X-Git-Url: https://git.auder.net/?a=blobdiff_plain;f=epclust%2FR%2Fde_serialize.R;h=eba6772c69b8052add0567a13d7d2c6e3bcee6a1;hb=282342bafdc9ff65c5df98c6e2304d63b33b9fb2;hp=682db53c18a2c129af70431b5d9dc85b0c192331;hpb=56857861dc15088cf58e7438968fe5714b22168e;p=epclust.git

diff --git a/epclust/R/de_serialize.R b/epclust/R/de_serialize.R
index 682db53..eba6772 100644
--- a/epclust/R/de_serialize.R
+++ b/epclust/R/de_serialize.R
@@ -1,73 +1,150 @@
-#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 Either a 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 (big.matrix or connection)
+#' @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()}, 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.
+#'
+#' @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_length = readBin(data_bin, "integer", 1, 8, endian)
-	#Ou t(sapply(...)) (+ rapide ?)
-	data_ascii = do.call( rbind, lapply( indices, function(i) {
-		ignored = seek(data_bin, 8+((i-1)*data_length*nbytes))
-		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)
-	data_ascii
+
+	data_ascii #retrieved data, in columns
 }