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#' Parse a Risoe SEQ-file to a sequence neccessary for simulating quartz luminescence
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#'
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#' A SEQ-file created by the Risoe Sequence Editor can be imported to simulate the sequence written
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#' in the sequence editor.
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#'
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#' \bold{Supported versions}: Supppored and tested: version 4.36.
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#'
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#' @param file \code{\link{character}} (\bold{required}): a *.seq file created by the Risoe Sequence Editor
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#'
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#' @param lab.dose_rate \code{\link{character}} (with default): set the dose rate of the radiation source
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#' in the laboratory Gy/s. Default: 1 Gy/s
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#'
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#' @param txtProgressBar \code{\link{logical}} (with default): enables or disables the txtProgressBar for a visuell
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#' control of the progress. Default: txtProgressBar = TRUE
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#'
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#' @return This function returns a \code{\link{list}} with the parsed *.seq file and the required steps for
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#' \code{\link{model_LuminescenceSignals}}.
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#'
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#' @section Function version: 0.1.0
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#'
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#' @author Johannes Friedrich, University of Bayreuth (Germany),
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#'
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#' @references
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#'
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#' Riso: Sequence Editor User Manual.
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#' Available at: http://www.nutech.dtu.dk/english/-/media/Andre_Universitetsenheder/Nutech/Produkter
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#' %20og%20services/Dosimetri/radiation_measurement_instruments/tl_osl_reader/Manuals/
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#' SequenceEditor.ashx?la=da
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#'
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#' @seealso \code{\link{model_LuminescenceSignals}}, \code{\link{readLines}}
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#'
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#' @examples
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#' ##search "example_SAR_cycle.SEQ" in "extdata" in package "RLumModel"
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#' path <- system.file("extdata", "example_SAR_cycle.SEQ", package="RLumModel")
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#'
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#' sequence <- read_SEQ2R(file = path, txtProgressBar = FALSE)
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#'
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#' @export
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read_SEQ2R <- function(
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file,
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lab.dose_rate = 1,
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txtProgressBar = TRUE
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){
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# Integrity tests and conversion --------------------------------------------------------------
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if(class(file)!= "character")
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stop("[read_SEQ2R()] class of file has to be a character.")
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if(!file.exists(file))
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stop("[read_SEQ2R()] file name doesn't seem to exist.")
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if(lab.dose_rate < 0)
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stop("[read_SEQ2R()] Argument 'lab.dose_rate' has to be positiv.")
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# parse *.SEQ file --------------------------------------------------------
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file2read <- readLines(file, encoding = "UTF-8")
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##(1)
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##get all rows with the term "[Cell(...)]" - that's what we are interested in and it defines
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##the number of elements we need
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records.row_number <- grep(pattern = "\\[Cell\\(", x = file2read)
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##(2)
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##make a list with data of each sequence step
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data.list <- lapply(1:length(records.row_number), function(x) {
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##grep each element
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if (!is.na(records.row_number[x + 1])) {
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return(file2read[records.row_number[x]:(records.row_number[x + 1] - 1)])
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}
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else{
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return(file2read[records.row_number[x]:length(file2read)])
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}
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})
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##PROGRESS BAR
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if(txtProgressBar){
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cat("\n [read_SEQ2R()] \n\t Parse *.seq file to sequence for RLumModel\n")
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pb <- txtProgressBar(min=0,max=length(data.list), char = "=", style=3)
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}
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sequence <- list()
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names <- character()
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for(x in 1:length(data.list)){
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##get length of record
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sequence.ID <- as.numeric(gsub("Command=", "", data.list[[x]][2]))
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#identify ID with sequence step
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if(sequence.ID >= 1 && sequence.ID <=5){
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stop(paste("[read_SEQ2R()] Step ",x," of your sequence is not supported!", sep = ""))
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}
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if(sequence.ID == 6){#TL
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temp_begin <- as.numeric(gsub("Low=", "", data.list[[x]][grep(pattern = "^Low=",x = data.list[[x]])]))
