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exec/1-Templates/HIT_XML.Create_Plan.R
In HITXML: Planning tools for ion beam therapy
#!/usr/bin/Rscript
############################################
# Script to create HIT irradiation plans for
# simple, homogenous fields
#
# E0408, DKFZ Heidelberg
# Oct2015
# Maintainer: s.greilich@dkfz.de
############################################
# Please see README for more information
############################################
############################################
# TODOs
############################################
# Fine tuning parameters
# Time estimate (completed in Oct. 2014 - Yukihara)
############################################
# Modifications implemented (Oct. 2014, Yukihara)
# - small fixes to the code to allow it to generate multiple IES with
# different energies.
# - Modified to allow the repetition of IES without repeating the optimization.
# - The code now saves by default the plans in the new format (tested successfully
# at HIT)
#
# Known problems
# - The function that gathers user input does not contain He ion and, therefore,
# does not ask for intensity. As a result, time estimate does not work. The plan
# should work without problems, since intensity information is not included
# in the plans.
# Clear workspace, set version
rm(list =ls())
# load package
library(HITXML)
program.version <- packageDescription("HITXML")$Version
program.date <- packageDescription("HITXML")$Date
# Structure to hold all input data
# This approach allows to run the script interactively, too,
# e.g. for debugging. Normal mode is non-interactively
# by Rscript from command line.
user.input <- list( basic = list( date = 20160920,
name.exp.series = "anTest",
name.exp.run = "ab0001Test",
chosen.particle = 1, # c("Protons", "Helium-4 ions", "Carbon ions", "Oxygen ions")
chosen.rifi.idx = 1, # c("None", "3 mm")
intensity = 1,
resolution.mm = 1,
spot.distance.mm = -1), # If <= 0, do spot distance optimization, otherwise use given value
fixed = list( time = format(Sys.time(), "%Y-%m-%dT%H:%M:%S.1111111+02:00"), # Due to POSIX/Windows problem hardcode fractions of second and time zone for timestamp, TODO: Fix by more flexible solution
room.name = "Room4",
patient.id = "PT-2004-01",
tumor.name = "Sacral Chordoma",
patient.birth = "2004-01-01",
patient.sex = "M",
therapist.name = "USER NAME"),
IES = list( list( energy.value.MeV.u = 50.6, # value will be adjusted to closest available in libC
chosen.idx = NA, # if given, overrides energy value
focus.FWHM.mm = 0.0, # value will be adjusted to closest available in libC
chosen.foc.idx = 3, # if given, overrides focus value
field.shape.idx = 1, # c("square", "circular", "shells")
fluence.cm2.or.dose.Gy = 2e5,
field.size.mm = 50,
r.min.mm = 0.0)))
# Script run interactively or non-interactively, set connection accordingly
interactive.run.mode <- interactive()
if(!interactive.run.mode){
input.con <-file("stdin")
}else{
input.con <-stdin()
}
# Read defaults
default.input <- HX.read.defaults()
# Say hello to user
welcome.message <- paste( "\n",
"#####################################################################\n",
"#####################################################################\n",
"## THIS IS HIT_XML\n## E0408, DKFZ Heidelberg\n## Version ",
program.version,
" as of ",
program.date,
"\n",
"#####################################################################\n",
sep = "")
message(welcome.message)
message("#####################################################################\n\n")
#################################
## Set up data frames for choices
df.particles <- data.frame( particle.name = c("PROTON", "ION", "ION", "ION"),
nice.particle.name = c("Protons", "Helium ions", "Carbon ions", "Oxygen ions"),
mass = c(1,4,12,16),
charge = c(1,2,6,8),
atomicNumber = c(1,2,6,8),
minParticles = c(165000, 0, 5000, 0),
libC.file.name = c( "LIBC HIT Version 1.4 p V11.txt",
"LIBC HIT Version 1.5 He4 V1.txt",
"LIBC HIT Version 1.4 C12 V8.txt",
"LIBC HIT Version 1.5 O16 V2.txt"),
stringsAsFactors = FALSE)
df.particles$particle.no <- libamtrack::AT.particle.no.from.Z.and.A( Z = df.particles$charge,
A = df.particles$mass)$particle.no
df.rippleFilter <- data.frame( filter.name = c("None", "3mm"),
filter.code = c(254, 3),
stringsAsFactors = FALSE)
df.fields <- data.frame( shape = c( "square", "circle", "shells"),
stringsAaFactors = FALSE)
# TODO: Add variables for field shape here
#######################################
## Get user inputs (if non-interactive)
# There is currently a problem wiht the function HX.get.user.input.basic.
# The function does not include He ions in a list of possible particles,
# so it is necessary to update it.
# (Yukihara, 30 Oct 14)
if(!interactive.run.mode){
user.input <- HX.get.user.input.basic(user.input = user.input,
default.input = default.input,
df.particles = df.particles,
df.rippleFilter = df.rippleFilter,
input.con = input.con)
}
# Translate ripple filter code
rippleFilter <- df.rippleFilter$filter.name[user.input$basic$chosen.rifi.idx]
ripplefilter.code <- df.rippleFilter$filter.code[user.input$basic$chosen.rifi.idx]
# load libC for chosen particle
df.libc.HIT <- read.table( system.file( "extdata", "libC",
df.particles$libC.file.name[user.input$basic$chosen.particle],
package = "HITXML"),
sep = "",
col.names = c( "energy.no", "energy.MeV.u",
paste("F", 1:6, ".mm", sep = ""),
paste("I", 1:15, ".1.s", sep = "")))
# Simple path (Yukihara, Oct. 2014)
path.save <- file.path( gsub( "\\",
"/",
paste( "./",
user.input$basic$date,
sep = ""),
fixed = TRUE))
dir.create(path.save,
recursive = TRUE,
showWarnings = FALSE)
if(!interactive.run.mode){
pdf(file = paste(path.save,"/",user.input$basic$name.exp.run, ".pdf", sep = ""))
}
title.doc <- paste(welcome.message,
"\n\nHIT_XML plan documentation\n\n",
"Plan name:",
user.input$basic$date, "/",
