R/read-egsnrc-plot-function.R
In claus-e-andersen/clanEGSnrc: R functions for reading output from EGSnrc
Defines functions
read.egsnrc.plot
Documented in
read.egsnrc.plot
#' @title Read plot file produced by the EGSnrc usercode dosrznrc or flurznrc
#' @description Read plot file produced by the EGSnrc usercode dosrznrc or flurznrc. These
#' plots are in a format designed for Grace. With this script we can get the data into
#' an R dataframe.
#' @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.egsnrc.plot
#' @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.egsnrc.plot
read.egsnrc.plot <- 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){
# Created: December 7, 2009
# Revised: December 7, 2009
# Revised: June 24, 2012
# Revised: June 16, 2013
# Revised: June 17, 2013
# Revised: July 30, 2014 (can now handle both xydy and xy graphs).
# Revised: August 1, 2014
# 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. Not implemented.
# 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.
# Notes : This version is based on the following syntax-separation
# of the egsnrc plotfile:
# (1) Each line is terminated by "LF".
# (2) Each "graph" is terminated by a "&".
# (3) The header consists of lines starting with "@" (i.e. the
# first character is a header line is "@").
# (4) The remaining lines are assumed to be data-lines with
# x,y,dy-data or x,y-data.
# Name : Claus E. Andersen
###########################################################
# Sample code
###########################################################
# 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)
# fp <- "C:/data/projects/Theoretical-Dosimetry"
###########################################################
print("read.egsnrc")
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")
ok <- substring(file.txt,1,1) == "&"
line.index <- 1:length(file.txt)
line.stops <- line.index[ok]-1
no.of.graphs <- length(line.stops)
line.starts <- c(1,line.stops[1:no.of.graphs-1]+2)
# no.of.graphs
df <- NULL
txt.title <- NA
txt.subtitle <- NA
txt.legend <- NA
txt.xaxis <- NA
txt.yaxis <- NA
txt.type <- NA
for (i in 1:no.of.graphs){
#Grand loop
if(is.element(i,read.vec)){
line.start <- line.starts[i]
line.stop <- line.stops[i]
raw.txt <- file.txt[line.start:line.stop]
ok <- substring(raw.txt,1,1) == "@"
raw.head <- raw.txt[ok]
raw.data <- raw.txt[!ok]
if(trace){
print(paste("Graph no",i))
print(raw.head)
print(raw.data)
}
##############################
# Header
##############################
for (k in 1:length(raw.head)){
xxx <- raw.head[k]
ee <- '@[[:space:]]+title'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.title <- yyy
}
ee <- '@[[:space:]]+subtitle'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.subtitle <- yyy
}
ee <- '@[[:space:]]+legend[[:space:]]+string[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.legend <- yyy
}
ee <- '@[[:space:]]+xaxis[[:space:]]+label[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.xaxis <- yyy
}
ee <- '@[[:space:]]+yaxis[[:space:]]+label[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.yaxis <- yyy
}
ee <- '@TYPE[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.type <- yyy
}
} # raw.header line loop
if(trace){
if(!is.na(txt.title )) print(txt.title)
