read_XSYG2R: Import XSYG files to R

In R-Lum/Luminescence: Comprehensive Luminescence Dating Data Analysis

Import XSYG files to R

Description

Imports XSYG-files produced by a Freiberg Instruments lexsyg reader into R.

Usage

read_XSYG2R(
  file,
  recalculate.TL.curves = TRUE,
  fastForward = FALSE,
  import = TRUE,
  pattern = ".xsyg",
  verbose = TRUE,
  txtProgressBar = TRUE
)

Arguments

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 this case the 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.
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 or disable verbose mode. If verbose is FALSE the txtProgressBar is also switched off
txtProgressBar	logical (with default): enables TRUE or disables FALSE the progression bar during import

Details

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:

1. HE: Heating element

2. PMT: Photomultiplier tube

3. Interpolation is done using the function approx

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.

Value

Using the option import = FALSE

A list consisting of two elements is shown:

• data.frame with information on file.

• data.frame with information on the sequences stored in the XSYG file.

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.

Function version

0.6.8

How to cite

Kreutzer, S., 2023. read_XSYG2R(): Import XSYG files to R. Function version 0.6.8. 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., 2023. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.23. https://CRAN.R-project.org/package=Luminescence

Note

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.

Author(s)

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team

References

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

See Also

xml, RLum.Analysis, RLum.Data.Curve, approx

Examples

##(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)

R-Lum/Luminescence documentation built on March 2, 2024, 12:39 p.m.