R/read-flurznrc-lst-function.R
In claus-e-andersen/clanEGSnrc: R functions for reading output from EGSnrc
Defines functions
read.flurznrc.lst
Documented in
read.flurznrc.lst
#' @title Read fluence spactre in lst file produced by the EGSnrc usercode flurznrc
#' @description Read fluence spactre in lst file produced by the EGSnrc usercode flurznrc.
#' See body of function for further details.
#' @usage
#' df1 <- read.egsnrc( file.path="C:/data/projects/Theoretical-Dosimetry",
#' file.name="mcclan-10410-thin-slab.spectra",
#' file.name.save="mcclan-10410-thin-slab",
#' read.vec=c(1,3),
#' trace=!TRUE)
# xyplot(y~x|paste("plt.no",plt.no),data=df1)
#' @name read.flurznrc.lst
#' @author Claus E. Andersen
#' @return A single dataframe (which can be stacked, if more data files of the same type are read).
#' @param file.path: Path to folder where file to be read is located.
#' @param file.name: Name of file to be read
#' @param file.name.save: If "" then nothing is saved. Otherwise files
#' are saved for each individual plot. Not implemented.
#' @param read.vec: Vector of element that should be processes. c(1,5) means
#' that only plot 1 and 5 should be processed. 1:99 means that
#' all plots up to 99 should be processed.
#' @param plot.wanted: Not implemented.
#' @param trace: TRUE means that the function becomes verbose. FALSE means silience.