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temp_end <- as.numeric(gsub("High=", "", data.list[[x]][grep(pattern = "^High=",x = data.list[[x]])]))
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b <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate",x = data.list[[x]])]))
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PH_time <- as.numeric(gsub("PhTime=", "", data.list[[x]][grep(pattern = "^PhTime",x = data.list[[x]])]))
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PH_temp <- as.numeric(gsub("PhTemp=", "", data.list[[x]][grep(pattern = "^PhTemp",x = data.list[[x]])]))
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names[x] <- "TL"
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sequence[[x]] <- c(temp_begin,temp_end,b,PH_time,PH_temp)
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}
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if(sequence.ID == 7){#OSL
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temp <- as.numeric(gsub("Temperature=", "", data.list[[x]][grep(pattern = "^Temperature=",x = data.list[[x]])]))
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duration <- as.numeric(gsub("High=", "", data.list[[x]][grep(pattern = "^High=",x = data.list[[x]])]))
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optical_power <- as.numeric(gsub("Current=", "", data.list[[x]][grep(pattern = "^Current=",x = data.list[[x]])]))
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b <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate=",x = data.list[[x]])]))
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lightsource <- as.numeric(gsub("Lightsource=", "", data.list[[x]][grep(pattern = "^Lightsource=",x = data.list[[x]])]))
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if(lightsource == 2){
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names[x] <- "IR_OSL"
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}
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if(lightsource == 4){
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names[x] <- "OSL"
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}
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sequence[[x]] <- c(temp,duration,optical_power,b)
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}
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if(sequence.ID == 8){#TOL
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stop(paste("[read_SEQ2R()] Step ",x," \"TOL\" of your sequence is not supported!", sep = ""))
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}
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if(sequence.ID == 9){#TR-POSL
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stop(paste("[read_SEQ2R()] Step ",x," \"TR-POSL\" of your sequence is not supportel!", sep = ""))
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}
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if(sequence.ID == 10){# Irradiation
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temp <- as.numeric(gsub("An_Temp=", "", data.list[[x]][grep(pattern = "^An_Temp=",x = data.list[[x]])]))
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duration <- as.numeric(gsub("Irr_Time=", "", data.list[[x]][grep(pattern = "^Irr_Time",x = data.list[[x]])]))
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if(duration == 0){
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duration <- 1e-13
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}
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dose <- duration*lab.dose_rate
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b <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate",x = data.list[[x]])]))
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PH_time <- as.numeric(gsub("An_Time=", "", data.list[[x]][grep(pattern = "^An_Time",x = data.list[[x]])]))
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names[x] <- "IRR"
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sequence[[x]] <- c(temp,dose,lab.dose_rate,b,PH_time)
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}
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if(sequence.ID == 11){# illumination
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temp <- as.numeric(gsub("Temperature=", "", data.list[[x]][grep(pattern = "^Temperature=",x = data.list[[x]])]))
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duration <- as.numeric(gsub("^Bl_Time=", "", data.list[[x]][grep(pattern = "^Bl_Time",x = data.list[[x]])]))
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optical_power <- as.numeric(gsub("Power=", "", data.list[[x]][grep(pattern = "^Power",x = data.list[[x]])]))
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b <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate",x = data.list[[x]])]))
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PH_time <- as.numeric(gsub("An_Time=", "", data.list[[x]][grep(pattern = "^An_Time",x = data.list[[x]])]))
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names[x] <- "ILL"
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sequence[[x]] <- c(temp,duration,optical_power,b,PH_time)
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}
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if(sequence.ID == 12){# PH
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PH_temp <- as.numeric(gsub("An_Temp=", "", data.list[[x]][grep(pattern = "^An_Temp",x = data.list[[x]])]))
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PH_time <- as.numeric(gsub("An_Time=", "", data.list[[x]][grep(pattern = "^An_Time",x = data.list[[x]])]))
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b <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate",x = data.list[[x]])]))
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names[x] <- "PH"
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sequence[[x]] <- c(PH_temp,PH_time,b)
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}
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if(sequence.ID == 13){# set temp
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PH_temp <- as.numeric(gsub("An_Temp=", "", data.list[[x]][grep(pattern = "^An_Temp",x = data.list[[x]])]))
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names[x] <- "PH"
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sequence[[x]] <- c(PH_temp)
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}
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if(sequence.ID == 14){# Pause
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Pause_time <- as.numeric(gsub("An_Time=", "", data.list[[x]][grep(pattern = "^An_Time",x = data.list[[x]])]))
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names[x] <- "PAUSE"
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sequence[[x]] <- c(Pause_time)
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}
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if(sequence.ID == 15){
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stop(paste("[read_SEQ2R()] Step ",x," of your sequence is not supported!", sep = ""))
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}
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if(sequence.ID == 16){
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stop(paste("[read_SEQ2R()] Step ",x," of your sequence is not supported!", sep = ""))
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}
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if(sequence.ID == 17){
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stop("[read_seq2R()] Low-Level: Not supported!")