if(!is.na(txt.legend)) print(txt.legend)
if(!is.na(txt.xaxis)) print(txt.xaxis)
if(!is.na(txt.yaxis)) print(txt.yaxis)
if(!is.na(txt.type)) print(txt.type)
}
txt.IRL <- NA
txt.IQ <- NA
txt.IP <- NA
ee <- 'IRL[[:space:]]*=[[:space:]]*[+]*[-]*[0-9]+'
ok <- length(y <- grep(ee, txt.legend, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt.legend)
txt.IRL <- substring(txt.legend,ii,ii+attr(ii,"match.length"))
txt.IRL <- extract.given.number(txt.IRL,1)
}
ee <- 'IQ[[:space:]]*=[[:space:]]*[+]*[-]*[0-9]+'
ok <- length(y <- grep(ee, txt.legend, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt.legend)
txt.IQ <- substring(txt.legend,ii,ii+attr(ii,"match.length"))
txt.IQ <- extract.given.number(txt.IQ,1)
}
ee <- 'IP[[:space:]]*=[[:space:]]*[+]*[-]*[0-9]+'
ok <- length(y <- grep(ee, txt.legend, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt.legend)
txt.IP <- substring(txt.legend,ii,ii+attr(ii,"match.length"))
txt.IP <- extract.given.number(txt.IP,1)
}
if(trace){
if(!is.na(txt.IRL)) print(paste('IRL =', txt.IRL))
if(!is.na(txt.IQ )) print(paste('IQ =', txt.IQ ))
if(!is.na(txt.IP )) print(paste('IP =', txt.IP ))
}
##############################
# Data
##############################
if(txt.type=="xydy"){
xx.txt <- paste(raw.data,collapse=" ")
#xx <- unlist(strsplit(xx.txt,split=". "))
xx <- unlist(strsplit(xx.txt,split="[[:space:]]+"))
ok <- !xx==""
xx <- as.numeric(as.character(xx[ok]))
if(trace){print(xx[ok])}
nn <- length(xx)/3
vec <- data.frame(value=xx,group=rep(c("x","y","dy"),nn))
ok.x <- vec$group=="x"
ok.y <- vec$group=="y"
ok.dy <- vec$group=="dy"
df0 <- data.frame(plt.no=i,x=vec$value[ok.x],y=vec$value[ok.y],dy=vec$value[ok.dy],
title=txt.title, subtitle=txt.subtitle, legend=txt.legend, xaxis=txt.xaxis,
yaxis=txt.yaxis,graph.type=txt.type,IRL=txt.IRL,IQ=txt.IQ,IP=txt.IP,file.name=file.name)
}#xydy
if(txt.type=="xy"){
xx.txt <- paste(raw.data,collapse=" ")
#xx <- unlist(strsplit(xx.txt,split=". "))
xx <- unlist(strsplit(xx.txt,split="[[:space:]]+"))
ok <- !xx==""
xx <- as.numeric(as.character(xx[ok]))
if(trace){print(xx[ok])}
nn <- length(xx)/2
vec <- data.frame(value=xx,group=rep(c("x","y"),nn))
ok.x <- vec$group=="x"
ok.y <- vec$group=="y"
ok.dy <- vec$group=="y"
df0 <- data.frame(plt.no=i, x=vec$value[ok.x],y=vec$value[ok.y],dy=0*vec$value[ok.dy],
title=txt.title, subtitle=txt.subtitle, legend=txt.legend, xaxis=txt.xaxis,
yaxis=txt.yaxis,graph.type=txt.type,IRL=txt.IRL,IQ=txt.IQ,IP=txt.IP,file.name=file.name)
}#xy
if(!file.name.save==""){
fn <- paste(file.name.save,'-read-egsnrc-',leading.zeros(i,4),".txt",sep="")
write.table(df0,fn,quote=TRUE,row.names=FALSE,col.names=names(df0))
print(paste("Saved file:",fn))
}
if(is.null(df)){ df <- df0 }else {df <- rbind(df,df0)}
} # End read.vec test
} # End Grand loop
df
}
claus-e-andersen/clanEGSnrc documentation built on Jan. 30, 2022, 9:22 p.m.
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Defines functions read.egsnrc.plot
Documented in read.egsnrc.plot
#' @title Read plot file produced by the EGSnrc usercode dosrznrc or flurznrc
#' @description Read plot file produced by the EGSnrc usercode dosrznrc or flurznrc. These
#' plots are in a format designed for Grace. With this script we can get the data into
#' an R dataframe.
