Luminescence (version 0.4.1)

readXSYG2R: Import XSYG files to R

Description

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

Usage

readXSYG2R(file, recalculate.TL.curves = TRUE, import = TRUE, 
    txtProgressBar = TRUE)

Arguments

file

character (required): path and file name of the XSYG file.

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

import

logical (with default): if set to FALSE, only the XSYG file structure is shown.

txtProgressBar

logical (with default): enables TRUE or disables FALSE the progression bar during import

Value

• Using the option import = FALSE A list consisting of two elements is shown:
• Sample
  data.frame with information on file.
• Sequences
  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

0.4 (2014-12-02 11:50:22)

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 x0 , y0 ; x1 , y1 ; x2 , y2 ; x3 , y3 So far, each XSYG file can only contain one , 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: HE: Heating element PMT: Photomultiplier tube 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 mutiple count values exists for each temperature value and temperature values may also decrease during heating, not only increase.

References

Grehl, S., Kreutzer, S., Hoehne, M., 2013. Documentation of the XSYG file format. Unpublished Technical Note. Freiberg, Germany Further reading XML: http://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 <- readXSYG2R(FILE)

##(2) additional examples for pure XML import using the package XML
##    (uncomment for usage)

  ##import entire XML file 
  #FILE <- file.choose()
  #temp <- xmlRoot(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.Analysis(OSL.SARMeasurement$Sequence.Object, recordType="OSL")[[1]]

##(3) How to see the structure of an object?
get_structure.RLum.Analysis(OSL.SARMeasurement$Sequence.Object)