user.input$basic$name.exp.series, "/",
user.input$basic$name.exp.run, "\n",
"Projectile: ",
df.particles$nice.particle.name[user.input$basic$chosen.particle],
"\n",
sep = "")
clan.txtplot(title.doc)
n.IES <- 1
nodes.IES <- list()
df.IES <- NULL
repeat{
cat("\n#####################################################################\n",
"Generating iso-energy slice (IES) no. ", n.IES, ".\n",
"#####################################################################\n\n",
sep = "")
if(!interactive.run.mode){
user.input <- HX.get.user.input.IES( n.IES = n.IES,
user.input = user.input,
default.input = default.input,
df.particles = df.particles,
df.fields = df.fields,
df.libc.HIT = df.libc.HIT,
input.con = input.con)
}else{
user.input <- HX.correct.user.input(user.input = user.input,
n.IES = n.IES,
df.libc.HIT = df.libc.HIT)
}
cat("Compute dose from fluence or vice versa\n")
# Compute dose from fluence or vice versa
if(user.input$IES[[n.IES]]$fluence.cm2.or.dose.Gy < 0.0){
dose.Gy <- -1.0 * user.input$IES[[n.IES]]$fluence.cm2.or.dose.Gy
fluence.cm2 <- libamtrack::AT.fluence.cm2.from.dose.Gy( E.MeV.u = user.input$IES[[n.IES]]$energy.value.MeV.u,
D.Gy = dose.Gy,
particle.no = df.particles$particle.no[user.input$basic$chosen.particle],
material.no = 1, # i.e. liquid water
stopping.power.source.no = 3)$fluence.cm2 # use ICRU49/73 data
}else{
fluence.cm2 <- user.input$IES[[n.IES]]$fluence.cm2.or.dose.Gy
dose.Gy <- libamtrack::AT.dose.Gy.from.fluence.cm2( E.MeV.u = user.input$IES[[n.IES]]$energy.value.MeV.u,
fluence.cm2 = fluence.cm2,
particle.no = df.particles$particle.no[user.input$basic$chosen.particle],
material.no = 1, # i.e. liquid water
stopping.power.source.no = 3)$dose.Gy # use ICRU49/73 data
}
cat("Prepare start and field parameters\n")
# Prepare start and field parameters
if(df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx] == "shells"){
par.start <- user.input$IES[[n.IES]]$focus.FWHM.mm * 0.99
field.par <- user.input$IES[[n.IES]]$field.size.mm
}
if(df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx] == "circle"){
par.start <- c(user.input$IES[[n.IES]]$focus.FWHM.mm / 2,
user.input$IES[[n.IES]]$focus.FWHM.mm / 3)
field.par <- c(user.input$IES[[n.IES]]$field.size.mm,
user.input$IES[[n.IES]]$r.min.mm)
}
if(df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx] == "square"){
par.start <- user.input$IES[[n.IES]]$focus.FWHM.mm * 0.99
field.par <- user.input$IES[[n.IES]]$field.size.mm
}
cat("Optimize field\n")
# Optimize field
optim.beam.spot.grid <- HX.optimize.field( field.shape = df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx],
par.start = par.start,
focus.FWHM.mm = user.input$IES[[n.IES]]$focus.FWHM.mm,
field.par = field.par,
fluence.cm2 = fluence.cm2,
N.min = df.particles$minParticles[user.input$basic$chosen.particle],
resolution.mm = user.input$basic$resolution.mm,
spot.distance.mm = user.input$basic$spot.distance.mm,
n.IES = n.IES,
plot = TRUE)$beam.spot.grid
# TODO: Add time estimate for plan
# TODO: Add robustness analysis by MC (see older versions in svn for autofocus routine)
## Translate beam spot grid into XLM structure
voxel.node.list <- list()
for (i in 1:nrow(optim.beam.spot.grid)){
# i <- 1
voxel.node.list[[i]] <- XML::xmlNode("Voxel",
attrs = c( x = optim.beam.spot.grid$x.mm[i],
y = optim.beam.spot.grid$y.mm[i],
particles = optim.beam.spot.grid$N.particles[i]))
}
nodes.IES[[n.IES]] <- XML::xmlNode("IES",
attrs = c(number = as.numeric(n.IES),
energy = as.numeric(user.input$IES[[n.IES]]$energy.value.MeV.u),
focus = as.numeric(user.input$IES[[n.IES]]$focus.FWHM.mm)),
.children = voxel.node.list)
# Add to IES overview data frame
df.IES <- rbind(df.IES,
data.frame( IES.no = n.IES,
E.MeV.u = user.input$IES[[n.IES]]$energy.value.MeV.u,
focus.FWHM.mm = user.input$IES[[n.IES]]$focus.FWHM.mm,
fluence.cm2 = fluence.cm2,
dose.Gy = dose.Gy,
n.spots = nrow(optim.beam.spot.grid), # new field added to table (Yukihara, Oct. 2014)
part.spot = optim.beam.spot.grid$N.particles[1] # new field added to table (Yukihara, Oct. 2014)
))
#Repeat IES? (Yukihara, Oct 2014)
if(!interactive.run.mode){
cat("\nRepeat IES? Enter TOTAL number of identical IES [press return for 1]?\n-->",sep="")
answer<-readLines(con=input.con,n=1)
n.repeats=as.numeric(answer)-1
if(!is.na(n.repeats) & n.repeats>0){
cat("\nCreating ",n.repeats," IES's, for a total of ",n.repeats+1," identical IES's.\n",sep="")
for(i in (n.IES+1):(n.IES+n.repeats)){
#repeat user input
user.input$IES[[i]]=user.input$IES[[i-1]]
# Repeat node
nodes.IES[[i]] <- XML::xmlNode("IES",
attrs = c(number = as.numeric(i),
energy = as.numeric(user.input$IES[[i]]$energy.value.MeV.u),
focus = as.numeric(user.input$IES[[i]]$focus.FWHM.mm)),
.children = voxel.node.list)
# Add to IES overview data frame
df.IES <- rbind(df.IES,
data.frame( IES.no = i,
E.MeV.u = user.input$IES[[i]]$energy.value.MeV.u,
focus.FWHM.mm = user.input$IES[[i]]$focus.FWHM.mm,
fluence.cm2 = fluence.cm2,
dose.Gy = dose.Gy,
n.spots = nrow(optim.beam.spot.grid), # new field added to table (Yukihara, Oct. 2014)
part.spot = optim.beam.spot.grid$N.particles[1] # new field added to table (Yukihara, Oct. 2014)
))
}
n.IES=n.IES+n.repeats
}
}
# Another IES?
if(!interactive.run.mode){
cat( "\nGenerate another IES [y/n (default, press return)]?\n--> ",
sep = "")
answer <- readLines(con = input.con,
n = 1)
if(answer != 'y'){
break
}
user.input$IES=c(user.input$IES,list(list())) # Increase dimention to add IES (Yukihara, Oct. 2014)
}else{
break
}
n.IES <- n.IES + 1
} # repeat IES
row.names(df.IES) <- 1:nrow(df.IES)
clan.txtplot(df.IES)
# Estimate irradiation time (Yukihara, Oct. 2014)
total.particles=sum(df.IES$n.spots*df.IES$part.spot)
duty.cycle=0.4
if(user.input$basic$intensity == 0){
spill.intensity <- df.libc.HIT[1, 8+10]
cat("\n\n=====================================================")
cat("\nIntensity not defined.")
