## parse character vector from Cadplan DVH file
## courseAsID ignored
parseCadplan <- function(x, planInfo=FALSE, courseAsID=FALSE) {
## function to extract one information element from a number of lines
getElem <- function(pattern, ll, trim=TRUE, iCase=FALSE, collWS=TRUE) {
line <- ll[grep(pattern, ll)]
elem <- sub("^.+?:[[:blank:]]*([[:alnum:][:punct:][:blank:]]+$)", "\\1",
line, ignore.case=iCase, perl=TRUE)
elem <- if(trim) {
trimWS(elem, side="both")
} else {
elem
}
if(collWS) {
collWS(elem)
} else {
elem
}
}
getPlan <- function(pattern, ll, trim=TRUE, iCase=FALSE, collWS=TRUE) {
line <- ll[grep(pattern, ll)]
elem <- sub("^[[:alpha:]]+[[:blank:]]+([[:alnum:]]+[[:alnum:][:blank:]]*)", "\\1",
line, ignore.case=iCase, perl=TRUE)
elem <- if(trim) {
trimWS(elem, side="both")
} else {
elem
}
if(collWS) {
collWS(elem)
} else {
elem
}
}
getDose <- function(pattern, ll, doseRx, percent=TRUE) {
line <- ll[grep(pattern, ll)]
elem <- sub("^.+?:[[:blank:]]+([[:alnum:][:punct:]]+[[:blank:]]*$)", "\\1", line, perl=TRUE)
num <- trimWS(elem)
if(percent && any(grepl("%", line))) {
if(!missing(doseRx)) {
doseRx * as.numeric(num)/100
} else {
NA_real_
}
} else {
as.numeric(num)
}
}
getDoseUnit <- function(ll) {
line <- ll[grep("^Prescr\\. dose.+:", ll)]
elem <- sub("^.+\\((GY|CGY)\\)[[:blank:]]*:.+", "\\1", line, perl=TRUE, ignore.case=TRUE)
toupper(trimWS(elem))
}
getVolUnit <- function(ll) {
line <- ll[grep("^Volume.+:", ll)]
elem <- sub("^.+\\((CC)\\)[[:blank:]]*:.+", "\\1", line, perl=TRUE, ignore.case=TRUE)
toupper(trimWS(elem))
}
getDVHtype <- function(ll) {
line <- ll[grep("^(Cumulative|Differential) (Dose Volume.+|DVH)", ll)]
elem <- sub("^(Cumulative|Differential).+", "\\1", line, perl=TRUE, ignore.case=TRUE)
tolower(trimWS(elem))
}
## split file into list of structure sections
sStart <- grep("^Histogram[[:blank:]]+: [[:alnum:][:punct:]]+", x) # start of sections
sLen <- diff(c(sStart, length(x)+1)) # length of sections
if((length(sLen) < 1L) || all(sLen < 1L)) {
stop("No structures found")
}
structList <- Map(function(start, len) x[start:(start+len-1)], sStart, sLen)
## extract file header and header info
header <- x[seq_len(sStart[1]-1)] # header
patName <- getElem("Patient Name[[:blank:]]*:", header) # patient name
patID <- getElem("^Patient ID[[:blank:]]*:", header) # patient id
plan <- getPlan("^PLAN", header, iCase=TRUE, collWS=TRUE) # treatment plan
DVHdate <- getElem("^Date[[:blank:]]+:", header) # export date
DVHtype <- getDVHtype(header)
## prescribed dose may be encoded in plan
if(tolower(planInfo) == "doserx") {
doseRxUnit <- toupper(sub("^.+_([.[:digit:]]+)(GY|CGY)_.*", "\\2",
plan, perl=TRUE, ignore.case=TRUE))
if(!grepl("^(GY|CGY)$", doseRxUnit)) {
warning("Could not determine dose Rx unit")
doseRxUnit <- NA_character_
}
drx <- sub("^[[:alnum:]]+_([.[:digit:]]+)(GY|CGY)_[[:alnum:]]*", "\\1",
plan, perl=TRUE, ignore.case=TRUE)
doseRx <- as.numeric(drx)
} else {
doseRx <- NA_real_
doseRxUnit <- NA_character_
}
## extract DVH from one structure section and store in a list
## with DVH itself as a matrix
getDVH <- function(strct, info) {
plan <- info$plan
## extract structure, prescribed dose, volume, completed to 100% dose Rx,
## dose min, max, mean, median, mode, and sd
structure <- getElem("^Histogram.*:", strct)
isoDoseRx0 <- getElem("^% for dose[[:blank:]]*:", strct)
## check if sum plan
isoDoseRx <- if((length(isoDoseRx0) > 0) && (isoDoseRx0 != "not defined")) {
as.numeric(isoDoseRx0)
} else { # sum plan -> use plan info?
