epclust/R/de_serialize.R

   1 #data: matrix of double or connection
   2 serialize = function(data_ascii, data_bin_file, nb_per_chunk,
   3     sep=",", nbytes=4, endian=.Platform$endian)
   4 {
   5     if (is.character(data_ascii))
   6         data_ascii = file(data_ascii, open="r")
   7     else if (is(data_ascii,"connection") && !isOpen(data_ascii))
   8         open(data_ascii)
   9
  10     first_write = (!file.exists(data_bin_file) || file.info(data_bin_file)$size == 0)
  11     data_bin = file(data_bin_file, open=ifelse(first_write,"wb","ab"))
  12
  13     #write data length on first call
  14     if (first_write)
  15     {
  16         #number of items always on 8 bytes
  17         writeBin(0L, data_bin, size=8) #,endian="little")
  18         if (is.matrix(data_ascii))
  19             data_length = ncol(data_ascii)
  20         else #if (is(data, "connection"))
  21         {
  22             data_line = scan(data_ascii, double(), sep=sep, nlines=1, quiet=TRUE)
  23             writeBin(data_line, data_bin, size=nbytes)
  24             data_length = length(data_line)
  25         }
  26     }
  27
  28     if (is.matrix(data_ascii))
  29         index = 1
  30     repeat
  31     {
  32         if (is.matrix(data_ascii))
  33         {
  34             range = index:min(nrow(data_ascii),index+nb_per_chunk)
  35             data_chunk =
  36                 if (range[1] <= nrow(data_ascii))
  37                     as.double(t(data_ascii[range,]))
  38                 else
  39                     integer(0)
  40             index = index + nb_per_chunk
  41         }
  42         else
  43             data_chunk = scan(data_ascii, double(), sep=sep, nlines=nb_per_chunk, quiet=TRUE)
  44         if (length(data_chunk)==0)
  45             break
  46         writeBin(data_chunk, data_bin, size=nbytes)
  47     }
  48
  49     if (first_write)
  50     {
  51         #ecrire file_size-1 / (nbytes*nbWritten) en 0 dans bin_data ! ignored == file_size
  52         ignored = seek(data_bin, 0)
  53         writeBin(data_length, data_bin, size=8)
  54     }
  55     close(data_bin)
  56
  57     if (is(data_ascii,"connection"))
  58         close(data_ascii)
  59 }
  60
  61 #read in binary file, always same structure
  62 getDataInFile = function(indices, data_bin_file, nbytes=4, endian=.Platform$endian)
  63 {
  64     data_bin = file(data_bin_file, "rb")
  65     data_size = file.info(data_bin)$size
  66     data_length = readBin(data_bin, "integer", 1, 8, endian)
  67     #Ou t(sapply(...)) (+ rapide ?)
  68     data_ascii = do.call( rbind, lapply( indices, function(i) {
  69         offset = 8+(i-1)*data_length*nbytes
  70         if (offset > data_size)
  71             return (vector("double",0))
  72         ignored = seek(data_bin, offset)
  73         readBin(data_bin, "double", n=data_length, size=nbytes)
  74     } ) )
  75     close(data_bin)
  76     if (ncol(data_ascii)>0) data_ascii else NULL
  77 }