#####---------------------------------------------------------------------------
## parse character vector from ProSoma DVH file
## planInfo and courseAsID ignored
parseProSoma <- function(x, planInfo=FALSE, courseAsID=FALSE, ...) {
## function to extract patient name from first line
getPatName <- function(ll) {
paste(trimWS(rev(strsplit(ll, ",")[[1]])), collapse=" ")
}
## 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:]]+$)", "\\1",
line, ignore.case=iCase, perl=TRUE)
elem <- if(trim) {
trimWS(elem, side="both")
} else {
elem
}
if(collWS) {
collWS(elem)
} else {
elem
}
}
getDose <- function(pattern, ll, doseRx) {
line <- ll[grep(pattern, ll)]
pat <- "^.+?:[^[:digit:]]*([[:digit:][:punct:]]+)(Gy|cGy|%)*([[:alnum:][:punct:][:blank:]]*)$"
elem <- gsub(pat, "\\1", line, perl=TRUE, ignore.case=TRUE)
grp2 <- gsub(pat, "\\2", line, perl=TRUE, ignore.case=TRUE)
grp3 <- gsub(pat, "\\3", line, perl=TRUE, ignore.case=TRUE)
if(nzchar(grp2) || nzchar(grp3)) {
warning("Non-standard dose line found")
}
num <- as.numeric(trimWS(elem))
if(is.na(num)) {
warning("No dose found")
}
if(grepl("\\[%\\]", line)) {
## relative dose
if(!missing(doseRx)) {
doseRx * num/100
} else {
NA_real_
}
} else {
num
}
}
getDoseUnit <- function(ll) {
line <- ll[grep("^Average \\[.+\\]:.+", ll)]
elem <- sub("^.+\\[(GY|CGY)\\]:.+", "\\1", line, perl=TRUE, ignore.case=TRUE)
toupper(trimWS(elem))
}
getVolUnit <- function(ll) {
line <- ll[grep("^Volume \\[.+\\]:.+", ll)]
elem <- sub("^.+\\[(.+)\\]:.+", "\\1", line, perl=TRUE, ignore.case=TRUE)
toupper(trimWS(elem))
}
getDVHtype <- function(ll) {
line <- ll[grep("^(Cumulative|Differential) DVH", ll)]
elem <- sub("^(Cumulative|Differential).+", "\\1", line, perl=TRUE, ignore.case=TRUE)
tolower(trimWS(elem))
}
sStart <- grep("^Name:[[: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
## ProSoma file does not have a PatID
header <- x[seq_len(sStart[1]-1)] # header
patName <- getPatName(header[1]) # patient name
patID <- gsub("[^a-z0-9]", "\\1", tempfile(pattern="", tmpdir="")) # as.character(trunc(runif(1, 0, 10000001)))
plan <- NA_character_
doseRx <- NA_real_
DVHdate <- NA_character_
DVHtype <- getDVHtype(header)
doseRxUnit <- NA_character_
doseRx <- NA_real_
## 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$doseRx
doseRxUnit <- info$doseRxUnit
doseUnit <- getDoseUnit(strct)
if(!grepl("^(GY|CGY)$", doseUnit)) {
warning("Could not determine dose measurement unit")
doseUnit <- NA_character_
}
## 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
}
}
## extract structure, volume, dose min, max, mean, median and sd
structure <- getElem("^Name:", strct)
structVol <- as.numeric(getElem("^Volume \\[.+\\]:.+", strct))
doseMin <- getDose("^Min \\[.+\\]:.+", strct, doseRx)
doseMax <- getDose("^Max \\[.+\\]:.+", strct, doseRx)
doseAvg <- getDose("^Average \\[.+\\]:.+", strct, doseRx)
doseMed <- getDose("^D50% \\[.+\\]:.+", strct, doseRx)
doseMode <- NA_real_
doseSD <- NA_real_
volumeUnit <- getVolUnit(strct)
volumeUnit <- if(grepl("^CM.+", volumeUnit, useBytes=TRUE)) {
"CC"
} else if(grepl("^ML", volumeUnit)) {
## ml = cm^3
"CC"
} else if(grepl("^%", volumeUnit)) {
"PERCENT"
} else {
warning("Could not determine volume measurement unit")
NA_character_
}
## find DVH
## DVH column headers
colHead <- grep("DOSE \\[(%|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="\\t+", 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 \\[(GY|CGY)\\]"
patDoseRel <- "^dose \\[%\\]"
patVolRel <- "^volume"
patVolD <- "^volume" # differential DVH
hits <- sum(c(grepl(patDose, vars2, ignore.case=TRUE),
grepl(patDoseRel, vars2, ignore.case=TRUE),
grepl(patVolRel, vars2, ignore.case=TRUE),
grepl(patVolD, vars2, ignore.case=TRUE) &&
DVHtype == "differential"))
if(length(vars2) != hits) {
stop(c("Could not identify all DVH columns"),
paste(vars2, collapse=", "))
}
## replace column headers
vars3 <- vars2
vars3[grep(patDose, vars2, ignore.case=TRUE)] <- "dose"
vars3[grep(patDoseRel, vars2, ignore.case=TRUE)] <- "doseRel"
vars3[grep(patVolRel, vars2, ignore.case=TRUE)] <- "volumeRel"
vars3[grepl(patVolD, vars2, ignore.case=TRUE) &
(DVHtype == "differential")] <- "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 <- 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
## 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=DVHtype,
plan=info$plan,
structure=structure,
structVol=structVol,
doseUnit=doseUnit,
volumeUnit=volumeUnit,
doseMin=doseMin,
doseMax=doseMax,
doseRx=doseRx,
doseRxUnit=doseRxUnit,
doseAvg=doseAvg,
doseMed=doseMed,
doseMode=doseMode,
doseSD=doseSD)
## convert differential DVH (per unit dose) to cumulative
## and add differential DVH separately
if(info$DVHtype == "differential") {
# stop("differential DVH currently not supported")
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,
date=DVHdate,
DVHtype=DVHtype,
plan=plan,
doseRx=doseRx,
doseRxUnit=doseRxUnit)
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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