#####---------------------------------------------------------------------------
## parse character vector from Masterplan DVH file
## planInfo and courseAsID ignored
parseMasterplan <- function(x, planInfo=FALSE, courseAsID=FALSE, ...) {
## function to extract one information element from a number of lines
## make sure only first : is matched -> not greedy
getElem <- function(pattern, ll, trim=TRUE, iCase=FALSE, collWS=TRUE) {
line <- ll[grep(pattern, ll)]
elem <- sub("^.+?:[[:blank:]]+([[:alnum:][:punct:][:blank:]]+$)", "\\1",
line, ignore.case=iCase, perl=TRUE)
elem <- if(trim) {
trimWS(elem, side="both")
} else {
elem
}
if(collWS) {
collWS(elem)
} else {
elem
}
}
getDoseUnit <- function(ll) {
line <- ll[grep("^(Absolute|Relative) dose - ", ll, ignore.case=TRUE)]
elem <- sub("^.+\\[(GY|CGY)\\]", "\\1", line, perl=TRUE, ignore.case=TRUE)
toupper(trimWS(elem))
}
getVolUnit <- function(ll) {
line <- ll[grep("^(Absolute|Relative) volume - ", ll, ignore.case=TRUE)]
elem <- sub("^.+\\[(ccm|%)\\]", "\\1", line, perl=TRUE, ignore.case=TRUE)
toupper(trimWS(elem))
}
getDVHtype <- function(ll) {
line <- ll[grep("mode", ll)]
elem <- sub("^(Cumulative|Differential) mode", "\\1", line, perl=TRUE, ignore.case=TRUE)
tolower(trimWS(elem))
}
sStart <- grep("^ROI: .+$", x) # start of sections
## there may be preceding Dose: ... line
idx_preceding <- nzchar(x[sStart-1])
sStart[idx_preceding] <- (sStart-1)[idx_preceding]
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:", header) # patient name
if(length(patName) == 0L) {
patName <- gsub("[^a-z0-9]", "\\1", tempfile(pattern="", tmpdir=""))
}
patID <- getElem("^Patient Id:", header) # patient id
if(length(patID) == 0L) {
patID <- gsub("[^a-z0-9]", "\\1", tempfile(pattern="", tmpdir=""))
}
plan <- getElem("^Plan:", header) # treatment plan
DVHdate <- NA_character_
DVHtype <- getDVHtype(header)
doseRx <- NA_real_
doseUnit <- getDoseUnit(header)
if(!grepl("^(GY|CGY)$", doseUnit)) {
warning("Could not determine dose measurement unit")
doseUnit <- NA_character_
}
volumeUnit <- getVolUnit(header)
volumeUnit <- if(grepl("^CCM", volumeUnit)) {
"CC"
} else if(grepl("^%", volumeUnit)) {
"PERCENT"
} else {
warning("Could not determine volume measurement unit")
NA_character_
}
## extract DVH from one structure section and store in a list
## with DVH itself as a matrix
getDVH <- function(strct, info) {
## extract information from info list
doseRx <- info$doseRx
## extract structure, volume, dose min, max, mean, median and sd
structure <- getElem("^ROI*:", strct)
## find DVH
## DVH column headers
colHead <- grep("DOSE.+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="[[:blank:]]+", 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"
patVol <- "^volume"
patBin <- "^bin"
hits <- sum(c(grepl(patDose, vars2),
grepl(patVol, vars2),
grepl(patBin, vars2)))
if(length(vars2) != hits) {
stop(c("Could not identify all DVH columns"),
paste(vars2, collapse=", "))
}
## final column headers
## rename volume to relative volume if necessary
vars3 <- vars2
if(info$volumeUnit == "PERCENT") {
vars3[grepl(patVol, vars3)] <- "volumeRel"
}
## extract DVH as a matrix and store preceding information
## read line length(strct) for cases where file does not end with a
## blank line -> this will then be last DVH line, otherwise blank
## check if dvh is all blank -> no data
if(all(!nzchar(strct[dvhStart:length(strct)]))) {
return(NULL)
}
dvh_text <- strct[dvhStart:length(strct)]
dvh <- data.matrix(read.table(text=dvh_text,
header=FALSE, stringsAsFactors=FALSE,
colClasses=rep("numeric", length(vars3)),
comment.char="", nrows=dvhLen))
## remove bin numbers
colnames(dvh) <- vars3
dvh <- dvh[ , -grep(patBin, vars3, ignore.case=TRUE)]
## structVol is NA in Masterplan -> 100% or maximum of DVH volumes
structVol <- if(info$volumeUnit == "PERCENT") {
warning(c("No information on absolute structure volume available"))
NA_real_
} else {
if(info$DVHtype == "cumulative") {
max(dvh[ , "volume"])
} else {
## reconstruct volumes -> volume is per gray -> mult with bin width
volBin <- dvh[ , "volume"]*diff(c(-dvh[1, "dose"], dvh[ , "dose"]))
sum(volBin)
}
}
## add information we don't have yet: relative/absolute volume
if(( "volumeRel" %in% vars3) && !("volume" %in% vars3)) {
dvh <- cbind(dvh, volume=structVol*(dvh[ , "volumeRel"]/100))
} else if(("volume" %in% vars3) && !("volumeRel" %in% vars3)) {
dvh <- cbind(dvh, volumeRel=100*(dvh[ , "volume"]/structVol))
}
## add information we don't have yet: relative/absolute dose
## without considering isoDoseRx
isoDoseRxTmp <- 100
if(( "doseRel" %in% vars3) && !("dose" %in% vars3)) {
dvh <- cbind(dvh, dose=dvh[ , "doseRel"]*doseRx / isoDoseRxTmp)
# (doseRx/(isoDoseRxTmp/100))*(dvh$doseRel/100)
} else if(("dose" %in% vars3) && !("doseRel" %in% vars3)) {
dvh <- cbind(dvh, doseRel=dvh[ , "dose"]*isoDoseRxTmp / doseRx)
# 100*(dvh$dose/(doseRx/(isoDoseRxTmp/100)))
}
## check if dose is increasing
stopifnot(isIncreasing(dvh))
DVH <- list(dvh=dvh,
patName=info$patName,
patID=info$patID,
date=info$date,
DVHtype=info$DVHtype,
plan=info$plan,
structure=structure,
structVol=structVol,
doseUnit=info$doseUnit,
volumeUnit=info$volumeUnit,
doseRx=doseRx)
## convert differential DVH (per unit dose) to cumulative
## and add differential DVH separately
if(info$DVHtype == "differential") {
DVH$dvh <- convertDVH(dvh, toType="cumulative",
toDoseUnit="asis", perDose=TRUE)
DVH$dvhDiff <- dvh
}
## Masterplan does not export mean/min/max ...
DVH$doseMin <- NA_real_
DVH$doseMax <- NA_real_
DVH$doseMed <- NA_real_
DVH$doseAvg <- NA_real_
DVH$doseSD <- NA_real_
DVH$doseMode <- NA_real_
## set class
class(DVH) <- "DVHs"
return(DVH)
}
## list of DVH data frames with component name = structure
info <- list(patID=patID,
patName=patName,
date=DVHdate,
DVHtype=DVHtype,
plan=plan,
doseRx=doseRx,
doseUnit=doseUnit,
volumeUnit=volumeUnit)
dvhL <- lapply(structList, getDVH, info=info)
dvhL <- Filter(Negate(is.null), dvhL)
names(dvhL) <- sapply(dvhL, function(y) y$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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