#' @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.egsnrc.plot
#' @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.egsnrc.plot
read.egsnrc.plot <- 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){
# Created: December 7, 2009
# Revised: December 7, 2009
# Revised: June 24, 2012
# Revised: June 16, 2013
# Revised: June 17, 2013
# Revised: July 30, 2014 (can now handle both xydy and xy graphs).
# Revised: August 1, 2014
# 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. Not implemented.
# 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.
# Notes : This version is based on the following syntax-separation
# of the egsnrc plotfile:
# (1) Each line is terminated by "LF".
# (2) Each "graph" is terminated by a "&".
# (3) The header consists of lines starting with "@" (i.e. the
# first character is a header line is "@").
# (4) The remaining lines are assumed to be data-lines with
# x,y,dy-data or x,y-data.
# Name : Claus E. Andersen
###########################################################
# Sample code
###########################################################
# 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)
# fp <- "C:/data/projects/Theoretical-Dosimetry"
###########################################################
print("read.egsnrc")
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")
ok <- substring(file.txt,1,1) == "&"
line.index <- 1:length(file.txt)
line.stops <- line.index[ok]-1
no.of.graphs <- length(line.stops)
line.starts <- c(1,line.stops[1:no.of.graphs-1]+2)
# no.of.graphs
df <- NULL
txt.title <- NA
txt.subtitle <- NA
txt.legend <- NA
txt.xaxis <- NA
txt.yaxis <- NA
txt.type <- NA
for (i in 1:no.of.graphs){
#Grand loop
if(is.element(i,read.vec)){
line.start <- line.starts[i]
line.stop <- line.stops[i]
raw.txt <- file.txt[line.start:line.stop]
ok <- substring(raw.txt,1,1) == "@"
raw.head <- raw.txt[ok]
raw.data <- raw.txt[!ok]
if(trace){
print(paste("Graph no",i))
print(raw.head)
print(raw.data)
}
##############################
# Header
##############################
for (k in 1:length(raw.head)){
xxx <- raw.head[k]
ee <- '@[[:space:]]+title'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.title <- yyy
}
ee <- '@[[:space:]]+subtitle'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.subtitle <- yyy
}
ee <- '@[[:space:]]+legend[[:space:]]+string[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.legend <- yyy
}
ee <- '@[[:space:]]+xaxis[[:space:]]+label[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.xaxis <- yyy
}
ee <- '@[[:space:]]+yaxis[[:space:]]+label[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.yaxis <- yyy
}
ee <- '@TYPE[[:space:]]+'
ok <- length(grep(ee, xxx, value=FALSE)) > 0
if(ok){
yyy <- sub(ee,'', xxx)
yyy <- sub('\\\\N', '', yyy)
yyy <- sub('\\\\S', '', yyy)
yyy <- sub('\\"', '', yyy)
yyy <- sub('\\"', '', yyy)
txt.type <- yyy
}
} # raw.header line loop
if(trace){
if(!is.na(txt.title )) print(txt.title)
if(!is.na(txt.legend)) print(txt.legend)
if(!is.na(txt.xaxis)) print(txt.xaxis)
if(!is.na(txt.yaxis)) print(txt.yaxis)
if(!is.na(txt.type)) print(txt.type)
}
txt.IRL <- NA
txt.IQ <- NA
txt.IP <- NA
ee <- 'IRL[[:space:]]*=[[:space:]]*[+]*[-]*[0-9]+'
ok <- length(y <- grep(ee, txt.legend, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt.legend)
txt.IRL <- substring(txt.legend,ii,ii+attr(ii,"match.length"))
txt.IRL <- extract.given.number(txt.IRL,1)
}
ee <- 'IQ[[:space:]]*=[[:space:]]*[+]*[-]*[0-9]+'
ok <- length(y <- grep(ee, txt.legend, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt.legend)
txt.IQ <- substring(txt.legend,ii,ii+attr(ii,"match.length"))
txt.IQ <- extract.given.number(txt.IQ,1)
}
ee <- 'IP[[:space:]]*=[[:space:]]*[+]*[-]*[0-9]+'
ok <- length(y <- grep(ee, txt.legend, value=FALSE)) > 0
if(ok){
ii <- regexpr(ee, txt.legend)
txt.IP <- substring(txt.legend,ii,ii+attr(ii,"match.length"))
txt.IP <- extract.given.number(txt.IP,1)
}
if(trace){
if(!is.na(txt.IRL)) print(paste('IRL =', txt.IRL))
if(!is.na(txt.IQ )) print(paste('IQ =', txt.IQ ))
if(!is.na(txt.IP )) print(paste('IP =', txt.IP ))
}
##############################
# Data
##############################
if(txt.type=="xydy"){
xx.txt <- paste(raw.data,collapse=" ")
#xx <- unlist(strsplit(xx.txt,split=". "))
xx <- unlist(strsplit(xx.txt,split="[[:space:]]+"))
ok <- !xx==""
xx <- as.numeric(as.character(xx[ok]))
if(trace){print(xx[ok])}
nn <- length(xx)/3
vec <- data.frame(value=xx,group=rep(c("x","y","dy"),nn))
ok.x <- vec$group=="x"
ok.y <- vec$group=="y"
ok.dy <- vec$group=="dy"
df0 <- data.frame(plt.no=i,x=vec$value[ok.x],y=vec$value[ok.y],dy=vec$value[ok.dy],
title=txt.title, subtitle=txt.subtitle, legend=txt.legend, xaxis=txt.xaxis,
yaxis=txt.yaxis,graph.type=txt.type,IRL=txt.IRL,IQ=txt.IQ,IP=txt.IP,file.name=file.name)
}#xydy
if(txt.type=="xy"){
xx.txt <- paste(raw.data,collapse=" ")
#xx <- unlist(strsplit(xx.txt,split=". "))
xx <- unlist(strsplit(xx.txt,split="[[:space:]]+"))
ok <- !xx==""
xx <- as.numeric(as.character(xx[ok]))
if(trace){print(xx[ok])}
nn <- length(xx)/2
vec <- data.frame(value=xx,group=rep(c("x","y"),nn))
ok.x <- vec$group=="x"
ok.y <- vec$group=="y"
ok.dy <- vec$group=="y"
df0 <- data.frame(plt.no=i, x=vec$value[ok.x],y=vec$value[ok.y],dy=0*vec$value[ok.dy],
title=txt.title, subtitle=txt.subtitle, legend=txt.legend, xaxis=txt.xaxis,
yaxis=txt.yaxis,graph.type=txt.type,IRL=txt.IRL,IQ=txt.IQ,IP=txt.IP,file.name=file.name)
}#xy
if(!file.name.save==""){
fn <- paste(file.name.save,'-read-egsnrc-',leading.zeros(i,4),".txt",sep="")
write.table(df0,fn,quote=TRUE,row.names=FALSE,col.names=names(df0))
print(paste("Saved file:",fn))
}
if(is.null(df)){ df <- df0 }else {df <- rbind(df,df0)}
} # End read.vec test
} # End Grand loop
df
}
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