#' @export read.flurznrc.lst
read.flurznrc.lst <- function(file.path = "C://MC//egsnrc_mp//flurznrc",
file.name="flurznrc_template.spectra",
file.name.save="",
read.vec=1:999,
plot.wanted=FALSE,
trace=FALSE
){
# This function can read lst-files from the egsnrc user-code FLURZnrc.
# Created: July 31, 2013
# Revised: July 31, 2014
# Revised: August 1, 2014
# Name : Claus E. Andersen
# Input:
# file.path: Path to folder where file to be read is located.
# file.name: Name of file to be read
# file.name.save: If "" then nothing is saved. Otherwise files
# are saved for each individual plot.
# read.vec: Vector of element that should be processes. c(1,5) means
# that only plot 1 and 5 should be processed. 1:99 means that
# all plots up to 99 should be processed.
# plot.wanted: Not implemented.
# trace: TRUE means that the function becomes verbose. FALSE means
# silience.
# Return value: A single dataframe (which can be stacked, if more data files
# of the same type are read.
# The format of the individual data parts in a flurznrc lst-file is shown below.
# This is clearly not a very easy format to work with, and it is unknown
# if other types of output could produce other variations. The starting point
# is the \f-starting character. We then test for the occurance of a
# Depth coordinate line and a radial coordinate line 3 and 4 lines after the
# starting line, respectively.
#\f
#mcclan-10450-thin-slab
#Wed Jul 30 14:23:44 2014
#
# Depth coordinates: 0.0000 TO 0.1000 cm REGION = 2
#
# Radial coordinates: 0.0000 TO 10.0000 cm
#
# Total fluence/(MeV)/unit incident fluence
#
# Bintop electrons photons positrons e(-) + e(+)
# ------ --------- ------- --------- -----------
# 0.0010 1.689E+00+- 0.0% 0.000E+00+-99.9% 0.000E+00+-99.9% 1.689E+00+- 0.0%
# 0.0020 1.083E+00+- 0.0% 0.000E+00+-99.9% 0.000E+00+-99.9% 1.083E+00+- 0.0%
# 0.0030 8.652E-01+- 0.0% 0.000E+00+-99.9% 0.000E+00+-99.9% 8.652E-01+- 0.0%
#
# .....
#
# 0.9990 0.000E+00+-99.9% 0.000E+00+-99.9% 0.000E+00+-99.9% 0.000E+00+-99.9%
# 1.0000--0.000E+00+-99.9%-0.000E+00+-99.9%-0.000E+00+-99.9%-0.000E+00+-99.9%
# --------- ---------------- ---------------- ---------------- ----------------
# Totals 1.297E+00+- 0.0% 2.032E-02+- 0.4% 0.000E+00+-99.9% 1.297E+00+- 0.0%
# Avg E 7.696E-01+- 0.0% 1.147E-01+- 0.5% 0.000E+00+- NaN% 7.696E-01+- 0.0%
# Sample call:
# df <- read.flurznrc.lst(file.path="C://data//projects//Theoretical-Dosimetry",
# file.name="mcclan-10450-thin-slab.egslst",
# file.name.save="mcclan-10450-thin-slab",
# read.vec=c(1:3,8),
# plot.wanted=FALSE,
# trace=FALSE)
#
# xyplot(electrons~Bintop|paste("plt.no",plt.no),data=df)
# xyplot(photons~Bintop|paste("plt.no",plt.no),data=df)
# xyplot(electrons~Bintop|txt.legend,groups=paste("plt.no",plt.no),data=df,auto.key=list(TRUE,columns=4))
# xyplot(photons~Bintop|txt.legend,groups=paste("plt.no",plt.no),data=df,auto.key=list(TRUE,columns=4))
print("read.flurznrc.lst")
df <- NULL
file.full.path <- paste(file.path,file.name,sep='//')
file.full.path
# Read file first
file.txt <- scan(file.full.path, what="", multi.line=FALSE, sep="\n")
line.index <- 1:length(file.txt)
# All lines containing \f
ee <- "\\\\f"
ii1 <- grep(ee, file.txt, value=FALSE)
# All lines containing Depth coordinates:
# We subtract 3, because for the real header, it should appear as line 3
ee <- '[[:space:]]+Depth coordinates:[[:space:]]'
ii2 <- grep(ee, file.txt, value=FALSE) - 3
# All lines containing Radial coordinates:
# We subtract 3, because for the real header, it should appear as line 4
ee <- '[[:space:]]+Radial coordinates:[[:space:]]'
ii3 <- grep(ee, file.txt, value=FALSE) - 4
# All lines containing Totals:
ee <- '[[:space:]]+Totals[[:space:]]+[+]*[-]*[0-9]+'
ii4 <- grep(ee, file.txt, value=FALSE)
# All lines containing Avg E:
ee <- '[[:space:]]+Avg E[[:space:]]+[+]*[-]*[0-9]+'
ii5 <- grep(ee, file.txt, value=FALSE) - 1
header.starts <- intersect(intersect(ii1,ii2),ii3)
data.starts <- header.starts+8
data.stops <- intersect(ii4,ii5)-2
for(i in 1:length(data.starts)){
if(trace){
print("Data, first five:")
print(file.txt[data.starts[i]:(data.starts[i]+5)])
print("last five:")
print(file.txt[(data.stops[i]-5):(data.stops[i])])
}}
