Class

S4 class object for luminescence data in R. The object is produced as output of the function read_BIN2R.

Usage

# S4 method for class 'Risoe.BINfileData'
show(object)

# S4 method for class 'ANY'
set_Risoe.BINfileData(
  METADATA = data.frame(),
  DATA = list(),
  .RESERVED = list()
)

# S4 method for class 'Risoe.BINfileData'
get_Risoe.BINfileData(object, ...)

Arguments

object: an object of class Risoe.BINfileData
METADATA: Object of class "data.frame" containing the meta information for each curve.
DATA: Object of class "list" containing numeric vector with count data.
.RESERVED: Object of class "list" containing list of undocumented raw values for internal use only.
...: other arguments that might be passed

Methods (by generic)

show(Risoe.BINfileData): Show structure of RLum and Risoe.BINfile class objects
set_Risoe.BINfileData(ANY): The Risoe.BINfileData is normally produced as output of the function read_BIN2R. This construction method is intended for internal usage only.
get_Risoe.BINfileData(Risoe.BINfileData): Formal get-method for Risoe.BINfileData object. It does not allow accessing the object directly, it is just showing a terminal message.

Slots

METADATA: Object of class "data.frame" containing the meta information for each curve.
DATA: Object of class "list" containing numeric vector with count data.
.RESERVED: Object of class "list" containing list of undocumented raw values for internal use only.

Note

Internal METADATA - object structure

This structure is compatible with BIN/BINX-files version 03-08, however, it does not follow (in its sequential arrangement) the manual provided by the manufacturer, but an own structure accounting for the different versions.

