| 1 | #' @name de_serialize |
| 2 | #' @rdname de_serialize |
| 3 | #' @aliases binarize binarizeTransform getDataInFile |
| 4 | #' |
| 5 | #' @title (De)Serialization of a [big]matrix or data stream |
| 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. Finally, |
| 10 | #' \code{binarizeTransform()} serialize transformations of all data chunks; to use it, |
| 11 | #' a data-retrieval function must be provided, thus \code{binarize} will most likely be |
| 12 | #' used first (and then a function defined to seek in generated binary file) |
| 13 | #' |
| 14 | #' @param data_ascii Either a matrix or CSV file, with items in rows |
| 15 | #' @param indices Indices of the lines to retrieve |
| 16 | #' @param data_bin_file Name of binary file on output (\code{binarize}) |
| 17 | #' or intput (\code{getDataInFile}) |
| 18 | #' @param nb_per_chunk Number of lines to process in one batch |
| 19 | #' @inheritParams claws |
| 20 | #' @param getData Function to retrieve data chunks |
| 21 | #' @param transform Transformation function to apply on data chunks |
| 22 | #' |
| 23 | #' @return For \code{getDataInFile()}, the matrix with rows corresponding to the |
| 24 | #' requested indices. \code{binarizeTransform} returns the number of processed lines. |
| 25 | #' \code{binarize} is designed to serialize in several calls, thus returns nothing. |
| 26 | NULL |
| 27 | |
| 28 | #' @rdname de_serialize |
| 29 | #' @export |
| 30 | binarize = function(data_ascii, data_bin_file, nb_per_chunk, |
| 31 | sep=",", nbytes=4, endian=.Platform$endian) |
| 32 | { |
| 33 | if (is.character(data_ascii)) |
| 34 | data_ascii = file(data_ascii, open="r") |
| 35 | else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii)) |
| 36 | open(data_ascii) |
| 37 | is_matrix = !methods::is(data_ascii,"connection") |
| 38 | |
| 39 | first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0) |
| 40 | data_bin = file(data_bin_file, open=ifelse(first_write,"wb","ab")) |
| 41 | |
| 42 | #write data length on first call |
| 43 | if (first_write) |
| 44 | { |
| 45 | #number of items always on 8 bytes |
| 46 | writeBin(0L, data_bin, size=8, endian=endian) |
| 47 | if ( is_matrix ) |
| 48 | data_length = nrow(data_ascii) |
| 49 | else #connection |
| 50 | { |
| 51 | data_line = scan(data_ascii, double(), sep=sep, nlines=1, quiet=TRUE) |
| 52 | writeBin(data_line, data_bin, size=nbytes, endian=endian) |
| 53 | data_length = length(data_line) |
| 54 | } |
| 55 | } |
| 56 | |
| 57 | if (is_matrix) |
| 58 | index = 1 |
| 59 | repeat |
| 60 | { |
| 61 | if ( is_matrix ) |
| 62 | { |
| 63 | data_chunk = |
| 64 | if (index <= ncol(data_ascii)) |
| 65 | as.double(data_ascii[,index:min(nrow(data_ascii),index+nb_per_chunk-1)]) |
| 66 | else |
| 67 | double(0) |
| 68 | index = index + nb_per_chunk |
| 69 | } |
| 70 | else |
| 71 | data_chunk = scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE) |
| 72 | if (length(data_chunk)==0) |
| 73 | break |
| 74 | writeBin(data_chunk, data_bin, size=nbytes, endian=endian) |
| 75 | } |
| 76 | |
| 77 | if (first_write) |
| 78 | { |
| 79 | # Write data_length, = (file_size-1) / (nbytes*nbWritten) at offset 0 in data_bin |
| 80 | ignored = seek(data_bin, 0) |
| 81 | writeBin(data_length, data_bin, size=8, endian=endian) |
| 82 | } |
| 83 | close(data_bin) |
| 84 | |
| 85 | if ( ! is_matrix ) |
| 86 | close(data_ascii) |
| 87 | } |
| 88 | |
| 89 | #' @rdname de_serialize |
| 90 | #' @export |
| 91 | binarizeTransform = function(getData, transform, data_bin_file, nb_per_chunk, |
| 92 | nbytes=4, endian=.Platform$endian) |
| 93 | { |
| 94 | nb_items = 0 |
| 95 | index = 1 |
| 96 | repeat |
| 97 | { |
| 98 | data_chunk = getData((index-1)+seq_len(nb_per_chunk)) |
| 99 | if (is.null(data_chunk)) |
| 100 | break |
| 101 | transformed_chunk = transform(data_chunk) |
| 102 | binarize(transformed_chunk, data_bin_file, nb_per_chunk, ",", nbytes, endian) |
| 103 | index = index + nb_per_chunk |
| 104 | nb_items = nb_items + nrow(data_chunk) |
| 105 | } |
| 106 | nb_items |
| 107 | } |
| 108 | |
| 109 | #' @rdname de_serialize |
| 110 | #' @export |
| 111 | getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian) |
| 112 | { |
| 113 | data_bin = file(data_bin_file, "rb") |
| 114 | data_size = file.info(data_bin_file)$size |
| 115 | data_length = readBin(data_bin, "integer", n=1, size=8, endian=endian) |
| 116 | data_ascii = sapply( indices, function(i) { |
| 117 | offset = 8+(i-1)*data_length*nbytes |
| 118 | if (offset > data_size) |
| 119 | return (vector("double",0)) |
| 120 | ignored = seek(data_bin, offset) |
| 121 | readBin(data_bin, "double", n=data_length, size=nbytes, endian=endian) |
| 122 | } ) |
| 123 | close(data_bin) |
| 124 | if (ncol(data_ascii)>0) data_ascii else NULL |
| 125 | } |