file.txt[data.starts]
for(iii in 1:length(header.starts)){
# Grand loop
if(is.element(iii,read.vec)){
i <- header.starts[iii]
txt.depth <- trim.whitespace(file.txt[i+3])
txt.radial <- trim.whitespace(file.txt[i+4])
txt.legend <- trim.whitespace(file.txt[i+5])
if(trace){
print("Header:")
print(i)
print(file.txt[i:(i+5)])
print(txt.depth)
print(txt.radial)
print(txt.legend)
}
txt <- txt.depth
txt.x <- NA
ee <- 'Depth coordinates:[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.depth.start <- txt.x
txt <- txt.depth
txt.x <- NA
ee <- 'TO[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.depth.stop <- txt.x
txt <- txt.depth
txt.x <- NA
ee <- 'REGION =[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.region <- txt.x
txt <- txt.radial
txt.x <- NA
ee <- 'Radial coordinates:[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.radial.start <- txt.x
txt <- txt.radial
txt.x <- NA
ee <- 'TO[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.radial.stop <- txt.x
txt.columns <- file.txt[i+6]
txt <- txt.columns
xx <- strsplit(txt," ")[[1]]
ok <- !xx==""
txt.columns <- xx[ok]
N.columns <- length(txt.columns)
if(trace){
print(txt.columns)
print(N.columns)
print("Data, first five:")
print(file.txt[data.starts[iii]:(data.starts[iii]+5)])
print("last five:")
print(file.txt[(data.stops[iii]-5):(data.stops[iii])])
}
txt.columns <- gsub(" ",".",trim.whitespace(txt.columns))
xxx <- rep(txt.columns[-1],each=2)
yyy <- rep(c("","u.pct."),length(txt.columns[-1]))
txt.columns.final <- c(txt.columns[1],paste(yyy,xxx,sep=""))
# Clean up the data part (remove -- +/- and %)
txt <- file.txt[data.starts[iii]:(data.stops[iii])]
txt <- gsub("--", " ", txt)
txt <- gsub("\\+-", " ", txt)
txt <- gsub("%-", " ", txt)
txt <- gsub("%", " ", txt)
df0 <- read.table(text=txt,sep="")
names(df0)<- txt.columns.final
if(!file.name.save==""){
fn <- paste(file.name.save,'-flurznrc-spectrum-',leading.zeros(iii,4),".txt",sep="")
write.table(df0,fn,quote=TRUE,row.names=FALSE,col.names=txt.columns.final)
print(paste("Saved file:",fn))
}
header.list <- list(region=txt.region,
depth.start=txt.depth.start,
depth.stop=txt.depth.stop,
radial.start=txt.radial.start,
radial.stop=txt.radial.stop,
N.columns=N.columns,
txt.columns=txt.columns,
txt.columns.final=txt.columns.final,
txt.depth=txt.depth,
txt.radial=txt.radial,
txt.legend=txt.legend,
df0=df0[1:10,])
#print(header.list)
df0 <- data.frame(plt.no=iii,
df0,
region=txt.region,
depth.start=txt.depth.start,
depth.stop=txt.depth.stop,
radial.start=txt.radial.start,
radial.stop=txt.radial.stop,
N.columns=N.columns,
txt.depth=txt.depth,
txt.radial=txt.radial,
txt.legend=txt.legend,
file.name=file.name)
if(is.null(df)){df <- df0} else {df <- rbind(df,df0)}
}# Test if it is in the read.vec
}# Grand loop
df
}# End read.egsnrc.lst
claus-e-andersen/clanEGSnrc documentation built on Jan. 30, 2022, 9:22 p.m.
R Package Documentation
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Defines functions read.flurznrc.lst
Documented in read.flurznrc.lst
#' @title Read fluence spactre in lst file produced by the EGSnrc usercode flurznrc
#' @description Read fluence spactre in lst file produced by the EGSnrc usercode flurznrc.
#' See body of function for further details.
#' @usage
#' df1 <- read.egsnrc( file.path="C:/data/projects/Theoretical-Dosimetry",
#' file.name="mcclan-10410-thin-slab.spectra",
#' file.name.save="mcclan-10410-thin-slab",
#' read.vec=c(1,3),
#' trace=!TRUE)
# xyplot(y~x|paste("plt.no",plt.no),data=df1)
#' @name read.flurznrc.lst
#' @author Claus E. Andersen
#' @return A single dataframe (which can be stacked, if more data files of the same type are read).
#' @param file.path: Path to folder where file to be read is located.
#' @param file.name: Name of file to be read
#' @param file.name.save: If "" then nothing is saved. Otherwise files
#' are saved for each individual plot. Not implemented.
#' @param read.vec: Vector of element that should be processes. c(1,5) means
#' that only plot 1 and 5 should be processed. 1:99 means that
#' all plots up to 99 should be processed.
#' @param plot.wanted: Not implemented.
#' @param trace: TRUE means that the function becomes verbose. FALSE means silience.
