Import XSYG files to R
Imports XSYG-files produced by a Freiberg Instruments lexsyg reader into R.
read_XSYG2R( file, recalculate.TL.curves = TRUE, n_records = NULL, fastForward = FALSE, import = TRUE, pattern = ".xsyg", verbose = TRUE, txtProgressBar = TRUE )
file: character or list (required ): path and file name of the XSYG file. If input is a list it should comprise only characters representing each valid path and XSYG-file names. Alternatively, the input character can be just a directory (path), in which case the function tries to detect and import all XSYG-files found in the directory.
recalculate.TL.curves: logical (with default): if set to TRUE, TL curves are returned as temperature against count values (see details for more information) Note: The option overwrites the time vs. count TL curve. Select FALSE to import the raw data delivered by the lexsyg. Works for TL curves and spectra.
n_records: numeric (with default): set the number of records to be imported; by default the function attempts to import all records
fastForward: logical (with default): if TRUE for a more efficient data processing only a list of RLum.Analysis
objects is returned.
import: logical (with default): if set to FALSE, only the XSYG file structure is shown.
pattern: regex (with default): optional regular expression if file is a link to a folder, to select just specific XSYG-files
verbose: logical (with default): enable/disable output to the terminal. If verbose is FALSE the txtProgressBar is also switched off
txtProgressBar: logical (with default): enable/disable the progress bar during import. Ignored if verbose = FALSE.
Using the option ‘import = FALSE’
A list consisting of two elements is shown:
Using the option ‘import = TRUE’ (default)
A list is provided, the list elements contain: - Sequence.Header: data.frame with information on the sequence. - Sequence.Object: RLum.Analysis
containing the curves.
How does the import function work?
The function uses the 'XML' package to parse the file structure. Each sequence is subsequently translated into an RLum.Analysis object.
General structure XSYG format
<?xml?>
<Sample>
<Sequence>
<Record>
<Curve name="first curve" />
<Curve name="curve with data">x0 , y0 ; x1 , y1 ; x2 , y2 ; x3 , y3</Curve>
</Record>
</Sequence>
</Sample>
So far, each XSYG file can only contain one <Sample></Sample>, but multiple sequences.
Each record may comprise several curves.
TL curve recalculation
On the FI lexsyg device TL curves are recorded as time against count values. Temperature values are monitored on the heating plate and stored in a separate curve (time vs. temperature). If the option recalculate.TL.curves = TRUE is chosen, the time values for each TL curve are replaced by temperature values.
Practically, this means combining two matrices (Time vs. Counts and Time vs. Temperature) with different row numbers by their time values. Three cases are considered:
CASE (1): nrow(matrix(PMT)) > nrow(matrix(HE))
Missing temperature values from the heating element are calculated using time values from the PMT measurement.
CASE (2): nrow(matrix(PMT)) < nrow(matrix(HE))
Missing count values from the PMT are calculated using time values from the heating element measurement.
CASE (3): nrow(matrix(PMT)) == nrow(matrix(HE))
A new matrix is produced using temperature values from the heating element and count values from the PMT.
Note:
Please note that due to the recalculation of the temperature values based on values delivered by the heating element, it may happen that multiple count values exists for each temperature value and temperature values may also decrease during heating, not only increase.
Advanced file import
To allow for a more efficient usage of the function, instead of single path to a file just a directory can be passed as input. In this particular case the function tries to extract all XSYG-files found in the directory and import them all. Using this option internally the function constructs as list of the XSYG-files found in the directory. Please note no recursive detection is supported as this may lead to endless loops.
This function is a beta version as the XSYG file format is not yet fully specified. Thus, further file operations (merge, export, write) should be done using the functions provided with the package 'XML'.
So far, no image data import is provided!
Corresponding values in the XSXG file are skipped.
0.6.14
##(1) import XSYG file to R (uncomment for usage) #FILE <- file.choose() #temp <- read_XSYG2R(FILE) ##(2) additional examples for pure XML import using the package XML ## (uncomment for usage) ##import entire XML file #FILE <- file.choose() #temp <- XML::xmlRoot(XML::xmlTreeParse(FILE)) ##search for specific subnodes with curves containing 'OSL' #getNodeSet(temp, "//Sample/Sequence/Record[@recordType = 'OSL']/Curve") ##(2) How to extract single curves ... after import data(ExampleData.XSYG, envir = environment()) ##grep one OSL curves and plot the first curve OSLcurve <- get_RLum(OSL.SARMeasurement$Sequence.Object, recordType="OSL")[[1]] ##(3) How to see the structure of an object? structure_RLum(OSL.SARMeasurement$Sequence.Object)
Kreutzer, S., 2025. read_XSYG2R(): Import XSYG files to R. Function version 0.6.14. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., Colombo, M., Steinbuch, L., Boer, A.d., 2025. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 1.0.1. https://r-lum.github.io/Luminescence/
Grehl, S., Kreutzer, S., Hoehne, M., 2013. Documentation of the XSYG file format. Unpublished Technical Note. Freiberg, Germany
Further reading
XML: https://en.wikipedia.org/wiki/XML
'XML', RLum.Analysis , RLum.Data.Curve , approx
Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team