cat("\n=====================================================\n")
}else{
spill.intensity <- df.libc.HIT[1,8 + user.input$basic$intensity]
}
cat("\nCalculating irradiation time with intensity = ",spill.intensity," particles/s")
# spill.intensity=user.input$IES[[1]]$spill.intensity
total.time.s=total.particles/spill.intensity/duty.cycle
time.estimation.message=paste(
"\nTime of irradiation (estimate) and total dose",
"\n=================================================================",
"\n Total number of particles =",total.particles,
"\n Spill intensity (particles/s) =",spill.intensity,
"\n Duty cycle =",duty.cycle,
"\n=================================================================",
"\n Estimated time (s) =",total.time.s,
"\n Estimate time (min), =",total.time.s/60,
"\n=================================================================",
"\n Total dose (Gy) =",sum(df.IES$dose.Gy),
"\n=================================================================\n"
)
cat(time.estimation.message)
clan.txtplot(time.estimation.message)
# Write plan documentation in detail (Yukihara, Oct. 2014)
documentation <- paste("\n\nHIT_XML detailed plan documentation\n\n",
"Plan name:",
user.input$basic$date, "/",
user.input$basic$name.exp.series, "/",
user.input$basic$name.exp.run, "\n",
"Projectile: ",
df.particles$nice.particle.name[user.input$basic$chosen.particle],
"\n",
sep = "")
for (i in 1:length(user.input$basic)){
documentation <- paste(documentation,
names(user.input$basic)[i]," \t\t\t = \t\t\t",as.character(user.input$basic[i]),"\n",
sep="")}
for (i in 1:length(user.input$IES)){
documentation <- paste(documentation, "\nIES no.", i, "\n", sep = "")
for (j in 1:length(user.input$IES[[i]])){
documentation <- paste(documentation,
names(user.input$IES[[i]][j])," = ",as.character(user.input$IES[[i]][[j]]),"\n",
sep = "")
}
}
clan.txtplot(documentation)
if(!interactive.run.mode){
dev.off()
}
# new or old plan format? Non-interactive --> always 2 == new
if(!interactive.run.mode){
plan.format <- as.numeric( HX.prompt.user( prompt = "\nWrite plan in new or old format?",
choices = c("Old", "New"),
default = 2,
input.con = input.con))
}else{
plan.format <- 2
}
first.name.exp.run <- user.input$basic$name.exp.run
repeat{
# Write back defaults
HX.save.defaults(user.input)
# Write request
file.name.plan <- paste(user.input$basic$name.exp.run, ".xml", sep = "")
file.name.request <- paste("req_", file.name.plan, sep = "")
file.name.result <- paste(user.input$basic$name.exp.run, "_result.xml", sep = "")
file.name.PBR <- paste(user.input$basic$name.exp.run, "_PBR.xml", sep = "")
file.name.MBR <- paste(user.input$basic$name.exp.run, "_MBR.xml", sep = "")
path.main <- "E:\\Rtt-Pt-Sim-WorkDir\\HIT-Exp\\"
path.plans <- paste(path.main, user.input$basic$date, "\\", user.input$basic$name.exp.series, "\\", sep = "")
path.result <- paste(path.plans, "OUTPUT\\", sep = "")
path.PBR <- paste(path.result, "PhysicalBeamRecordFile\\", file.name.PBR, sep = "")
path.MBR <- paste(path.result, "MachineBeamRecordFile\\", file.name.MBR, sep = "")
# # Old directory structure from Steffen (removed by Yukihara, Oct. 2014)
# path.save <- file.path( gsub( "\\",
# "/",
# paste( "./Rtt-Pt-Sim-WorkDir/HIT-Exp/",
# user.input$basic$date,
# "/",
# user.input$basic$name.exp.series,
# sep = ""),
# fixed = TRUE))
program.context <- paste(path.plans, file.name.plan, sep = "")
md5.checksum <- digest::digest(program.context, algo = "md5")
node.GroupParameter <- XML::xmlNode( "GroupParameter",
attrs = c(name = "ExecuteSFP"),
.children = list(XML::xmlNode("Parameter",
attrs = c(name = "ProgramID"),
value = "TCsPerformIrradiation"),
XML::xmlNode("Parameter",
attrs = c(name = "ProgramContext"),
value = program.context),
XML::xmlNode("Parameter",
attrs = c(name = "ProgramContextMd5CheckSum"),
value = md5.checksum),
XML::xmlNode("Parameter",
attrs = c(name = "ProgramResult"),
value = (paste(path.result, file.name.result, sep = ""))),
XML::xmlNode("Parameter",
attrs = c(name = "Timeout"),
value = "3000000")))
node.Message <- XML::xmlNode( "Message",
attrs = c( type = "SET",
timestamp = user.input$basic$time,
device = "SFPGM"),
.children = list(node.GroupParameter))
