#' @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
+#' or input (\code{getDataInFile})
+#' @param nb_per_chunk Number of lines to process in one batch (big.matrix or connection)
#' @inheritParams claws
#' @param getData Function to retrieve data chunks
#' @param transform Transformation function to apply on data chunks
binarize = function(data_ascii, data_bin_file, nb_per_chunk,
sep=",", nbytes=4, endian=.Platform$endian)
{
+ # data_ascii can be of two types: [big.]matrix, or connection
if (is.character(data_ascii))
data_ascii = file(data_ascii, open="r")
else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii))
open(data_ascii)
is_matrix = !methods::is(data_ascii,"connection")
+ # At first call, the length of a stored row is written. So it's important to determine
+ # if the serialization process already started.
first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0)
+
+ # 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
+ # 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
{
+ # 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 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)
double(0)
index = index + nb_per_chunk
}
- else
+ 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
+
+ # Write this chunk of data to the binary file
writeBin(data_chunk, data_bin, size=nbytes, endian=endian)
}
binarizeTransform = function(getData, transform, data_bin_file, nb_per_chunk,
nbytes=4, endian=.Platform$endian)
{
- nb_items = 0
+ nb_items = 0 #side-effect: store the number of transformed items
index = 1
repeat
{
+ # Retrieve a chunk of data in a binary file (generally obtained by binarize())
data_chunk = getData((index-1)+seq_len(nb_per_chunk))
if (is.null(data_chunk))
break
+
+ # Apply transformation on the current chunk (by columns)
transformed_chunk = transform(data_chunk)
+
+ # Save the result in binary format
binarize(transformed_chunk, data_bin_file, nb_per_chunk, ",", nbytes, endian)
+
index = index + nb_per_chunk
nb_items = nb_items + nrow(data_chunk)
}
- nb_items
+ nb_items #number of transformed items
}
#' @rdname de_serialize
#' @export
getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
{
- data_bin = file(data_bin_file, "rb")
- data_size = file.info(data_bin_file)$size
+ data_bin = file(data_bin_file, "rb") #source binary file
+
+ data_size = file.info(data_bin_file)$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)
+ ignored = seek(data_bin, offset) #position cursor at computed offset
readBin(data_bin, "double", n=data_length, size=nbytes, endian=endian)
} ) )
close(data_bin)
- data_ascii
+
+ data_ascii #retrieved data, in columns
}