-#data: matrix of double or connection
-serialize = function(data_ascii, data_bin_file, nb_per_chunk,
+#' (De)Serialization of a [big]matrix or data stream
+#'
+#' \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 Matrix (by columns) or CSV file or connection (by rows)
+#' @param data_bin_file Name of binary file on output of \code{binarize()}
+#' or input of \code{getDataInFile()}
+#' @param nb_per_chunk Number of lines to process in one batch
+#' @param getData Function to retrieve data chunks
+#' @param transform Transformation function to apply on data chunks
+#' @param indices Indices of the lines to retrieve
+#' @inheritParams claws
+#'
+#' @return For \code{getDataInFile()}, a matrix with columns 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.
+#'
+#' @name de_serialize
+#' @rdname de_serialize
+#' @aliases binarize binarizeTransform getDataInFile
+NULL
+
+#' @rdname de_serialize
+#' @export
+binarize <- function(data_ascii, data_bin_file, nb_per_chunk,
sep=",", nbytes=4, endian=.Platform$endian)
{
+ # data_ascii can be of two types: [big.]matrix, or connection
if (is.character(data_ascii))
- data_ascii = file(data_ascii, open="r")
- else if (is(data_ascii,"connection") && !isOpen(data_ascii))
+ data_ascii <- file(data_ascii, open="r")
+ else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii))
open(data_ascii)
+ is_matrix <- !methods::is(data_ascii,"connection")
+
+ # At first call, the length of a stored row is written. So it's important to determine
+ # if the serialization process already started.
+ first_write <- (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0)
- 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"))
+ # Open the binary file for writing (or 'append' if already exists)
+ data_bin <- file(data_bin_file, open=ifelse(first_write,"wb","ab"))
- #write data length on first call
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"))
+ # Write data length on first call: number of items always on 8 bytes
+ 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)
- data_length = length(data_line)
+ # Read the first line to know data length, and write it then
+ data_line <- scan(data_ascii, double(), sep=sep, nlines=1, quiet=TRUE)
+ writeBin(data_line, data_bin, size=nbytes, endian=endian)
+ data_length <- length(data_line)
}
}
- if (is.matrix(data_ascii))
- index = 1
+ if (is_matrix)
+ {
+ # Data is processed by chunks; although this may not be so useful for (normal) matrix
+ # input, it could for a file-backed big.matrix. It's easier to follow a unified pattern.
+ 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,]))
+ data_chunk <-
+ if (index <= ncol(data_ascii))
+ as.double(data_ascii[,index:min(ncol(data_ascii),index+nb_per_chunk-1)])
else
- integer(0)
- index = index + nb_per_chunk
+ double(0)
+ index <- index + nb_per_chunk
}
- else
- data_chunk = scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE)
+ else #connection
+ data_chunk <- scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE)
+
+ # Data size is unknown in the case of a connection
if (length(data_chunk)==0)
break
- writeBin(data_chunk, data_bin, size=nbytes)
+
+ # Write this chunk of data to the binary file
+ 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)
+ # 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, endian=endian)
}
close(data_bin)
- if (is(data_ascii,"connection"))
+ if ( ! is_matrix )
close(data_ascii)
}
-#read in binary file, always same structure
-getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
+#' @rdname de_serialize
+#' @export
+binarizeTransform <- function(getData, transform, data_bin_file, nb_per_chunk,
+ 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) {
- 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)
+ nb_items <- 0 #side-effect: store the number of transformed items
+ index <- 1
+ repeat
+ {
+ # Retrieve a chunk of data in a binary file (generally obtained by binarize())
+ data_chunk <- getData((index-1)+seq_len(nb_per_chunk))
+ if (is.null(data_chunk))
+ break
+
+ # Apply transformation on the current chunk (by columns)
+ transformed_chunk <- transform(data_chunk)
+
+ # Save the result in binary format
+ binarize(transformed_chunk, data_bin_file, nb_per_chunk, ",", nbytes, endian)
+
+ index <- index + nb_per_chunk
+ nb_items <- nb_items + ncol(data_chunk)
+ }
+ nb_items #number of transformed items
+}
+
+#' @rdname de_serialize
+#' @export
+getDataInFile <- function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
+{
+ data_bin <- file(data_bin_file, "rb") #source binary file
+
+ data_size <- file.info(data_bin_file)$size #number of bytes in the file
+ # data_length: length of a vector in the binary file (first element, 8 bytes)
+ data_length <- readBin(data_bin, "integer", n=1, size=8, endian=endian)
+
+ # Seek all 'indices' columns in the binary file, using data_length and nbytes
+ # to compute the offset ( index i at 8 + i*data_length*nbytes )
+ data_ascii <- do.call( cbind, lapply( indices, function(i) {
+ offset <- 8+(i-1)*data_length*nbytes
+ if (offset >= data_size)
+ return (NULL)
+ ignored <- seek(data_bin, offset) #position cursor at computed offset
+ readBin(data_bin, "double", n=data_length, size=nbytes, endian=endian)
} ) )
close(data_bin)
- if (ncol(data_ascii)>0) data_ascii else NULL
+
+ data_ascii #retrieved data, in columns
}
projects / epclust.git / blobdiff