Risoe.BINfileData-class: Class '"Risoe.BINfileData"'
In Luminescence: Comprehensive Luminescence Dating Data Analysis
Risoe.BINfileData-class R Documentation
Class "Risoe.BINfileData"
Description
S4 class object for luminescence data in R. The object is produced as output
of the function read_BIN2R.
Usage
## S4 method for signature 'Risoe.BINfileData'
show(object)
## S4 method for signature 'ANY'
set_Risoe.BINfileData(
METADATA = data.frame(),
DATA = list(),
.RESERVED = list()
)
## S4 method for signature '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
METADATAObject of class "data.frame" containing the meta information for each curve.
DATAObject of class "list" containing numeric vector with count data.
.RESERVEDObject of class "list" containing list of undocumented raw values for internal use only.
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., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.24. https://CRAN.R-project.org/package=Luminescence
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)
Author(s)
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
References
Risø DTU, 2013. The Sequence Editor User Manual - Feb 2013 and Risø DTU, 2016.
The Sequence Editor User Manual - February 2016
See Also
plot_Risoe.BINfileData, read_BIN2R, write_R2BIN,
merge_Risoe.BINfileData, Risoe.BINfileData2RLum.Analysis
Examples
showClass("Risoe.BINfileData")
Luminescence documentation built on June 22, 2024, 9:54 a.m.
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| Risoe.BINfileData-class | R Documentation |
Class "Risoe.BINfileData"
Description
S4 class object for luminescence data in R. The object is produced as output of the function read_BIN2R.
Usage
## S4 method for signature 'Risoe.BINfileData'
show(object)
## S4 method for signature 'ANY'
set_Risoe.BINfileData(
METADATA = data.frame(),
DATA = list(),
.RESERVED = list()
)
## S4 method for signature '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
METADATAObject of class "data.frame" containing the meta information for each curve.
DATAObject of class "list" containing numeric vector with count data.
.RESERVEDObject of class "list" containing list of undocumented raw values for internal use only.
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., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.24. https://CRAN.R-project.org/package=Luminescence
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 forRECTYPE:= (0,1)): is a vector with the length defined throughNPOINTS. 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 byNPOINTSin@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)
Author(s)
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
References
Risø DTU, 2013. The Sequence Editor User Manual - Feb 2013 and Risø DTU, 2016.
The Sequence Editor User Manual - February 2016
See Also
plot_Risoe.BINfileData, read_BIN2R, write_R2BIN, merge_Risoe.BINfileData, Risoe.BINfileData2RLum.Analysis
Examples
showClass("Risoe.BINfileData")
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