#	Name	Data Type	V	Description
`[,1]`	`ID`	`numeric`	RLum	Unique record ID (same ID as in slot `DATA`)
`[,2]`	`SEL`	`logic`	RLum	Record selection, not part official BIN-format, triggered by TAG
`[,3]`	`VERSION`	`raw`	03-08	BIN-file version number
`[,4]`	`LENGTH`	`integer`	03-08	Length of this record
`[,5]`	`PREVIOUS`	`integer`	03-08	Length of previous record
`[,6]`	`NPOINTS`	`integer`	03-08	Number of data points in the record
`[,7]`	`RECTYPE`	`integer`	08	Record type
`[,8]`	`RUN`	`integer`	03-08	Run number
`[,9]`	`SET`	`integer`	03-08	Set number
`[,10]`	`POSITION`	`integer`	03-08	Position number
`[,11]`	`GRAIN`	`integer`	03-04	Grain number
`[,12]`	`GRAINNUMBER`	`integer`	05-08	Grain number
`[,13]`	`CURVENO`	`integer`	05-08	Curve number
`[,14]`	`XCOORD`	`integer`	03-08	X position of a single grain
`[,15]`	`YCOORD`	`integer`	03-08	Y position of a single grain
`[,16]`	`SAMPLE`	`factor`	03-08	Sample name
`[,17]`	`COMMENT`	`factor`	03-08	Comment name
`[,18]`	`SYSTEMID`	`integer`	03-08	Risø system id
`[,19]`	`FNAME`	`factor`	05-08	File name (.bin/.binx)
`[,20]`	`USER`	`factor`	03-08	User name
`[,21]`	`TIME`	`character`	03-08	Data collection time (`hh-mm-ss`)
`[,22]`	`DATE`	`factor`	03-08	Data collection date (`ddmmyy`)
`[,23]`	`DTYPE`	`character`	03-08	Data type
`[,24]`	`BL_TIME`	`numeric`	03-08	Bleaching time
`[,25]`	`BL_UNIT`	`integer`	03-08	Bleaching unit (mJ, J, s, min, h)
`[,26]`	`NORM1`	`numeric`	03-08	Normalisation factor (1)
`[,27]`	`NORM2`	`numeric`	03-08	Normalisation factor (2)
`[,28]`	`NORM3`	`numeric`	03-08	Normalisation factor (3)
`[,29]`	`BG`	`numeric`	03-08	Background level
`[,30]`	`SHIFT`	`integer`	03-08	Number of channels to shift data
`[,31]`	`TAG`	`integer`	03-08	Tag, triggers `SEL`
`[,32]`	`LTYPE`	`character`	03-08	Luminescence type
`[,33]`	`LIGHTSOURCE`	`character`	03-08	Light source
`[,34]`	`LPOWER`	`numeric`	03-08	Optical stimulation power
`[,35]`	`LIGHTPOWER`	`numeric`	05-08	Optical stimulation power
`[,36]`	`LOW`	`numeric`	03-08	Low (temperature, time, wavelength)
`[,37]`	`HIGH`	`numeric`	03-08	High (temperature, time, wavelength)
`[,38]`	`RATE`	`numeric`	03-08	Rate (heating rate, scan rate)
`[,39]`	`TEMPERATURE`	`integer`	03-08	Sample temperature
`[,40]`	`MEASTEMP`	`integer`	05-08	Measured temperature
`[,41]`	`AN_TEMP`	`numeric`	03-08	Annealing temperature
`[,42]`	`AN_TIME`	`numeric`	03-08	Annealing time
`[,43]`	`TOLDELAY`	`integer`	03-08	TOL 'delay' channels
`[,44]`	`TOLON`	`integer`	03-08	TOL 'on' channels
`[,45]`	`TOLOFF`	`integer`	03-08	TOL 'off' channels
`[,46]`	`IRR_TIME`	`numeric`	03-08	Irradiation time
`[,47]`	`IRR_TYPE`	`integer`	03-08	Irradiation type (alpha, beta or gamma)
`[,48]`	`IRR_UNIT`	`integer`	03-04	Irradiation unit (Gy, rad, s, min, h)
`[,49]`	`IRR_DOSERATE`	`numeric`	05-08	Irradiation dose rate (Gy/s)
`[,50]`	`IRR_DOSERATEERR`	`numeric`	06-08	Irradiation dose rate error (Gy/s)
`[,51]`	`TIMESINCEIRR`	`integer`	05-08	Time since irradiation (s)
`[,52]`	`TIMETICK`	`numeric`	05-08	Time tick for pulsing (s)
`[,53]`	`ONTIME`	`integer`	05-08	On-time for pulsing (in time ticks)
`[,54]`	`OFFTIME`	`integer`	03	Off-time for pulsed stimulation (in s)
`[,55]`	`STIMPERIOD`	`integer`	05-08	Stimulation period (on+off in time ticks)
`[,56]`	`GATE_ENABLED`	`raw`	05-08	PMT signal gating enabled
`[,57]`	`ENABLE_FLAGS`	`raw`	05-08	PMT signal gating enabled
`[,58]`	`GATE_START`	`integer`	05-08	Start gating (in time ticks)
`[,59]`	`GATE_STOP`	`integer`	05-08	Stop gating (in time ticks), `'Gateend'` for version 04, here only GATE_STOP is used
`[,60]`	`PTENABLED`	`raw`	05-08	Photon time enabled
`[,61]`	`DTENABLED`	`raw`	05-08	PMT dead time correction enabled
`[,62]`	`DEADTIME`	`numeric`	05-08	PMT dead time (s)
`[,63]`	`MAXLPOWER`	`numeric`	05-08	Stimulation power to 100 percent (mW/cm^2)
`[,64]`	`XRF_ACQTIME`	`numeric`	05-08	XRF acquisition time (s)
`[,65]`	`XRF_HV`	`numeric`	05-08	XRF X-ray high voltage (V)
`[,66]`	`XRF_CURR`	`integer`	05-08	XRF X-ray current (µA)
`[,67]`	`XRF_DEADTIMEF`	`numeric`	05-08	XRF dead time fraction
`[,68]`	`DETECTOR_ID`	`raw`	07-08	Detector ID
`[,69]`	`LOWERFILTER_ID`	`integer`	07-08	Lower filter ID in reader
`[,70]`	`UPPERFILTER_ID`	`integer`	07-08	Upper filter ID in reader
`[,71]`	`ENOISEFACTOR`	`numeric`	07-08	Excess noise filter, usage unknown
`[,72]`	`MARKPOS_X1`	`numeric`	08	Coordinates marker position 1
`[,73]`	`MARKPOS_Y1`	`numeric`	08	Coordinates marker position 1
`[,74]`	`MARKPOS_X2`	`numeric`	08	Coordinates marker position 2
`[,75]`	`MARKPOS_Y2`	`numeric`	08	Coordinates marker position 2
`[,76]`	`MARKPOS_X3`	`numeric`	08	Coordinates marker position 3
`[,77]`	`MARKPOS_Y3`	`numeric`	08	Coordinates marker position 3
`[,78]`	`EXTR_START`	`numeric`	08	usage unknown
`[,79]`	`EXTR_END`	`numeric`	08	usage unknown
`[,80]`	`SEQUENCE`	`character`	03-04	Sequence name

V = BIN-file version (RLum means that it does not depend on a specific BIN version)

Note that the Risoe.BINfileData object combines all values from different versions from the BIN-file, reserved bits are skipped, however, the function write_R2BIN reset arbitrary reserved bits. Invalid values for a specific version are set to NA. Furthermore, the internal R data types do not necessarily match the required data types for the BIN-file data import! Data types are converted during data import.