#' @export read.flurznrc.lst
read.flurznrc.lst <- function(file.path = "C://MC//egsnrc_mp//flurznrc",
file.name="flurznrc_template.spectra",
file.name.save="",
read.vec=1:999,
plot.wanted=FALSE,
trace=FALSE
){
# This function can read lst-files from the egsnrc user-code FLURZnrc.
# Created: July 31, 2013
# Revised: July 31, 2014
# Revised: August 1, 2014
# Name : Claus E. Andersen
# Input:
# file.path: Path to folder where file to be read is located.
# file.name: Name of file to be read
# file.name.save: If "" then nothing is saved. Otherwise files
# are saved for each individual plot.
# read.vec: Vector of element that should be processes. c(1,5) means
# that only plot 1 and 5 should be processed. 1:99 means that
# all plots up to 99 should be processed.
# plot.wanted: Not implemented.
# trace: TRUE means that the function becomes verbose. FALSE means
# silience.
# Return value: A single dataframe (which can be stacked, if more data files
# of the same type are read.
# The format of the individual data parts in a flurznrc lst-file is shown below.
# This is clearly not a very easy format to work with, and it is unknown
# if other types of output could produce other variations. The starting point
# is the \f-starting character. We then test for the occurance of a
# Depth coordinate line and a radial coordinate line 3 and 4 lines after the
# starting line, respectively.
#\f
#mcclan-10450-thin-slab
#Wed Jul 30 14:23:44 2014
#
# Depth coordinates: 0.0000 TO 0.1000 cm REGION = 2
#
# Radial coordinates: 0.0000 TO 10.0000 cm
#
# Total fluence/(MeV)/unit incident fluence
#
# Bintop electrons photons positrons e(-) + e(+)
# ------ --------- ------- --------- -----------
# 0.0010 1.689E+00+- 0.0% 0.000E+00+-99.9% 0.000E+00+-99.9% 1.689E+00+- 0.0%
# 0.0020 1.083E+00+- 0.0% 0.000E+00+-99.9% 0.000E+00+-99.9% 1.083E+00+- 0.0%
# 0.0030 8.652E-01+- 0.0% 0.000E+00+-99.9% 0.000E+00+-99.9% 8.652E-01+- 0.0%
#
# .....
#
# 0.9990 0.000E+00+-99.9% 0.000E+00+-99.9% 0.000E+00+-99.9% 0.000E+00+-99.9%
# 1.0000--0.000E+00+-99.9%-0.000E+00+-99.9%-0.000E+00+-99.9%-0.000E+00+-99.9%
# --------- ---------------- ---------------- ---------------- ----------------
# Totals 1.297E+00+- 0.0% 2.032E-02+- 0.4% 0.000E+00+-99.9% 1.297E+00+- 0.0%
# Avg E 7.696E-01+- 0.0% 1.147E-01+- 0.5% 0.000E+00+- NaN% 7.696E-01+- 0.0%
# Sample call:
# df <- read.flurznrc.lst(file.path="C://data//projects//Theoretical-Dosimetry",
# file.name="mcclan-10450-thin-slab.egslst",
# file.name.save="mcclan-10450-thin-slab",
# read.vec=c(1:3,8),
# plot.wanted=FALSE,
# trace=FALSE)
#
# xyplot(electrons~Bintop|paste("plt.no",plt.no),data=df)
# xyplot(photons~Bintop|paste("plt.no",plt.no),data=df)
# xyplot(electrons~Bintop|txt.legend,groups=paste("plt.no",plt.no),data=df,auto.key=list(TRUE,columns=4))
# xyplot(photons~Bintop|txt.legend,groups=paste("plt.no",plt.no),data=df,auto.key=list(TRUE,columns=4))
print("read.flurznrc.lst")
df <- NULL
file.full.path <- paste(file.path,file.name,sep='//')
file.full.path
# Read file first
file.txt <- scan(file.full.path, what="", multi.line=FALSE, sep="\n")
line.index <- 1:length(file.txt)
# All lines containing \f
ee <- "\\\\f"
ii1 <- grep(ee, file.txt, value=FALSE)
# All lines containing Depth coordinates:
# We subtract 3, because for the real header, it should appear as line 3
ee <- '[[:space:]]+Depth coordinates:[[:space:]]'
ii2 <- grep(ee, file.txt, value=FALSE) - 3
# All lines containing Radial coordinates:
# We subtract 3, because for the real header, it should appear as line 4
ee <- '[[:space:]]+Radial coordinates:[[:space:]]'
ii3 <- grep(ee, file.txt, value=FALSE) - 4
