| 1 | #' @name de_serialize |
| 2 | #' @rdname de_serialize |
| 3 | #' @aliases binarize getDataInFile |
| 4 | #' |
| 5 | #' @title (De)Serialization of a matrix |
| 6 | #' |
| 7 | #' @description \code{binarize()} serializes a matrix or CSV file with minimal overhead, |
| 8 | #' into a binary file. \code{getDataInFile()} achieves the inverse task: she retrieves |
| 9 | #' (ASCII) data rows from indices in the binary file |
| 10 | #' |
| 11 | #' @param data_ascii Either a matrix or CSV file, with items in rows |
| 12 | #' @param indices Indices of the lines to retrieve |
| 13 | #' @param data_bin_file Name of binary file on output (\code{binarize}) |
| 14 | #' or intput (\code{getDataInFile}) |
| 15 | #' @param nb_per_chunk Number of lines to process in one batch |
| 16 | #' @inheritParams claws |
| 17 | #' |
| 18 | #' @return For \code{getDataInFile()}, the matrix with rows corresponding to the |
| 19 | #' requested indices |
| 20 | NULL |
| 21 | |
| 22 | #' @rdname de_serialize |
| 23 | #' @export |
| 24 | binarize = function(data_ascii, data_bin_file, nb_per_chunk, |
| 25 | sep=",", nbytes=4, endian=.Platform$endian) |
| 26 | { |
| 27 | if (is.character(data_ascii)) |
| 28 | data_ascii = file(data_ascii, open="r") |
| 29 | else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii)) |
| 30 | open(data_ascii) |
| 31 | |
| 32 | first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0) |
| 33 | data_bin = file(data_bin_file, open=ifelse(first_write,"wb","ab")) |
| 34 | |
| 35 | #write data length on first call |
| 36 | if (first_write) |
| 37 | { |
| 38 | #number of items always on 8 bytes |
| 39 | writeBin(0L, data_bin, size=8, endian=endian) |
| 40 | if (is.matrix(data_ascii)) |
| 41 | data_length = ncol(data_ascii) |
| 42 | else #if (is(data, "connection")) |
| 43 | { |
| 44 | data_line = scan(data_ascii, double(), sep=sep, nlines=1, quiet=TRUE) |
| 45 | writeBin(data_line, data_bin, size=nbytes, endian=endian) |
| 46 | data_length = length(data_line) |
| 47 | } |
| 48 | } |
| 49 | |
| 50 | if (is.matrix(data_ascii)) |
| 51 | index = 1 |
| 52 | repeat |
| 53 | { |
| 54 | if (is.matrix(data_ascii)) |
| 55 | { |
| 56 | range = index:min(nrow(data_ascii),index+nb_per_chunk) |
| 57 | data_chunk = |
| 58 | if (range[1] <= nrow(data_ascii)) |
| 59 | as.double(t(data_ascii[range,])) |
| 60 | else |
| 61 | integer(0) |
| 62 | index = index + nb_per_chunk |
| 63 | } |
| 64 | else |
| 65 | data_chunk = scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE) |
| 66 | if (length(data_chunk)==0) |
| 67 | break |
| 68 | writeBin(data_chunk, data_bin, size=nbytes, endian=endian) |
| 69 | } |
| 70 | |
| 71 | if (first_write) |
| 72 | { |
| 73 | #ecrire file_size-1 / (nbytes*nbWritten) en 0 dans bin_data ! ignored == file_size |
| 74 | ignored = seek(data_bin, 0) |
| 75 | writeBin(data_length, data_bin, size=8, endian=endian) |
| 76 | } |
| 77 | close(data_bin) |
| 78 | |
| 79 | if (methods::is(data_ascii,"connection")) |
| 80 | close(data_ascii) |
| 81 | } |
| 82 | |
| 83 | #' @rdname de_serialize |
| 84 | #' @export |
| 85 | getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian) |
| 86 | { |
| 87 | data_bin = file(data_bin_file, "rb") |
| 88 | data_size = file.info(data_bin_file)$size |
| 89 | data_length = readBin(data_bin, "integer", n=1, size=8, endian=endian) |
| 90 | #Ou t(sapply(...)) (+ rapide ?) |
| 91 | data_ascii = do.call( rbind, lapply( indices, function(i) { |
| 92 | offset = 8+(i-1)*data_length*nbytes |
| 93 | if (offset > data_size) |
| 94 | return (vector("double",0)) |
| 95 | ignored = seek(data_bin, offset) |
| 96 | readBin(data_bin, "double", n=data_length, size=nbytes, endian=endian) |
| 97 | } ) ) |
| 98 | close(data_bin) |
| 99 | if (ncol(data_ascii)>0) data_ascii else NULL |
| 100 | } |