LTYPE values

VALUE	TYPE	DESCRIPTION
`[0]`	`TL`	: Thermoluminescence
`[1]`	`OSL`	: Optically stimulated luminescence
`[2]`	`IRSL`	: Infrared stimulated luminescence
`[3]`	`M-IR`	: Infrared monochromator scan
`[4]`	`M-VIS`	: Visible monochromator scan
`[5]`	`TOL`	: Thermo-optical luminescence
`[6]`	`TRPOSL`	: Time Resolved Pulsed OSL
`[7]`	`RIR`	: Ramped IRSL
`[8]`	`RBR`	: Ramped (Blue) LEDs
`[9]`	`USER`	: User defined
`[10]`	`POSL`	: Pulsed OSL
`[11]`	`SGOSL`	: Single Grain OSL
`[12]`	`RL`	: Radio Luminescence
`[13]`	`XRF`	: X-ray Fluorescence

DTYPE values

VALUE	DESCRIPTION
`[0]`	Natural
`[1]`	N+dose
`[2]`	Bleach
`[3]`	Bleach+dose
`[4]`	Natural (Bleach)
`[5]`	N+dose (Bleach)
`[6]`	Dose
`[7]`	Background

LIGHTSOURCE values

VALUE	DESCRIPTION
`[0]`	None
`[1]`	Lamp
`[2]`	IR diodes/IR Laser
`[3]`	Calibration LED
`[4]`	Blue Diodes
`[5]`	White light
`[6]`	Green laser (single grain)
`[7]`	IR laser (single grain)

Internal DATA - object structure

With version 8 of the BIN/BINX file format, slot @DATA (byte array DPOINTS) can contain two different values:

DPOINTS (standard for RECTYPE := (0,1)): is a vector with the length defined through NPOINTS. This is the standard for xy-curves since version 03.
DPOINTS (RECTYPE := 128) is contains no count values but information about the definition of the regions of interest (ROI). Each definition is 504 bytes long. The number of definitions is defined by NPOINTS in @METADATA. The record describes basically the geometric features of the regions of interest. The representation in R is a nested list.

#	Name	Data Type	V	Description
`[,1]`	`NOFPOINTS`	`numeric`	08	number of points in the definition (e.g., if the ROI is a rectangle: 4)
`[,2]`	`USEDFOR`	`logical`	08	samples for which the ROI is used for; a maximum of 48 samples are allowed.
`[,3]`	`SHOWNFOR`	`logical`	08	samples for which the ROI is shown for; a maximum of 48 samples are allowed.
`[,4]`	`COLOR`	`numeric`	08	The colour values of the ROI.
`[,5]`	`X`	`numeric`	08	The x coordinates used to draw the ROI geometry (up to 50 points are allowed).
`[,6]`	`Y`	`numeric`	08	The y coordinates used to draw the ROI geometry (up to 50 points are allowed).

(information on the BIN/BINX file format are kindly provided by Risø, DTU Nutech)

Objects from the Class

Objects can be created by calls of the form new("Risoe.BINfileData", ...).

Function version

0.4.1

How to cite

Kreutzer, S., 2024. Risoe.BINfileData-class(): Class 'Risoe.BINfileData'. Function version 0.4.1. 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

Risø DTU, 2013. The Sequence Editor User Manual - Feb 2013 and Risø DTU, 2016.

The Sequence Editor User Manual - February 2016

https://www.fysik.dtu.dk

Author

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
based on information provided by Torben Lapp and Karsten Bracht Nielsen (Risø DTU, Denmark) , RLum Developer Team

Examples


showClass("Risoe.BINfileData")
#> Class "Risoe.BINfileData" [package "Luminescence"]
#> 
#> Slots:
#>                                        
#> Name:    METADATA       DATA  .RESERVED
#> Class: data.frame       list       list

Class `"Risoe.BINfileData"`