## Write plan
## The "Housekeeping", "Specifications", and "UI" nodes are not
## necessary and not used. Their generation code is kept
## in the svn of <0.6.2 versions. Maybe it will be useful one day.
node.PBR <- XML::xmlNode( "Parameter",
attrs = c(Name = "PhysicalBeamRecordFile"),
value = path.PBR)
node.MBR <- XML::xmlNode( "Parameter",
attrs = c(Name = "MachineBeamRecordFile"),
value = path.MBR)
node.Spill <- XML::xmlNode( "Parameter",
attrs = c(Name = "FullSpill"),
value = "false")
node.SpillIntensity <- XML::xmlNode("Parameter",
attrs = c(Name = "SpillIntensity"),
value = sprintf("%2.1e", user.input$IES[[1]]$spill.intensity))
node.PosCorrLoop <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnablePosCorrectionLoop"),
value = "true")
node.DosemeterName <- XML::xmlNode("Parameter",
attrs = c(Name = "DosemeterDeviceName"),
value = "none")
node.DosemeterCommand <- XML::xmlNode( "Parameter",
attrs = c(Name = "DosemeterCommand"),
value = "none")
node.Channel <- XML::xmlNode( "Parameter",
attrs = c(Name = "Channel"),
value = "All")
node.EnableIC1 <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnableIC1"),
value = "true")
node.EnableIC2 <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnableIC2"),
value = "true")
node.EnableIM <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnableIM"),
value = "true")
node.RstFormat <- XML::xmlNode( "RstFormat",
value = "PT_2004")
node.Patient <- XML::xmlNode("Patient",
attrs = c( id = user.input$fixed$patient.id,
name = user.input$fixed$tumor.name,
sex = user.input$fixed$patient.sex,
birthDate = user.input$fixed$patient.birth))
node.TxInitiation <- XML::xmlNode("TxInitiation",
attrs = c( therapist = user.input$fixed$therapist.name,
dateTime = "2007-01-23T13:52:27.2343750+01:00"))
node.BAMS <- XML::xmlNode( "BAMS",
attrs = c( rippleFilter = ripplefilter.code ,
rangeShifter = "3",
rangeShifterDistance = "20"))
node.table <- XML::xmlNode( "TxTable",
attrs = c( roll = "0",
pitch = "0",
lateral = "150",
longitudinal = "-400",
isocentricAngle = "0",
vertical = "-100.5"))
node.gantry <- XML::xmlNode( "Gantry",
attrs = c( angle = "90"))
tmp.projectile <- df.particles$particle.name[user.input$basic$chosen.particle]
tmp.charge <- df.particles$charge[user.input$basic$chosen.particle]
tmp.mass <- df.particles$mass[user.input$basic$chosen.particle]
tmp.atomicNumber <- df.particles$atomicNumber[user.input$basic$chosen.particle]
if(tmp.projectile == "PROTON"){ # Funny enough, but as from Jun06 mass/charge/atomic no for protons are "" rather than 1
tmp.charge <- ""
tmp.mass <- ""
tmp.atomicNumber<- ""
}
node.TxRoom <- XML::xmlNode("TxRoom",
attrs = c( name = user.input$fixed$room.name,
projectile = tmp.projectile,
charge = tmp.charge,
mass = tmp.mass,
atomicNumber = tmp.atomicNumber))
# REMARK: The beam UID could be changed in principle but it
# likely to cause problems as the same beam UID must be provided manually
# to cancel beam requests in the queueing system, so just leave it
# as it is
node.Beam <- XML::xmlNode("Beam",
attrs = c(uid = "bee035c5-03f6-4e9c-94b9-31f0fc484db1"),
.children = c(list( node.RstFormat,
node.Patient,
node.TxInitiation,
node.TxRoom,
node.BAMS,
node.table,
node.gantry),
nodes.IES))
node.PTTxPlan <- XML::xmlNode( "PTTxPlan",
.children = list(node.Beam))
node.BeamPlan <- XML::xmlNode( "Parameter",
attrs = c(Name = "BeamPlan"),
.children = list(node.PTTxPlan))
if(user.input$IES[[1]]$spill.intensity == 0){
node.SfpParameters <- XML::xmlNode( "SfpParameters",
.children = list( node.PBR,
node.MBR,
node.Spill,
node.PosCorrLoop,
node.DosemeterName,
node.DosemeterCommand,
node.Channel,
node.EnableIC1,
node.EnableIC2,
node.EnableIM,
node.BeamPlan))
}else{
node.SfpParameters <- XML::xmlNode( "SfpParameters",
.children = list( node.PBR,
node.MBR,
node.Spill,
node.SpillIntensity,
node.PosCorrLoop,
node.DosemeterName,
node.DosemeterCommand,
node.Channel,
node.EnableIC1,
node.EnableIC2,
node.EnableIM,
node.BeamPlan))
}
# It seems we do not need the first three node for a working plan
node.WorkflowContext <- XML::xmlNode( "WorkflowContext",
.children = list( #node.Housekeeping,
#node.Specifications,
#node.UIs,
node.SfpParameters))
# # THIS IS THE NEW PLAN FORMAT
# node.PTTxPlanMd5 <- xmlNode("PTTxPlanMd5",
# .children = node.PTTxPlan,
# attrs = c( md5 = "noMD5"))
# xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance",
# xsi:noNamespaceSchemaLocation = "RTT-PT-Plan.xsd"))
# THIS IS THE NEW PLAN FORMAT - with small fixes (Yukihara, Oct. 2014)
node.PTTxPlanMd5 <- XML::xmlNode("PTTxPlanMd5",
node.PTTxPlan,
attrs = c( md5 = "noMD5",
"xmlns:xsi" = "http://www.w3.org/2001/XMLSchema-instance",
"xsi:noNamespaceSchemaLocation" = "RTT-PT-Plan.xsd"))
# SAVE
dir.create(path.save,
recursive = TRUE,
showWarnings = FALSE)
prefix <- paste("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
"<!-- IRRADIATION PLAN CREATED WITH HIT_XML ",
program.version,
" (",
program.date,
")\n S. GREILICH, S. STEFANOWICZ, DKFZ -->\n",
sep = "")
if(plan.format == 1){
XML::saveXML( node.Message,
file = file.path(paste(path.save, "/", file.name.request, sep = "")),
prefix = prefix)
XML::saveXML( node.WorkflowContext,
file = file.path(paste(path.save, "/", file.name.plan, sep = "")),
prefix = prefix)
cat("\nSaved request file ",
file.name.request,
" and plan file ",
file.name.plan,
"\nto location ",
path.save,
"\n\nYou can directly copy this folder onto Rtt-Pt-Sim drive E:\n!!! IMPORTANT: If your plan does not work at HIT, esp. with only one ion species double check with accelerator team if MD% checksums for the control system have been updated after any kind of system maintainance. This is the most likely cause for HITXML plans to fail. !!!\nDone.\n",
sep = "")
}else{
# Save plan in the new format, according to Steffen's format (Yukihara, Oct. 2014)
XML::saveXML( node.PTTxPlanMd5,
file = file.path(paste(path.save, "/", file.name.plan, sep = "")),
prefix = prefix)
# # Save plan in simple new format, according to Julia's example (Yukihara, Oct. 2014)
# saveXML( node.PTTxPlan,
# file = file.path(paste(path.save, "/", file.name.plan, sep = "")),
# prefix = prefix)
cat("\nSaved plan file ",
file.name.plan,
"\nto location ",
path.save,
"\n\nYou can directly copy this folder onto Rtt-Pt-Sim drive E:\n!!! IMPORTANT: If your plan does not work at HIT, esp. with only one ion species double check with accelerator team if MD% checksums for the control system have been updated after any kind of system maintainance. This is the most likely cause for HITXML plans to fail. !!!\nDone.\n",
sep = "")
}
if(!interactive.run.mode){
cat( "\n\nSave same plan with different name [y/n (default, press return)]?\n--> ",
sep = "")
answer <- readLines(con = input.con,
n = 1)
if(answer != 'y'){
break
}
}else{
break
}
# Get new experiment run name
result <- HX.prompt.user( variable.name = "name.exp.run",
prompt = "Please give NEW experiment run name - unique, no whitespace",
df.defaults = df.defaults)
name.exp.run <- result$value
df.defaults <- result$df.defaults
}
# Start pdf viewer for results, Acrobat Reader will
# give problems here if alread open with same file
# Rather use a viewer as "evince" as default
# Check OS
if(!interactive.run.mode){
current.OS <- "Linux"
if (grepl("Windows", Sys.info()[[1]]) == TRUE){
current.OS <- "Windows"
}
switch( match(current.OS, c("Linux", "Windows", "Apple")),
system(paste("evince ./",path.save,"/",user.input$basic$name.exp.run, ".pdf", sep = "")),
system(paste("cmd /c start ", path.save,"\\",user.input$basic$name.exp.run, ".pdf", sep = "")),
system("Tba"))