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}
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222
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if(sequence.ID == 18){# LM-OSL
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temp <- as.numeric(gsub("Temperature=", "", data.list[[x]][grep(pattern = "^Temperature=",x = data.list[[x]])]))
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duration <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate",x = data.list[[x]])]))
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start_power <- as.numeric(gsub("Low=", "", data.list[[x]][grep(pattern = "^Low",x = data.list[[x]])]))
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end_power <- as.numeric(gsub("High=", "", data.list[[x]][grep(pattern = "^High",x = data.list[[x]])]))
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229
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b <- as.numeric(gsub("HeatRate=", "", data.list[[x]][grep(pattern = "^HeatRate",x = data.list[[x]])]))
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PH_time <- as.numeric(gsub("PreHeatTime=", "", data.list[[x]][grep(pattern = "^PreHeatTime",x = data.list[[x]])]))
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232
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0
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names[x] <- "LM_OSL"
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sequence[[x]] <- c(temp,duration,start_power,end_power,b,PH_time)
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234
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235
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236
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}
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if(sequence.ID == 19){
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239
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240
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0
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stop(paste("[read_SEQ2R()] Step ",x," \"SG OSL\" of your sequence is not supported!", sep = ""))
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241
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242
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}
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244
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if(sequence.ID == 20){
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245
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246
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0
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stop(paste("[read_SEQ2R()] Step ",x," \"User defined\" of your sequence is not supported!", sep = ""))
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247
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248
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}
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249
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250
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251
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5
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if(sequence.ID == 21){
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252
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253
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0
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stop(paste("[read_SEQ2R()] Step ",x," \"SG LM-OSL\" of your sequence is not supported!", sep = ""))
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254
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255
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}
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256
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257
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5
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if(sequence.ID == 22){
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258
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259
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0
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stop(paste("[read_SEQ2R()] Step ",x," of your sequence is not supported!", sep = ""))
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260
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261
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}
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262
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263
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5
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if(sequence.ID == 23){
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264
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265
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0
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stop(paste("[read_SEQ2R()] Step ",x," \"POSL\" of your sequence is not supported!", sep = ""))
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266
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267
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}
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268
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269
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270
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5
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if(sequence.ID == 28){#RL
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271
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272
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0
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temp <- as.numeric(gsub("Temperature=", "", data.list[[x]][grep(pattern = "^Temperature=",x = data.list[[x]])]))
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273
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0
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duration <- as.numeric(gsub("High=", "", data.list[[x]][grep(pattern = "^High",x = data.list[[x]])]))
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274
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0
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lab.dose_rate <- lab.dose_rate
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275
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276
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0
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dose <- duration*lab.dose_rate
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277
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b <- as.numeric(gsub("Rate=", "", data.list[[x]][grep(pattern = "^Rate",x = data.list[[x]])]))
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278
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279
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0
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names[x] <- "RL"
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280
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0
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sequence[[x]] <- c(temp,dose,lab.dose_rate,b)
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281
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}
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282
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283
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5
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if(sequence.ID == 29){
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284
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285
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0
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stop(paste("[read_SEQ2R()] Step ",x," \"XRF\" of your sequence is not supported!", sep = ""))
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286
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287
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}
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288
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|
|
|
289
|
5
|
if(sequence.ID == 30){
|
|
290
|
|
|
|
291
|
0
|
stop(paste("[read_SEQ2R()] Step ",x," \"Photo\" of your sequence is not supported!", sep = ""))
|
|
292
|
|
|
|
293
|
|
}
|
|
294
|
|
|
|
295
|
|
|
|
296
|
|
|
|
297
|
|
##update progress bar
|
|
298
|
5
|
if (txtProgressBar) {
|
|
299
|
5
|
setTxtProgressBar(pb, x)
|
|
300
|
|
}
|
|
301
|
|
|
|
302
|
|
|
|
303
|
|
}
|
|
304
|
|
##close ProgressBar
|
|
305
|
5
|
if(txtProgressBar){close(pb)}
|
|
306
|
|
|
|
307
|
5
|
return(sequence <- setNames(object = sequence, nm = names))
|
|
308
|
|
}
|
RLumSK