R/read_softmax6_xml.R

In briandconnelly/softermax: Read Exported Data from 'SoftMax Pro'

# Read absorbance information about a single well <Well>
read_softmax6_xml_plate_well_absorbance <- function(w) {
    well_attrs <- xml2::xml_attrs(w)
    rawdata <- xml2::xml_find_first(w, ".//RawData")
    timedata <- xml2::xml_find_first(w, ".//TimeData")

    softermax.well(
        name = well_attrs[["Name"]],
        times = as.numeric(strsplit(xml2::xml_text(timedata), " ")[[1]]),
        values = as.numeric(strsplit(xml2::xml_text(rawdata), " ")[[1]]),
        attrs = list(
            ID = well_attrs[["WellID"]],
            row = as.integer(well_attrs[["Row"]]),
            col = as.integer(well_attrs[["Col"]])
        )
    )
}


# Read information about a plate <PlateSection>
read_softmax6_xml_plate <- function(p) {
    plate_attrs <- xml2::xml_attrs(p)
    inst_attrs <- xml2::xml_attrs(
        xml2::xml_find_first(p, ".//InstrumentSettings")
    )

    wavelengths <- unlist(
        lapply(
            X = xml2::xml_find_all(
                p,
                xpath = ".//InstrumentSettings/WavelengthSettings/Wavelength"
            ),
            FUN = function(x) as.numeric(xml2::xml_text(x))
        )
    )

    temps_raw <- xml2::xml_find_first(p, ".//TemperatureData")

    # TODO: maybe don't stop(), but just don't read the unsupported plate?
    read_mode <- inst_attrs[["ReadMode"]]
    well_fn <- switch(read_mode,
                      "Absorbance" = read_softmax6_xml_plate_well_absorbance,
                      #"Luminescence" = read_softmax6_xml_plate_well_luminescence,
                      stop(sprintf("'%s' read mode is unsupported", read_mode),
                           call. = FALSE))

    softermax.plate(
        name = plate_attrs[["Name"]],
        wavelengths = lapply(
            X = xml2::xml_find_all(p, ".//Wavelengths/Wavelength"),
            FUN = function(x) {
                softermax.wavelength(
                    wavelength = wavelengths[as.integer(xml2::xml_attr(x, "WavelengthIndex"))],
                    wells = lapply(
                        X = xml2::xml_find_all(x, ".//Well"),
                        FUN = well_fn
                    )
                )

            }
        ),
        temperatures = as.numeric(
            strsplit(xml2::xml_text(temps_raw), " ")[[1]]
        ),
        attrs = list(
            type = inst_attrs[["PlateType"]],
            barcode = xml2::xml_text(xml2::xml_find_first(p, ".//Barcode")),
            read_time = readr::parse_datetime(
                plate_attrs[["ReadTime"]],
                format = "%T %p %m/%d/%Y"
            ),
            instrument_info = plate_attrs[["InstrumentInfo"]],
            instrument_settings = list(
                read_mode = inst_attrs[["ReadMode"]],
                read_type = inst_attrs[["ReadType"]],
                # TODO: <Automix>
                # TODO: <MoreSettings>
                wavelengths = wavelengths
            )
        )
    )
}

read_softmax6_xml_experiment <- function(e) {
    softermax.experiment(
        name = "unknown",
        plates = lapply(
            X = xml2::xml_find_all(e, ".//PlateSections/PlateSection"),
            FUN = read_softmax6_xml_plate
        ),
        notes = list()
    )
}


#' @rdname read_softmax_xml
#' @export
read_softmax6_xml <- function(file, ...) {
    datafile <- xml2::read_xml(file, ...)

    d <- softermax(
        experiments = list(read_softmax6_xml_experiment(datafile))
    )

    class(d) <- append(class(d), "softermax6")
    d
}