# All lines containing Totals:
ee <- '[[:space:]]+Totals[[:space:]]+[+]*[-]*[0-9]+'
ii4 <- grep(ee, file.txt, value=FALSE)
# All lines containing Avg E:
ee <- '[[:space:]]+Avg E[[:space:]]+[+]*[-]*[0-9]+'
ii5 <- grep(ee, file.txt, value=FALSE) - 1
header.starts <- intersect(intersect(ii1,ii2),ii3)
data.starts <- header.starts+8
data.stops <- intersect(ii4,ii5)-2
for(i in 1:length(data.starts)){
if(trace){
print("Data, first five:")
print(file.txt[data.starts[i]:(data.starts[i]+5)])
print("last five:")
print(file.txt[(data.stops[i]-5):(data.stops[i])])
}}
file.txt[data.starts]
for(iii in 1:length(header.starts)){
# Grand loop
if(is.element(iii,read.vec)){
i <- header.starts[iii]
txt.depth <- trim.whitespace(file.txt[i+3])
txt.radial <- trim.whitespace(file.txt[i+4])
txt.legend <- trim.whitespace(file.txt[i+5])
if(trace){
print("Header:")
print(i)
print(file.txt[i:(i+5)])
print(txt.depth)
print(txt.radial)
print(txt.legend)
}
txt <- txt.depth
txt.x <- NA
ee <- 'Depth coordinates:[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.depth.start <- txt.x
txt <- txt.depth
txt.x <- NA
ee <- 'TO[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.depth.stop <- txt.x
txt <- txt.depth
txt.x <- NA
ee <- 'REGION =[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.region <- txt.x
txt <- txt.radial
txt.x <- NA
ee <- 'Radial coordinates:[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.radial.start <- txt.x
txt <- txt.radial
txt.x <- NA
ee <- 'TO[[:space:]]*[[:space:]]*[+]*[-]*[0-9]+[.]?[0-9]*'
ok <- length(y <- grep(ee, txt, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt)
txt.x <- substring(txt,ii,ii+attr(ii,"match.length"))
txt.x <- extract.given.number(txt.x,1)
}
txt.radial.stop <- txt.x
txt.columns <- file.txt[i+6]
txt <- txt.columns
xx <- strsplit(txt," ")[[1]]
ok <- !xx==""
txt.columns <- xx[ok]
N.columns <- length(txt.columns)
if(trace){
print(txt.columns)
print(N.columns)
print("Data, first five:")
print(file.txt[data.starts[iii]:(data.starts[iii]+5)])
print("last five:")
print(file.txt[(data.stops[iii]-5):(data.stops[iii])])
}
txt.columns <- gsub(" ",".",trim.whitespace(txt.columns))
xxx <- rep(txt.columns[-1],each=2)
yyy <- rep(c("","u.pct."),length(txt.columns[-1]))
txt.columns.final <- c(txt.columns[1],paste(yyy,xxx,sep=""))
# Clean up the data part (remove -- +/- and %)
txt <- file.txt[data.starts[iii]:(data.stops[iii])]
txt <- gsub("--", " ", txt)
txt <- gsub("\\+-", " ", txt)
txt <- gsub("%-", " ", txt)
txt <- gsub("%", " ", txt)
df0 <- read.table(text=txt,sep="")
names(df0)<- txt.columns.final
if(!file.name.save==""){
fn <- paste(file.name.save,'-flurznrc-spectrum-',leading.zeros(iii,4),".txt",sep="")
write.table(df0,fn,quote=TRUE,row.names=FALSE,col.names=txt.columns.final)
print(paste("Saved file:",fn))
}
header.list <- list(region=txt.region,
depth.start=txt.depth.start,
depth.stop=txt.depth.stop,
radial.start=txt.radial.start,
radial.stop=txt.radial.stop,
N.columns=N.columns,
txt.columns=txt.columns,
txt.columns.final=txt.columns.final,
txt.depth=txt.depth,
txt.radial=txt.radial,
txt.legend=txt.legend,
df0=df0[1:10,])
#print(header.list)
df0 <- data.frame(plt.no=iii,
df0,
region=txt.region,
depth.start=txt.depth.start,
depth.stop=txt.depth.stop,
radial.start=txt.radial.start,
radial.stop=txt.radial.stop,
N.columns=N.columns,
txt.depth=txt.depth,
txt.radial=txt.radial,
txt.legend=txt.legend,
file.name=file.name)
if(is.null(df)){df <- df0} else {df <- rbind(df,df0)}
}# Test if it is in the read.vec
}# Grand loop
df
}# End read.egsnrc.lst
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