warning("Iso-dose-Rx is assumed to be 100")
100
}
doseUnit <- getDoseUnit(strct)
if(!grepl("^(GY|CGY)$", doseUnit)) {
doseUnit <- NA_character_
warning("Could not determine dose measurement unit")
}
doseRx0 <- getElem("^Prescr\\. dose.*:", strct)
## check if sum plan
if((length(doseRx0) > 0) && (doseRx0 != "not defined")) {
doseRxUnit <- doseUnit
doseRx <- getDose("^Prescr\\. dose.*:", strct)
} else { # sum plan
## doseRx may be encoded in plan name
if(tolower(planInfo) == "doserx") {
doseRxUnit <- info$doseRxUnit
doseRx <- info$doseRx
} else {
warning("No info on prescribed dose")
doseRxUnit <- NA_character_
doseRx <- NA_real_
}
}
## check if we have dose Rx
## if so, does it have the same unit as doseUnit -> convert
if(!is.na(doseUnit) && !is.na(doseRxUnit)) {
if((doseUnit == "GY") && (doseRxUnit == "CGY")) {
doseRx <- doseRx/100
} else if((doseUnit == "CGY") && (doseRxUnit == "GY")) {
doseRx <- doseRx*100
}
}
volumeUnit <- getVolUnit(strct)
volumeUnit <- if(grepl("^CC$", volumeUnit)) {
"CC"
} else if(grepl("^%", volumeUnit)) {
"PERCENT"
} else {
warning("Could not determine volume measurement unit")
NA_character_
}
structVol <- as.numeric(getElem("^Volume.*:", strct))
doseMin <- getDose("^Dose minimum.*:", strct, doseRx)
doseMax <- getDose("^Dose maximum.*:", strct, doseRx)
doseAvg <- getDose("^Dose mean.*:", strct, doseRx)
doseMed <- getDose("^Dose median.*:", strct, doseRx)
doseMod <- getDose("^Dose modal.*:", strct, doseRx)
doseSD <- getDose("^Standard dev.*:", strct, doseRx, percent=FALSE)
## find DVH
## DVH column headers
colHead <- grep("DOSE[[:blank:]]*\\((%|GY|CGY)\\).+VOLUME", strct,
ignore.case=TRUE, perl=TRUE)
dvhStart <- colHead+1 # first numeric line of DVH
dvhLen <- length(strct) - dvhStart + 1
if((length(dvhLen) < 1L) || dvhLen < 1L) {
stop("No DVH data found")
}
## column headers
vars1 <- unlist(strsplit(strct[colHead],
split="\\([[:alpha:]%]+\\)", fixed=FALSE, perl=TRUE))
## remove leading and trailing white space
vars2 <- tolower(trimWS(vars1))
## make sure we recognize all columns in the DVH
patDose <- "^dose"
patDoseRel <- "^relative dose"
patVol <- "^volume.+cm3"
hits <- sum(c(grepl(patDose, vars2), grepl(patDoseRel, vars2), grepl(patVol, vars2)))
if(length(vars2) != hits) {
stop(c("Could not identify all DVH columns"),
paste(vars2, collapse=", "))
}
## replace column headers
vars3 <- vars2
vars3[grep(patDose, vars2)] <- "dose"
vars3[grep(patDoseRel, vars2)] <- "doseRel"
vars3[grep(patVol, vars2)] <- "volume"
## extract DVH as a matrix and store preceding information
## read line length(strct) for cases where file does not end with a
## blank line -> this will then be last DVH line, otherwise blank
## check if dvh is all blank -> no data
if(all(!nzchar(strct[dvhStart:length(strct)]))) {
