ignore generated binary files while debugging
[epclust.git] / epclust / R / de_serialize.R
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 }