code seems OK; still wavelets test to write
[epclust.git] / epclust / R / de_serialize.R
CommitLineData
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1#' @name de_serialize
2#' @rdname de_serialize
492cd9e7 3#' @aliases binarize binarizeTransform getDataInFile
4bcfdbee 4#'
492cd9e7 5#' @title (De)Serialization of a [big]matrix or data stream
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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
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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)
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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})
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17#' or input (\code{getDataInFile})
18#' @param nb_per_chunk Number of lines to process in one batch (big.matrix or connection)
4bcfdbee 19#' @inheritParams claws
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20#' @param getData Function to retrieve data chunks
21#' @param transform Transformation function to apply on data chunks
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22#'
23#' @return For \code{getDataInFile()}, the matrix with rows corresponding to the
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24#' requested indices. \code{binarizeTransform} returns the number of processed lines.
25#' \code{binarize} is designed to serialize in several calls, thus returns nothing.
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26NULL
27
28#' @rdname de_serialize
29#' @export
30binarize = function(data_ascii, data_bin_file, nb_per_chunk,
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31 sep=",", nbytes=4, endian=.Platform$endian)
32{
d9bb53c5 33 # data_ascii can be of two types: [big.]matrix, or connection
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34 if (is.character(data_ascii))
35 data_ascii = file(data_ascii, open="r")
4bcfdbee 36 else if (methods::is(data_ascii,"connection") && !isOpen(data_ascii))
56857861 37 open(data_ascii)
492cd9e7 38 is_matrix = !methods::is(data_ascii,"connection")
56857861 39
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40 # At first call, the length of a stored row is written. So it's important to determine
41 # if the serialization process already started.
56857861 42 first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0)
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43
44 # Open the binary file for writing (or 'append' if already exists)
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45 data_bin = file(data_bin_file, open=ifelse(first_write,"wb","ab"))
46
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47 if (first_write)
48 {
d9bb53c5 49 # Write data length on first call: number of items always on 8 bytes
4bcfdbee 50 writeBin(0L, data_bin, size=8, endian=endian)
0486fbad 51 if (is_matrix)
eef6f6c9 52 data_length = nrow(data_ascii)
492cd9e7 53 else #connection
56857861 54 {
d9bb53c5 55 # Read the first line to know data length, and write it then
56857861 56 data_line = scan(data_ascii, double(), sep=sep, nlines=1, quiet=TRUE)
4bcfdbee 57 writeBin(data_line, data_bin, size=nbytes, endian=endian)
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58 data_length = length(data_line)
59 }
60 }
61
492cd9e7 62 if (is_matrix)
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63 {
64 # Data is processed by chunks; although this may not be so useful for (normal) matrix
65 # input, it could for a file-backed big.matrix. It's easier to follow a unified pattern.
56857861 66 index = 1
d9bb53c5 67 }
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68 repeat
69 {
0486fbad 70 if (is_matrix)
56857861 71 {
56857861 72 data_chunk =
eef6f6c9 73 if (index <= ncol(data_ascii))
0486fbad 74 as.double(data_ascii[,index:min(ncol(data_ascii),index+nb_per_chunk-1)])
56857861 75 else
492cd9e7 76 double(0)
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77 index = index + nb_per_chunk
78 }
d9bb53c5 79 else #connection
56857861 80 data_chunk = scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE)
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81
82 # Data size is unknown in the case of a connection
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83 if (length(data_chunk)==0)
84 break
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85
86 # Write this chunk of data to the binary file
4bcfdbee 87 writeBin(data_chunk, data_bin, size=nbytes, endian=endian)
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88 }
89
90 if (first_write)
91 {
492cd9e7 92 # Write data_length, = (file_size-1) / (nbytes*nbWritten) at offset 0 in data_bin
56857861 93 ignored = seek(data_bin, 0)
4bcfdbee 94 writeBin(data_length, data_bin, size=8, endian=endian)
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95 }
96 close(data_bin)
97
492cd9e7 98 if ( ! is_matrix )
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99 close(data_ascii)
100}
101
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102#' @rdname de_serialize
103#' @export
104binarizeTransform = function(getData, transform, data_bin_file, nb_per_chunk,
105 nbytes=4, endian=.Platform$endian)
106{
d9bb53c5 107 nb_items = 0 #side-effect: store the number of transformed items
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108 index = 1
109 repeat
110 {
d9bb53c5 111 # Retrieve a chunk of data in a binary file (generally obtained by binarize())
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112 data_chunk = getData((index-1)+seq_len(nb_per_chunk))
113 if (is.null(data_chunk))
114 break
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115
116 # Apply transformation on the current chunk (by columns)
492cd9e7 117 transformed_chunk = transform(data_chunk)
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118
119 # Save the result in binary format
492cd9e7 120 binarize(transformed_chunk, data_bin_file, nb_per_chunk, ",", nbytes, endian)
d9bb53c5 121
492cd9e7 122 index = index + nb_per_chunk
a52836b2 123 nb_items = nb_items + ncol(data_chunk)
492cd9e7 124 }
d9bb53c5 125 nb_items #number of transformed items
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126}
127
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128#' @rdname de_serialize
129#' @export
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130getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
131{
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132 data_bin = file(data_bin_file, "rb") #source binary file
133
134 data_size = file.info(data_bin_file)$size #number of bytes in the file
135 # data_length: length of a vector in the binary file (first element, 8 bytes)
4bcfdbee 136 data_length = readBin(data_bin, "integer", n=1, size=8, endian=endian)
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137
138 # Seek all 'indices' columns in the binary file, using data_length and nbytes
139 # to compute the offset ( index i at 8 + i*data_length*nbytes )
0486fbad 140 data_ascii = do.call( cbind, lapply( indices, function(i) {
8702eb86 141 offset = 8+(i-1)*data_length*nbytes
a52836b2 142 if (offset >= data_size)
0486fbad 143 return (NULL)
d9bb53c5 144 ignored = seek(data_bin, offset) #position cursor at computed offset
4bcfdbee 145 readBin(data_bin, "double", n=data_length, size=nbytes, endian=endian)
0486fbad 146 } ) )
56857861 147 close(data_bin)
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148
149 data_ascii #retrieved data, in columns
56857861 150}