}
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#!/usr/bin/Rscript
############################################
# Script to create HIT irradiation plans for
# simple, homogenous fields
#
# E0408, DKFZ Heidelberg
# Oct2015
# Maintainer: s.greilich@dkfz.de
############################################
# Please see README for more information
############################################
############################################
# TODOs
############################################
# Fine tuning parameters
# Time estimate (completed in Oct. 2014 - Yukihara)
############################################
# Modifications implemented (Oct. 2014, Yukihara)
# - small fixes to the code to allow it to generate multiple IES with
# different energies.
# - Modified to allow the repetition of IES without repeating the optimization.
# - The code now saves by default the plans in the new format (tested successfully
# at HIT)
#
# Known problems
# - The function that gathers user input does not contain He ion and, therefore,
# does not ask for intensity. As a result, time estimate does not work. The plan
# should work without problems, since intensity information is not included
# in the plans.
# Clear workspace, set version
rm(list =ls())
# load package
library(HITXML)
program.version <- packageDescription("HITXML")$Version
program.date <- packageDescription("HITXML")$Date
# Structure to hold all input data
# This approach allows to run the script interactively, too,
# e.g. for debugging. Normal mode is non-interactively
# by Rscript from command line.
user.input <- list( basic = list( date = 20160920,
name.exp.series = "anTest",
name.exp.run = "ab0001Test",
chosen.particle = 1, # c("Protons", "Helium-4 ions", "Carbon ions", "Oxygen ions")
chosen.rifi.idx = 1, # c("None", "3 mm")
intensity = 1,
resolution.mm = 1,
spot.distance.mm = -1), # If <= 0, do spot distance optimization, otherwise use given value
fixed = list( time = format(Sys.time(), "%Y-%m-%dT%H:%M:%S.1111111+02:00"), # Due to POSIX/Windows problem hardcode fractions of second and time zone for timestamp, TODO: Fix by more flexible solution
room.name = "Room4",
patient.id = "PT-2004-01",
tumor.name = "Sacral Chordoma",
patient.birth = "2004-01-01",
patient.sex = "M",
therapist.name = "USER NAME"),
IES = list( list( energy.value.MeV.u = 50.6, # value will be adjusted to closest available in libC
chosen.idx = NA, # if given, overrides energy value
focus.FWHM.mm = 0.0, # value will be adjusted to closest available in libC
chosen.foc.idx = 3, # if given, overrides focus value
field.shape.idx = 1, # c("square", "circular", "shells")
fluence.cm2.or.dose.Gy = 2e5,
field.size.mm = 50,
r.min.mm = 0.0)))
# Script run interactively or non-interactively, set connection accordingly
interactive.run.mode <- interactive()
if(!interactive.run.mode){
input.con <-file("stdin")
}else{
input.con <-stdin()
}
# Read defaults
default.input <- HX.read.defaults()
# Say hello to user
welcome.message <- paste( "\n",
"#####################################################################\n",
"#####################################################################\n",
"## THIS IS HIT_XML\n## E0408, DKFZ Heidelberg\n## Version ",
program.version,
" as of ",
program.date,
"\n",
"#####################################################################\n",
sep = "")
message(welcome.message)
message("#####################################################################\n\n")
#################################
## Set up data frames for choices
df.particles <- data.frame( particle.name = c("PROTON", "ION", "ION", "ION"),
nice.particle.name = c("Protons", "Helium ions", "Carbon ions", "Oxygen ions"),
mass = c(1,4,12,16),
charge = c(1,2,6,8),
atomicNumber = c(1,2,6,8),
minParticles = c(165000, 0, 5000, 0),
libC.file.name = c( "LIBC HIT Version 1.4 p V11.txt",
"LIBC HIT Version 1.5 He4 V1.txt",
"LIBC HIT Version 1.4 C12 V8.txt",
"LIBC HIT Version 1.5 O16 V2.txt"),
stringsAsFactors = FALSE)
df.particles$particle.no <- libamtrack::AT.particle.no.from.Z.and.A( Z = df.particles$charge,
A = df.particles$mass)$particle.no
df.rippleFilter <- data.frame( filter.name = c("None", "3mm"),
filter.code = c(254, 3),
stringsAsFactors = FALSE)
df.fields <- data.frame( shape = c( "square", "circle", "shells"),
stringsAaFactors = FALSE)
# TODO: Add variables for field shape here
#######################################
## Get user inputs (if non-interactive)
# There is currently a problem wiht the function HX.get.user.input.basic.
# The function does not include He ions in a list of possible particles,
# so it is necessary to update it.
# (Yukihara, 30 Oct 14)
if(!interactive.run.mode){
user.input <- HX.get.user.input.basic(user.input = user.input,
default.input = default.input,
df.particles = df.particles,
df.rippleFilter = df.rippleFilter,
input.con = input.con)
}
# Translate ripple filter code
rippleFilter <- df.rippleFilter$filter.name[user.input$basic$chosen.rifi.idx]
ripplefilter.code <- df.rippleFilter$filter.code[user.input$basic$chosen.rifi.idx]
# load libC for chosen particle
df.libc.HIT <- read.table( system.file( "extdata", "libC",
df.particles$libC.file.name[user.input$basic$chosen.particle],
package = "HITXML"),
sep = "",
col.names = c( "energy.no", "energy.MeV.u",
paste("F", 1:6, ".mm", sep = ""),
paste("I", 1:15, ".1.s", sep = "")))
# Simple path (Yukihara, Oct. 2014)
path.save <- file.path( gsub( "\\",
"/",
paste( "./",
user.input$basic$date,
sep = ""),
fixed = TRUE))
dir.create(path.save,
recursive = TRUE,
showWarnings = FALSE)
if(!interactive.run.mode){
pdf(file = paste(path.save,"/",user.input$basic$name.exp.run, ".pdf", sep = ""))
}
title.doc <- paste(welcome.message,
"\n\nHIT_XML plan documentation\n\n",
"Plan name:",
user.input$basic$date, "/",
user.input$basic$name.exp.series, "/",
