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read.abif <- function(filename, max.bytes.in.file = file.info(filename)$size,
pied.de.pilote = 1.2, verbose = FALSE){
#
# Suppress warnings when reading strings with internal nul character:
#
RTC <- function(x, ...) suppressWarnings(rawToChar(x, ...))
#
# Define some shortcuts:
#
SInt32 <- function(f, ...) readBin(f, what = "integer", signed = TRUE, endian = "big", size = 4, ...)
SInt16 <- function(f, ...) readBin(f, what = "integer", signed = TRUE, endian = "big", size = 2, ...)
SInt8 <- function(f, ...) readBin(f, what = "integer", signed = TRUE, endian = "big", size = 1, ...)
UInt32 <- function(f, ...) readBin(f, what = "integer", signed = FALSE, endian = "big", size = 4, ...)
UInt16 <- function(f, ...) readBin(f, what = "integer", signed = FALSE, endian = "big", size = 2, ...)
UInt8 <- function(f, ...) readBin(f, what = "integer", signed = FALSE, endian = "big", size = 1, ...)
f32 <- function(f, ...) readBin(f, what = "numeric", size = 4,endian="little", ...)
f64 <- function(f, ...) readBin(f, what = "numeric", size = 8, endian="little",...)
#
# Load raw data in memory:
#
fc <- file(filename, open = "rb")
rawdata <- readBin(fc, what = "raw", n = pied.de.pilote*max.bytes.in.file,endian="little")
if(verbose) print(paste("number of bytes in file", filename, "is", length(rawdata)))
close(fc)
#
# Make a list to store results:
#
res <- list(Header = NULL, Directory = NA, Data = NA)
#
# Header section is 128 bytes long, located at a fixed position at the
# beginning of the file. We essentially need the number of item and dataoffset
#
res$Header$abif <- RTC(rawdata[1:4])
if(res$Header$abif != "ABIF") stop("file not in ABIF format")
if(verbose) print("OK: File is in ABIF format")
res$Header$version <- SInt16(rawdata[5:6])
if(verbose) print(paste("File in ABIF version", res$Header$version/100))
res$Header$DirEntry.name <- rawdata[7:10]
if(verbose) print(paste("DirEntry name: ", RTC(res$Header$DirEntry.name)))
res$Header$DirEntry.number <- SInt32(rawdata[11:14])
if(verbose) print(paste("DirEntry number: ", res$Header$DirEntry.number))
res$Header$DirEntry.elementtype <- SInt16(rawdata[15:16])
if(verbose) print(paste("DirEntry elementtype: ", res$Header$DirEntry.elementtype))
res$Header$DirEntry.elementsize <- SInt16(rawdata[17:18])
if(verbose) print(paste("DirEntry elementsize: ", res$Header$DirEntry.elementsize))
# This one is important:
res$Header$numelements <- SInt32(rawdata[19:22])
if(verbose) print(paste("DirEntry numelements: ", res$Header$numelements))
# This one is important too:
res$Header$dataoffset <- SInt32(rawdata[27:30])
if(verbose) print(paste("DirEntry dataoffset: ", res$Header$dataoffset))
dataoffset <- res$Header$dataoffset + 1 # start position is 1 in R vectors
res$Header$datahandle <- SInt32(rawdata[31:34])
if(verbose) print(paste("DirEntry datahandle: ", res$Header$datahandle))
res$Header$unused <- SInt16(rawdata[35:128], n = 47)
# Should be ingnored and set to zero
res$Header$unused[1:length(res$Header$unused)] <- 0
if(verbose) print(paste("DirEntry unused: ", length(res$Header$unused), "2-byte integers"))
#
# The directory is located at the offset specified in the header,
# and consist of an array of directory entries.
# We scan the directory to put values in a data.frame:
#
dirdf <- data.frame(list(name = character(0)))
dirdf$name <- as.character(dirdf$name) # force to characters
for(i in seq_len(res$Header$numelements)){
deb <- (i-1)*res$Header$DirEntry.elementsize + dataoffset
direntry <- rawdata[deb:(deb + res$Header$DirEntry.elementsize)]
dirdf[i, "name"] <- RTC(direntry[1:4])
dirdf[i, "tagnumber"] <- SInt32(direntry[5:8])
dirdf[i, "elementtype"] <- SInt16(direntry[9:10])
dirdf[i, "elementsize"] <- SInt16(direntry[11:12])
dirdf[i, "numelements"] <- SInt32(direntry[13:16])
dirdf[i, "datasize"] <- SInt32(direntry[17:20])
dirdf[i, "dataoffset"] <- SInt32(direntry[21:24])
}
if(verbose){
print("Element found:")
print(dirdf$name)
}
#
# Save Directory and make a list to store data:
#
res$Directory <- dirdf
res$Data <- vector("list", nrow(dirdf))
names(res$Data) <- paste(dirdf$name, dirdf$tagnumber, sep = ".")
#
# Data extraction:
#
for(i in seq_len(res$Header$numelements)){
deb <- (i-1)*res$Header$DirEntry.elementsize + dataoffset
# Short data are stored in dataoffset directly:
if(dirdf[i, "datasize"] > 4){
debinraw <- dirdf[i, "dataoffset"] + 1
} else {
debinraw <- deb + 20
}
elementtype <- dirdf[i, "elementtype"]
numelements <- dirdf[i, "numelements"]
elementsize <- dirdf[i, "elementsize"]
data <- rawdata[debinraw:(debinraw + numelements*elementsize)]
# unsigned 8 bits integer:
if(elementtype == 1) res$Data[[i]] <- UInt8(data, n = numelements)
# char or signed 8 bits integer
if(elementtype == 2){
res$Data[[i]] <- tryCatch(RTC(data),finally=paste(rawToChar(data,multiple=TRUE),collapse=""),error=function(er){cat(paste("an error was detected with the following message:",er," but this error was fixed\n",sep=" "))})
}
# unsigned 16 bits integer:
if(elementtype == 3) res$Data[[i]] <- UInt16(data, n = numelements)
# short:
if(elementtype == 4) res$Data[[i]] <- SInt16(data, n = numelements)
# long:
if(elementtype == 5) res$Data[[i]] <- SInt32(data, n = numelements)
# float:
if(elementtype == 7) res$Data[[i]] <- f32(data, n = numelements)
# double:
if(elementtype == 8) res$Data[[i]] <- f64(data, n = numelements)
# date:
if(elementtype == 10)
res$Data[[i]] <- list(year = SInt16(data, n = 1),
month = UInt8(data[-(1:2)], n = 1), day = UInt8(data[-(1:3)], n = 1))
# time:
if(elementtype == 11)
res$Data[[i]] <- list(hour = UInt8(data, n = 1),
minute = UInt8(data[-1], n = 1), second = UInt8(data[-(1:2)], n = 1),
hsecond = UInt8(data[-(1:3)], n = 1))
# pString:
if(elementtype == 18){
n <- SInt8(rawdata[debinraw])
pString <- RTC(rawdata[(debinraw+1):(debinraw+n)])
res$Data[[i]] <- pString
}
# cString:
if(elementtype == 19) res$Data[[i]] <- RTC(data[1:(length(data) - 1) ])
# user:
if(elementtype >= 1024) res$Data[[i]] <- data
# legacy:
if(elementtype %in% c(12, 13))
warning("unimplemented legacy type found in file")
if(elementtype %in% c(6, 9, 14, 15, 16, 17, 20, 128, 256, 384))
warning("unsupported legacy type found in file")
}
return(res)
}
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