-#data: matrix of double or connection
-serialize = function(data_ascii, data_bin_file, nb_per_chunk,
+#' @name de_serialize
+#' @rdname de_serialize
+#' @aliases binarize binarizeTransform getDataInFile
+#'
+#' @title (De)Serialization of a [big]matrix or data stream
+#'
+#' @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. Finally,
+#' \code{binarizeTransform()} serialize transformations of all data chunks; to use it,
+#' a data-retrieval function must be provided, thus \code{binarize} will most likely be
+#' used first (and then a function defined to seek in generated 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
+#' @param getData Function to retrieve data chunks
+#' @param transform Transformation function to apply on data chunks
+#'
+#' @return For \code{getDataInFile()}, the matrix with rows corresponding to the
+#' requested indices. \code{binarizeTransform} returns the number of processed lines.
+#' \code{binarize} is designed to serialize in several calls, thus returns nothing.
+NULL
+
+#' @rdname de_serialize
+#' @export
+binarize = function(data_ascii, data_bin_file, nb_per_chunk,
sep=",", nbytes=4, endian=.Platform$endian)
{
if (is.character(data_ascii))
data_ascii = file(data_ascii, open="r")
- else if (is(data_ascii,"connection") && !isOpen(data_ascii))
+ else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii))
open(data_ascii)
+ is_matrix = !methods::is(data_ascii,"connection")
first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0)
data_bin = file(data_bin_file, open=ifelse(first_write,"wb","ab"))
if (first_write)
{
#number of items always on 8 bytes
- writeBin(0L, data_bin, size=8) #,endian="little")
- if (is.matrix(data_ascii))
- data_length = ncol(data_ascii)
- else #if (is(data, "connection"))
+ writeBin(0L, data_bin, size=8, endian=endian)
+ if ( is_matrix )
+ data_length = nrow(data_ascii)
+ else #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)
}
}
- if (is.matrix(data_ascii))
+ if (is_matrix)
index = 1
repeat
{
- if (is.matrix(data_ascii))
+ if ( is_matrix )
{
- range = index:min(nrow(data_ascii),index+nb_per_chunk)
data_chunk =
- if (range[1] <= nrow(data_ascii))
- as.double(t(data_ascii[range,]))
+ if (index <= ncol(data_ascii))
+ as.double(data_ascii[,index:min(nrow(data_ascii),index+nb_per_chunk-1)])
else
- integer(0)
+ double(0)
index = index + nb_per_chunk
}
else
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
+ # Write data_length, = (file_size-1) / (nbytes*nbWritten) at offset 0 in data_bin
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 ( ! is_matrix )
close(data_ascii)
}
-#read in binary file, always same structure
+#' @rdname de_serialize
+#' @export
+binarizeTransform = function(getData, transform, data_bin_file, nb_per_chunk,
+ nbytes=4, endian=.Platform$endian)
+{
+ nb_items = 0
+ index = 1
+ repeat
+ {
+ data_chunk = getData((index-1)+seq_len(nb_per_chunk))
+ if (is.null(data_chunk))
+ break
+ transformed_chunk = transform(data_chunk)
+ binarize(transformed_chunk, data_bin_file, nb_per_chunk, ",", nbytes, endian)
+ index = index + nb_per_chunk
+ nb_items = nb_items + nrow(data_chunk)
+ }
+ nb_items
+}
+
+#' @rdname de_serialize
+#' @export
getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
{
data_bin = file(data_bin_file, "rb")
- data_size = file.info(data_bin)$size
- data_length = readBin(data_bin, "integer", 1, 8, endian)
- #Ou t(sapply(...)) (+ rapide ?)
- data_ascii = do.call( rbind, lapply( indices, function(i) {
+ data_size = file.info(data_bin_file)$size
+ data_length = readBin(data_bin, "integer", n=1, size=8, endian=endian)
+ data_ascii = sapply( 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
}
projects / epclust.git / blobdiff