user.input$basic$name.exp.run, "\n",
"Projectile: ",
df.particles$nice.particle.name[user.input$basic$chosen.particle],
"\n",
sep = "")
clan.txtplot(title.doc)
n.IES <- 1
nodes.IES <- list()
df.IES <- NULL
repeat{
cat("\n#####################################################################\n",
"Generating iso-energy slice (IES) no. ", n.IES, ".\n",
"#####################################################################\n\n",
sep = "")
if(!interactive.run.mode){
user.input <- HX.get.user.input.IES( n.IES = n.IES,
user.input = user.input,
default.input = default.input,
df.particles = df.particles,
df.fields = df.fields,
df.libc.HIT = df.libc.HIT,
input.con = input.con)
}else{
user.input <- HX.correct.user.input(user.input = user.input,
n.IES = n.IES,
df.libc.HIT = df.libc.HIT)
}
cat("Compute dose from fluence or vice versa\n")
# Compute dose from fluence or vice versa
if(user.input$IES[[n.IES]]$fluence.cm2.or.dose.Gy < 0.0){
dose.Gy <- -1.0 * user.input$IES[[n.IES]]$fluence.cm2.or.dose.Gy
fluence.cm2 <- libamtrack::AT.fluence.cm2.from.dose.Gy( E.MeV.u = user.input$IES[[n.IES]]$energy.value.MeV.u,
D.Gy = dose.Gy,
particle.no = df.particles$particle.no[user.input$basic$chosen.particle],
material.no = 1, # i.e. liquid water
stopping.power.source.no = 3)$fluence.cm2 # use ICRU49/73 data
}else{
fluence.cm2 <- user.input$IES[[n.IES]]$fluence.cm2.or.dose.Gy
dose.Gy <- libamtrack::AT.dose.Gy.from.fluence.cm2( E.MeV.u = user.input$IES[[n.IES]]$energy.value.MeV.u,
fluence.cm2 = fluence.cm2,
particle.no = df.particles$particle.no[user.input$basic$chosen.particle],
material.no = 1, # i.e. liquid water
stopping.power.source.no = 3)$dose.Gy # use ICRU49/73 data
}
cat("Prepare start and field parameters\n")
# Prepare start and field parameters
if(df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx] == "shells"){
par.start <- user.input$IES[[n.IES]]$focus.FWHM.mm * 0.99
field.par <- user.input$IES[[n.IES]]$field.size.mm
}
if(df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx] == "circle"){
par.start <- c(user.input$IES[[n.IES]]$focus.FWHM.mm / 2,
user.input$IES[[n.IES]]$focus.FWHM.mm / 3)
field.par <- c(user.input$IES[[n.IES]]$field.size.mm,
user.input$IES[[n.IES]]$r.min.mm)
}
if(df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx] == "square"){
par.start <- user.input$IES[[n.IES]]$focus.FWHM.mm * 0.99
field.par <- user.input$IES[[n.IES]]$field.size.mm
}
cat("Optimize field\n")
# Optimize field
optim.beam.spot.grid <- HX.optimize.field( field.shape = df.fields$shape[user.input$IES[[n.IES]]$field.shape.idx],
par.start = par.start,
focus.FWHM.mm = user.input$IES[[n.IES]]$focus.FWHM.mm,
field.par = field.par,
fluence.cm2 = fluence.cm2,
N.min = df.particles$minParticles[user.input$basic$chosen.particle],
resolution.mm = user.input$basic$resolution.mm,
spot.distance.mm = user.input$basic$spot.distance.mm,
n.IES = n.IES,
plot = TRUE)$beam.spot.grid
# TODO: Add time estimate for plan
# TODO: Add robustness analysis by MC (see older versions in svn for autofocus routine)
## Translate beam spot grid into XLM structure
voxel.node.list <- list()
for (i in 1:nrow(optim.beam.spot.grid)){
# i <- 1
voxel.node.list[[i]] <- XML::xmlNode("Voxel",
attrs = c( x = optim.beam.spot.grid$x.mm[i],
y = optim.beam.spot.grid$y.mm[i],
particles = optim.beam.spot.grid$N.particles[i]))
}
nodes.IES[[n.IES]] <- XML::xmlNode("IES",
attrs = c(number = as.numeric(n.IES),
energy = as.numeric(user.input$IES[[n.IES]]$energy.value.MeV.u),
focus = as.numeric(user.input$IES[[n.IES]]$focus.FWHM.mm)),
.children = voxel.node.list)
# Add to IES overview data frame
df.IES <- rbind(df.IES,
data.frame( IES.no = n.IES,
E.MeV.u = user.input$IES[[n.IES]]$energy.value.MeV.u,
focus.FWHM.mm = user.input$IES[[n.IES]]$focus.FWHM.mm,
fluence.cm2 = fluence.cm2,
dose.Gy = dose.Gy,
n.spots = nrow(optim.beam.spot.grid), # new field added to table (Yukihara, Oct. 2014)
part.spot = optim.beam.spot.grid$N.particles[1] # new field added to table (Yukihara, Oct. 2014)
))
#Repeat IES? (Yukihara, Oct 2014)
if(!interactive.run.mode){
cat("\nRepeat IES? Enter TOTAL number of identical IES [press return for 1]?\n-->",sep="")
answer<-readLines(con=input.con,n=1)
n.repeats=as.numeric(answer)-1
if(!is.na(n.repeats) & n.repeats>0){
cat("\nCreating ",n.repeats," IES's, for a total of ",n.repeats+1," identical IES's.\n",sep="")
for(i in (n.IES+1):(n.IES+n.repeats)){
#repeat user input
user.input$IES[[i]]=user.input$IES[[i-1]]
# Repeat node
nodes.IES[[i]] <- XML::xmlNode("IES",
attrs = c(number = as.numeric(i),
energy = as.numeric(user.input$IES[[i]]$energy.value.MeV.u),
focus = as.numeric(user.input$IES[[i]]$focus.FWHM.mm)),
.children = voxel.node.list)
# Add to IES overview data frame
df.IES <- rbind(df.IES,
data.frame( IES.no = i,
E.MeV.u = user.input$IES[[i]]$energy.value.MeV.u,
focus.FWHM.mm = user.input$IES[[i]]$focus.FWHM.mm,
fluence.cm2 = fluence.cm2,
dose.Gy = dose.Gy,
n.spots = nrow(optim.beam.spot.grid), # new field added to table (Yukihara, Oct. 2014)
part.spot = optim.beam.spot.grid$N.particles[1] # new field added to table (Yukihara, Oct. 2014)
))
}
n.IES=n.IES+n.repeats
}
}
# Another IES?
if(!interactive.run.mode){
cat( "\nGenerate another IES [y/n (default, press return)]?\n--> ",
sep = "")
answer <- readLines(con = input.con,
n = 1)
if(answer != 'y'){
break
}
user.input$IES=c(user.input$IES,list(list())) # Increase dimention to add IES (Yukihara, Oct. 2014)
}else{
break
}
n.IES <- n.IES + 1
} # repeat IES
row.names(df.IES) <- 1:nrow(df.IES)
clan.txtplot(df.IES)
# Estimate irradiation time (Yukihara, Oct. 2014)
total.particles=sum(df.IES$n.spots*df.IES$part.spot)
duty.cycle=0.4
if(user.input$basic$intensity == 0){
spill.intensity <- df.libc.HIT[1, 8+10]
cat("\n\n=====================================================")
cat("\nIntensity not defined.")
