ||
| }) | ||
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| # infer times from "PDA.1.Method" stream | ||
| # method_metadata <- read_sz_method(path, stream = c("GUMM_Information", "ShimadzuGC.1", | ||
| # "GUC.1.METHOD")) | ||
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| if (data_format == "wide"){ | ||
| dat <- lapply(dat, function(x){ | ||
| data.frame(int = x$int, row.names = x$rt) | ||
| }) | ||
| } | ||
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| if (format_out == "matrix"){ | ||
| dat <- lapply(dat, function(x){ | ||
| as.matrix(x) | ||
| }) | ||
| } | ||
| if (length(dat) == 1){ | ||
| dat <- dat[[1]] | ||
| } | ||
| dat | ||
| } | ||
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| #' @noRd | ||
| decode_shimadzu_gcd <- function(path, stream){ | ||
| path_stream <- export_stream(path, stream = stream) | ||
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| f <- file(path_stream, "rb") | ||
| on.exit(close(f)) | ||
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| block_start <- seek(f, NA, "current") | ||
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| readBin(f, what = "integer", n = 1, size = 4) #skip | ||
| interval <- readBin(f, what = "integer",size = 4,endian = "little") | ||
| nval <- readBin(f, what = "integer", size = 4, endian = "little") | ||
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| readBin(f, what="double", size=4, n = 3, endian = "little") #skip | ||
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| signal <- readBin(f, what = "double", n = nval, endian = "little") | ||
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| times <- seq(40, nval*interval, interval)/60000 | ||
| data.frame(rt = times, int=signal) | ||
| } |
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