-#data: matrix of double or connection
-serialize = function(data_ascii, data_bin_file, nb_per_chunk,
+#' @name de_serialize
+#' @rdname de_serialize
+#' @aliases binarize getDataInFile
+#'
+#' @title (De)Serialization of a matrix
+#'
+#' @description \code{binarize()} serializes a matrix or CSV file with minimal overhead,
+#' into a binary file. \code{getDataInFile()} achieves the inverse task: she retrieves
+#' (ASCII) data rows from indices in the binary file
+#'
+#' @param data_ascii Either a matrix or CSV file, with items in rows
+#' @param indices Indices of the lines to retrieve
+#' @param data_bin_file Name of binary file on output (\code{binarize})
+#' or intput (\code{getDataInFile})
+#' @param nb_per_chunk Number of lines to process in one batch
+#' @inheritParams claws
+#'
+#' @return For \code{getDataInFile()}, the matrix with rows corresponding to the
+#' requested indices
+NULL
+
+#' @rdname de_serialize
+#' @export
+binarize = function(data_ascii, data_bin_file, nb_per_chunk,
sep=",", nbytes=4, endian=.Platform$endian)
{
if (is.character(data_ascii))
data_ascii = file(data_ascii, open="r")
- else if (is(data_ascii,"connection") && !isOpen(data_ascii))
+ else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii))
open(data_ascii)
first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0)
if (first_write)
{
#number of items always on 8 bytes
- writeBin(0L, data_bin, size=8) #,endian="little")
+ writeBin(0L, data_bin, size=8, endian=endian)
if (is.matrix(data_ascii))
data_length = ncol(data_ascii)
else #if (is(data, "connection"))
{
data_line = scan(data_ascii, double(), sep=sep, nlines=1, quiet=TRUE)
- writeBin(data_line, data_bin, size=nbytes)
+ writeBin(data_line, data_bin, size=nbytes, endian=endian)
data_length = length(data_line)
}
}
data_chunk = scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE)
if (length(data_chunk)==0)
break
- writeBin(data_chunk, data_bin, size=nbytes)
+ writeBin(data_chunk, data_bin, size=nbytes, endian=endian)
}
if (first_write)
{
#ecrire file_size-1 / (nbytes*nbWritten) en 0 dans bin_data ! ignored == file_size
ignored = seek(data_bin, 0)
- writeBin(data_length, data_bin, size=8)
+ writeBin(data_length, data_bin, size=8, endian=endian)
}
close(data_bin)
- if (is(data_ascii,"connection"))
+ if (methods::is(data_ascii,"connection"))
close(data_ascii)
}
-#read in binary file, always same structure
+#' @rdname de_serialize
+#' @export
getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
{
data_bin = file(data_bin_file, "rb")
- data_size = file.info(data_bin)$size
- data_length = readBin(data_bin, "integer", 1, 8, endian)
+ data_size = file.info(data_bin_file)$size
+ data_length = readBin(data_bin, "integer", n=1, size=8, endian=endian)
#Ou t(sapply(...)) (+ rapide ?)
data_ascii = do.call( rbind, lapply( indices, function(i) {
offset = 8+(i-1)*data_length*nbytes
if (offset > data_size)
return (vector("double",0))
ignored = seek(data_bin, offset)
- readBin(data_bin, "double", n=data_length, size=nbytes)
+ readBin(data_bin, "double", n=data_length, size=nbytes, endian=endian)
} ) )
close(data_bin)
if (ncol(data_ascii)>0) data_ascii else NULL