Import Princeton Instruments (TM) SPE-file into R

Function imports Princeton Instruments (TM) SPE-files into R environment and provides RLum.Data.Image objects as output.

Usage

read_SPE2R(
  file,
  output.object = "RLum.Data.Image",
  frame.range,
  txtProgressBar = TRUE,
  verbose = TRUE,
  ...
)

Arguments

file

character (required): SPE-file name (including path), e.g.

[WIN]: read_SPE2R("C:/Desktop/test.spe")
[MAC/LINUX]: read_SPE2R("/User/test/Desktop/test.spe"). Additionally, it can be a URL starting with http:// or https://.

output.object

character (with default): set RLum output object. Allowed types are "RLum.Data.Spectrum", "RLum.Data.Image" or "matrix"

frame.range

vector (optional): limit frame range, e.g. select first 100 frames by frame.range = c(1,100)

txtProgressBar

logical (with default): enables or disables txtProgressBar.

verbose

logical (with default): enables or disables verbose mode

...

not used, for compatibility reasons only

Value

Depending on the chosen option the functions returns three different type of objects:

output.object

RLum.Data.Spectrum

An object of type RLum.Data.Spectrum is returned. Row sums are used to integrate all counts over one channel.

RLum.Data.Image

An object of type RLum.Data.Image is returned. Due to performance reasons the import is aborted for files containing more than 100 frames. This limitation can be overwritten manually by using the argument frame.range.

matrix

Returns a matrix of the form: Rows = Channels, columns = Frames. For the transformation the function get_RLum is used, meaning that the same results can be obtained by using the function get_RLum on an RLum.Data.Spectrum or RLum.Data.Image object.

Details

Function provides an R only import routine for the Princeton Instruments SPE format. Import functionality is based on the file format description provided by Princeton Instruments and a MatLab script written by Carl Hall (see references).

Note

The function does not test whether the input data are spectra or pictures for spatial resolved analysis!

The function has been successfully tested for SPE format versions 2.x.

Currently not all information provided by the SPE format are supported.

Function version

0.1.5

How to cite

Kreutzer, S., 2024. read_SPE2R(): Import Princeton Instruments (TM) SPE-file into R. Function version 0.1.5. 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., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.26. https://r-lum.github.io/Luminescence/

References

Princeton Instruments, 2014. Princeton Instruments SPE 3.0 File Format Specification, Version 1.A (for document URL please use an internet search machine)

Hall, C., 2012: readSPE.m. https://www.mathworks.com/matlabcentral/fileexchange/35940-readspe

Author

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

Examples


## to run examples uncomment lines and run the code

##(1) Import data as RLum.Data.Spectrum object
#file <- file.choose()
#temp <- read_SPE2R(file)
#temp

##(2) Import data as RLum.Data.Image object
#file <- file.choose()
#temp <- read_SPE2R(file, output.object = "RLum.Data.Image")
#temp

##(3) Import data as matrix object
#file <- file.choose()
#temp <- read_SPE2R(file, output.object = "matrix")
#temp

##(4) Export raw data to csv, if temp is a RLum.Data.Spectrum object
# write.table(x = get_RLum(temp),
#             file = "[your path and filename]",
#             sep = ";", row.names = FALSE)