return(NULL)
}
dvh <- data.matrix(read.table(text=strct[dvhStart:length(strct)],
header=FALSE, stringsAsFactors=FALSE,
colClasses=rep("numeric", length(vars3)),
comment.char="", nrows=dvhLen))
## rename
colnames(dvh) <- vars3
## catch special case: structVol is 0.0 due to limited precision
if("volume" %in% vars3) {
structVol <- if(info$DVHtype == "cumulative") {
max(c(structVol, dvh[ , "volume"]))
} else {
## reconstruct volumes -> volume is per gray -> mult with bin width
volBin <- dvh[ , "volume"]*diff(c(-dvh[1, "dose"], dvh[ , "dose"]))
max(c(structVol, sum(volBin)))
}
}
## add information we don't have yet: relative/absolute volume
if(( "volumeRel" %in% vars3) && !("volume" %in% vars3)) {
dvh <- cbind(dvh, volume=structVol*(dvh[ , "volumeRel"]/100))
} else if(("volume" %in% vars3) && !("volumeRel" %in% vars3)) {
dvh <- cbind(dvh, volumeRel=100*(dvh[ , "volume"]/structVol))
}
## add information we don't have yet: relative/absolute dose
## considering isoDoseRx
if(( "doseRel" %in% vars3) && !("dose" %in% vars3)) {
dvh <- cbind(dvh, dose=dvh[ , "doseRel"]*doseRx / isoDoseRx)
# (doseRx/(isoDoseRx/100))*(dvh$doseRel/100)
} else if(("dose" %in% vars3) && !("doseRel" %in% vars3)) {
dvh <- cbind(dvh, doseRel=dvh[ , "dose"]*isoDoseRx / doseRx)
# 100*(dvh$dose/(doseRx/(isoDoseRx/100)))
}
## check if dose is increasing
stopifnot(isIncreasing(dvh))
DVH <- list(dvh=dvh,
patID=info$patID,
patName=info$patName,
date=info$date,
DVHtype=info$DVHtype,
plan=info$plan,
structure=structure,
structVol=structVol,
doseUnit=doseUnit,
volumeUnit=volumeUnit,
doseMin=doseMin,
doseMax=doseMax,
doseRx=doseRx,
doseRxUnit=doseRxUnit,
isoDoseRx=isoDoseRx,
doseAvg=doseAvg,
doseMed=doseMed,
doseSD=doseSD)
## convert differential DVH (not per unit dose!) to cumulative
## and add differential DVH separately
if(info$DVHtype == "differential") {
DVH$dvh <- convertDVH(dvh, toType="cumulative",
toDoseUnit="asis", perDose=FALSE)
DVH$dvhDiff <- dvh
}
## set class
class(DVH) <- "DVHs"
return(DVH)
}
## list of DVH data frames with component name = structure
info <- list(patID=patID, patName=patName, plan=plan, date=DVHdate,
DVHtype=DVHtype, doseRx=doseRx, doseRxUnit=doseRxUnit)
dvhL <- lapply(structList, getDVH, info)
dvhL <- Filter(Negate(is.null), dvhL)
names(dvhL) <- sapply(dvhL, function(y) y$structure)
if(length(unique(names(dvhL))) < length(dvhL)) {
warning("Some structures have the same name - this can lead to problems")
}
class(dvhL) <- "DVHLst"
attr(dvhL, which="byPat") <- TRUE
return(dvhL)
}
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