cat("\n=====================================================\n")
}else{
spill.intensity <- df.libc.HIT[1,8 + user.input$basic$intensity]
}
cat("\nCalculating irradiation time with intensity = ",spill.intensity," particles/s")
# spill.intensity=user.input$IES[[1]]$spill.intensity
total.time.s=total.particles/spill.intensity/duty.cycle
time.estimation.message=paste(
"\nTime of irradiation (estimate) and total dose",
"\n=================================================================",
"\n Total number of particles =",total.particles,
"\n Spill intensity (particles/s) =",spill.intensity,
"\n Duty cycle =",duty.cycle,
"\n=================================================================",
"\n Estimated time (s) =",total.time.s,
"\n Estimate time (min), =",total.time.s/60,
"\n=================================================================",
"\n Total dose (Gy) =",sum(df.IES$dose.Gy),
"\n=================================================================\n"
)
cat(time.estimation.message)
clan.txtplot(time.estimation.message)
# Write plan documentation in detail (Yukihara, Oct. 2014)
documentation <- paste("\n\nHIT_XML detailed plan documentation\n\n",
"Plan name:",
user.input$basic$date, "/",
user.input$basic$name.exp.series, "/",
user.input$basic$name.exp.run, "\n",
"Projectile: ",
df.particles$nice.particle.name[user.input$basic$chosen.particle],
"\n",
sep = "")
for (i in 1:length(user.input$basic)){
documentation <- paste(documentation,
names(user.input$basic)[i]," \t\t\t = \t\t\t",as.character(user.input$basic[i]),"\n",
sep="")}
for (i in 1:length(user.input$IES)){
documentation <- paste(documentation, "\nIES no.", i, "\n", sep = "")
for (j in 1:length(user.input$IES[[i]])){
documentation <- paste(documentation,
names(user.input$IES[[i]][j])," = ",as.character(user.input$IES[[i]][[j]]),"\n",
sep = "")
}
}
clan.txtplot(documentation)
if(!interactive.run.mode){
dev.off()
}
# new or old plan format? Non-interactive --> always 2 == new
if(!interactive.run.mode){
plan.format <- as.numeric( HX.prompt.user( prompt = "\nWrite plan in new or old format?",
choices = c("Old", "New"),
default = 2,
input.con = input.con))
}else{
plan.format <- 2
}
first.name.exp.run <- user.input$basic$name.exp.run
repeat{
# Write back defaults
HX.save.defaults(user.input)
# Write request
file.name.plan <- paste(user.input$basic$name.exp.run, ".xml", sep = "")
file.name.request <- paste("req_", file.name.plan, sep = "")
file.name.result <- paste(user.input$basic$name.exp.run, "_result.xml", sep = "")
file.name.PBR <- paste(user.input$basic$name.exp.run, "_PBR.xml", sep = "")
file.name.MBR <- paste(user.input$basic$name.exp.run, "_MBR.xml", sep = "")
path.main <- "E:\\Rtt-Pt-Sim-WorkDir\\HIT-Exp\\"
path.plans <- paste(path.main, user.input$basic$date, "\\", user.input$basic$name.exp.series, "\\", sep = "")
path.result <- paste(path.plans, "OUTPUT\\", sep = "")
path.PBR <- paste(path.result, "PhysicalBeamRecordFile\\", file.name.PBR, sep = "")
path.MBR <- paste(path.result, "MachineBeamRecordFile\\", file.name.MBR, sep = "")
# # Old directory structure from Steffen (removed by Yukihara, Oct. 2014)
# path.save <- file.path( gsub( "\\",
# "/",
# paste( "./Rtt-Pt-Sim-WorkDir/HIT-Exp/",
# user.input$basic$date,
# "/",
# user.input$basic$name.exp.series,
# sep = ""),
# fixed = TRUE))
program.context <- paste(path.plans, file.name.plan, sep = "")
md5.checksum <- digest::digest(program.context, algo = "md5")
node.GroupParameter <- XML::xmlNode( "GroupParameter",
attrs = c(name = "ExecuteSFP"),
.children = list(XML::xmlNode("Parameter",
attrs = c(name = "ProgramID"),
value = "TCsPerformIrradiation"),
XML::xmlNode("Parameter",
attrs = c(name = "ProgramContext"),
value = program.context),
XML::xmlNode("Parameter",
attrs = c(name = "ProgramContextMd5CheckSum"),
value = md5.checksum),
XML::xmlNode("Parameter",
attrs = c(name = "ProgramResult"),
value = (paste(path.result, file.name.result, sep = ""))),
XML::xmlNode("Parameter",
attrs = c(name = "Timeout"),
value = "3000000")))
node.Message <- XML::xmlNode( "Message",
attrs = c( type = "SET",
timestamp = user.input$basic$time,
device = "SFPGM"),
.children = list(node.GroupParameter))
## Write plan
## The "Housekeeping", "Specifications", and "UI" nodes are not
## necessary and not used. Their generation code is kept
## in the svn of <0.6.2 versions. Maybe it will be useful one day.
node.PBR <- XML::xmlNode( "Parameter",
attrs = c(Name = "PhysicalBeamRecordFile"),
value = path.PBR)
node.MBR <- XML::xmlNode( "Parameter",
attrs = c(Name = "MachineBeamRecordFile"),
value = path.MBR)
node.Spill <- XML::xmlNode( "Parameter",
attrs = c(Name = "FullSpill"),
value = "false")
node.SpillIntensity <- XML::xmlNode("Parameter",
attrs = c(Name = "SpillIntensity"),
value = sprintf("%2.1e", user.input$IES[[1]]$spill.intensity))
node.PosCorrLoop <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnablePosCorrectionLoop"),
value = "true")
node.DosemeterName <- XML::xmlNode("Parameter",
attrs = c(Name = "DosemeterDeviceName"),
value = "none")
node.DosemeterCommand <- XML::xmlNode( "Parameter",
attrs = c(Name = "DosemeterCommand"),
value = "none")
node.Channel <- XML::xmlNode( "Parameter",
attrs = c(Name = "Channel"),
value = "All")
node.EnableIC1 <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnableIC1"),
value = "true")
node.EnableIC2 <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnableIC2"),
value = "true")
node.EnableIM <- XML::xmlNode( "Parameter",
attrs = c(Name = "EnableIM"),
value = "true")
node.RstFormat <- XML::xmlNode( "RstFormat",
value = "PT_2004")
node.Patient <- XML::xmlNode("Patient",
attrs = c( id = user.input$fixed$patient.id,
name = user.input$fixed$tumor.name,
sex = user.input$fixed$patient.sex,
birthDate = user.input$fixed$patient.birth))
node.TxInitiation <- XML::xmlNode("TxInitiation",
attrs = c( therapist = user.input$fixed$therapist.name,
dateTime = "2007-01-23T13:52:27.2343750+01:00"))
node.BAMS <- XML::xmlNode( "BAMS",
attrs = c( rippleFilter = ripplefilter.code ,
rangeShifter = "3",
rangeShifterDistance = "20"))
node.table <- XML::xmlNode( "TxTable",
attrs = c( roll = "0",
pitch = "0",
lateral = "150",
longitudinal = "-400",
isocentricAngle = "0",
vertical = "-100.5"))
node.gantry <- XML::xmlNode( "Gantry",
attrs = c( angle = "90"))
tmp.projectile <- df.particles$particle.name[user.input$basic$chosen.particle]
tmp.charge <- df.particles$charge[user.input$basic$chosen.particle]
tmp.mass <- df.particles$mass[user.input$basic$chosen.particle]
tmp.atomicNumber <- df.particles$atomicNumber[user.input$basic$chosen.particle]
if(tmp.projectile == "PROTON"){ # Funny enough, but as from Jun06 mass/charge/atomic no for protons are "" rather than 1
tmp.charge <- ""
tmp.mass <- ""
tmp.atomicNumber<- ""
}
node.TxRoom <- XML::xmlNode("TxRoom",
attrs = c( name = user.input$fixed$room.name,
projectile = tmp.projectile,
charge = tmp.charge,
mass = tmp.mass,
atomicNumber = tmp.atomicNumber))
# REMARK: The beam UID could be changed in principle but it
# likely to cause problems as the same beam UID must be provided manually
# to cancel beam requests in the queueing system, so just leave it
# as it is
node.Beam <- XML::xmlNode("Beam",
attrs = c(uid = "bee035c5-03f6-4e9c-94b9-31f0fc484db1"),
.children = c(list( node.RstFormat,
node.Patient,
node.TxInitiation,
node.TxRoom,
node.BAMS,
node.table,
node.gantry),
nodes.IES))
node.PTTxPlan <- XML::xmlNode( "PTTxPlan",
.children = list(node.Beam))
node.BeamPlan <- XML::xmlNode( "Parameter",
attrs = c(Name = "BeamPlan"),
.children = list(node.PTTxPlan))
if(user.input$IES[[1]]$spill.intensity == 0){
node.SfpParameters <- XML::xmlNode( "SfpParameters",
.children = list( node.PBR,
node.MBR,
node.Spill,
node.PosCorrLoop,
node.DosemeterName,
node.DosemeterCommand,
node.Channel,
node.EnableIC1,
node.EnableIC2,
node.EnableIM,
node.BeamPlan))
}else{
node.SfpParameters <- XML::xmlNode( "SfpParameters",
.children = list( node.PBR,
node.MBR,
node.Spill,
node.SpillIntensity,
node.PosCorrLoop,
node.DosemeterName,
node.DosemeterCommand,
node.Channel,
node.EnableIC1,
node.EnableIC2,
node.EnableIM,
node.BeamPlan))
}
# It seems we do not need the first three node for a working plan
node.WorkflowContext <- XML::xmlNode( "WorkflowContext",
.children = list( #node.Housekeeping,
#node.Specifications,
#node.UIs,
node.SfpParameters))
# # THIS IS THE NEW PLAN FORMAT
# node.PTTxPlanMd5 <- xmlNode("PTTxPlanMd5",
# .children = node.PTTxPlan,
# attrs = c( md5 = "noMD5"))
# xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance",
# xsi:noNamespaceSchemaLocation = "RTT-PT-Plan.xsd"))
# THIS IS THE NEW PLAN FORMAT - with small fixes (Yukihara, Oct. 2014)
node.PTTxPlanMd5 <- XML::xmlNode("PTTxPlanMd5",
node.PTTxPlan,
attrs = c( md5 = "noMD5",
"xmlns:xsi" = "http://www.w3.org/2001/XMLSchema-instance",
"xsi:noNamespaceSchemaLocation" = "RTT-PT-Plan.xsd"))
# SAVE
dir.create(path.save,
recursive = TRUE,
showWarnings = FALSE)
prefix <- paste("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
"<!-- IRRADIATION PLAN CREATED WITH HIT_XML ",
program.version,
" (",
program.date,
")\n S. GREILICH, S. STEFANOWICZ, DKFZ -->\n",
sep = "")
if(plan.format == 1){
XML::saveXML( node.Message,
file = file.path(paste(path.save, "/", file.name.request, sep = "")),
prefix = prefix)
XML::saveXML( node.WorkflowContext,
file = file.path(paste(path.save, "/", file.name.plan, sep = "")),
prefix = prefix)
cat("\nSaved request file ",
file.name.request,
" and plan file ",
file.name.plan,
"\nto location ",
path.save,
"\n\nYou can directly copy this folder onto Rtt-Pt-Sim drive E:\n!!! IMPORTANT: If your plan does not work at HIT, esp. with only one ion species double check with accelerator team if MD% checksums for the control system have been updated after any kind of system maintainance. This is the most likely cause for HITXML plans to fail. !!!\nDone.\n",
sep = "")
}else{
# Save plan in the new format, according to Steffen's format (Yukihara, Oct. 2014)
XML::saveXML( node.PTTxPlanMd5,
file = file.path(paste(path.save, "/", file.name.plan, sep = "")),
prefix = prefix)
# # Save plan in simple new format, according to Julia's example (Yukihara, Oct. 2014)
# saveXML( node.PTTxPlan,
# file = file.path(paste(path.save, "/", file.name.plan, sep = "")),
# prefix = prefix)
cat("\nSaved plan file ",
file.name.plan,
"\nto location ",
path.save,
"\n\nYou can directly copy this folder onto Rtt-Pt-Sim drive E:\n!!! IMPORTANT: If your plan does not work at HIT, esp. with only one ion species double check with accelerator team if MD% checksums for the control system have been updated after any kind of system maintainance. This is the most likely cause for HITXML plans to fail. !!!\nDone.\n",
sep = "")
}
if(!interactive.run.mode){
cat( "\n\nSave same plan with different name [y/n (default, press return)]?\n--> ",
sep = "")
answer <- readLines(con = input.con,
n = 1)
if(answer != 'y'){
break
}
}else{
break
}
# Get new experiment run name
result <- HX.prompt.user( variable.name = "name.exp.run",
prompt = "Please give NEW experiment run name - unique, no whitespace",
df.defaults = df.defaults)
name.exp.run <- result$value
df.defaults <- result$df.defaults
}
# Start pdf viewer for results, Acrobat Reader will
# give problems here if alread open with same file
# Rather use a viewer as "evince" as default
# Check OS
if(!interactive.run.mode){
current.OS <- "Linux"
if (grepl("Windows", Sys.info()[[1]]) == TRUE){
current.OS <- "Windows"
}
switch( match(current.OS, c("Linux", "Windows", "Apple")),
system(paste("evince ./",path.save,"/",user.input$basic$name.exp.run, ".pdf", sep = "")),
system(paste("cmd /c start ", path.save,"\\",user.input$basic$name.exp.run, ".pdf", sep = "")),
system("Tba"))
}
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