epclust/tests/testthat/test-de_serialize.R

   1 context("de_serialize")
   2
   3 test_that("serialization + getDataInFile retrieve original data / from matrix",
   4 {
   5     data_bin_file = ".epclust_test_m.bin"
   6     unlink(data_bin_file)
   7
   8     # Dataset 200 cols / 30 rows
   9     data_ascii = matrix(runif(200*30,-10,10),nrow=30)
  10     nbytes = 4 #lead to a precision of 1e-7 / 1e-8
  11     endian = "little"
  12
  13     # Simulate serialization in one single call
  14     binarize(data_ascii, data_bin_file, 500, ",", nbytes, endian)
  15     expect_equal(file.info(data_bin_file)$size, length(data_ascii)*nbytes+8)
  16     for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
  17     {
  18         data_lines = getDataInFile(indices, data_bin_file, nbytes, endian)
  19         expect_equal(data_lines, data_ascii[,indices], tolerance=1e-6)
  20     }
  21     unlink(data_bin_file)
  22
  23     # Serialization in several calls (last call complete, next call NULL)
  24     for (i in 1:20)
  25         binarize(data_ascii[,((i-1)*10+1):(i*10)], data_bin_file, 20, ",", nbytes, endian)
  26     expect_equal(file.info(data_bin_file)$size, length(data_ascii)*nbytes+8)
  27     for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
  28     {
  29         data_lines = getDataInFile(indices, data_bin_file, nbytes, endian)
  30         expect_equal(data_lines, data_ascii[,indices], tolerance=1e-6)
  31     }
  32     unlink(data_bin_file)
  33 })
  34
  35 test_that("serialization + transform + getDataInFile retrieve original transforms",
  36 {
  37     data_bin_file = ".epclust_test_t.bin"
  38     unlink(data_bin_file)
  39
  40     # Dataset 200 cols / 30 rows
  41     data_ascii = matrix(runif(200*30,-10,10),nrow=30)
  42     nbytes = 8
  43     endian = "little"
  44
  45     binarize(data_ascii, data_bin_file, 500, ",", nbytes, endian)
  46     # Serialize transformation (just compute range) into a new binary file
  47     trans_bin_file = ".epclust_test_t_trans.bin"
  48     unlink(trans_bin_file)
  49     getSeries = function(inds) getDataInFile(inds, data_bin_file, nbytes, endian)
  50     binarizeTransform(getSeries, function(series) apply(series, 2, range),
  51         trans_bin_file, 250, nbytes, endian)
  52     unlink(data_bin_file)
  53     expect_equal(file.info(trans_bin_file)$size, 2*ncol(data_ascii)*nbytes+8)
  54     for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
  55     {
  56         trans_cols = getDataInFile(indices, trans_bin_file, nbytes, endian)
  57         expect_equal(trans_cols, apply(data_ascii[,indices],2,range), tolerance=1e-6)
  58     }
  59     unlink(trans_bin_file)
  60 })
  61
  62 test_that("serialization + getDataInFile retrieve original data / from connection",
  63 {
  64     data_bin_file = ".epclust_test_c.bin"
  65     unlink(data_bin_file)
  66
  67     # Dataset 300 cols / 50 rows
  68     data_csv = system.file("testdata","de_serialize.csv",package="epclust")
  69     nbytes = 8
  70     endian = "big"
  71     data_ascii = t( as.matrix(read.table(data_csv, sep=";", header=FALSE)) ) #for ref
  72
  73     # Simulate serialization in one single call
  74     binarize(data_csv, data_bin_file, 350, ";", nbytes, endian)
  75     expect_equal(file.info(data_bin_file)$size, 300*50*8+8)
  76     for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
  77     {
  78         data_cols = getDataInFile(indices,data_bin_file,nbytes,endian)
  79         #HACK: rows naming required to match (ref) data structure
  80         rownames(data_cols) <- paste("V",seq_len(nrow(data_ascii)), sep="")
  81         expect_equal(data_cols, data_ascii[,indices])
  82     }
  83     unlink(data_bin_file)
  84
  85     # Serialization in several calls / chunks of 29 --> 29*10 + 10, incomplete last
  86     data_con = file(data_csv, "r")
  87     binarize(data_con, data_bin_file, 29, ";", nbytes, endian)
  88     expect_equal(file.info(data_bin_file)$size, 300*50*8+8)
  89     for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
  90     {
  91         data_cols = getDataInFile(indices,data_bin_file,nbytes,endian)
  92         rownames(data_cols) <- paste("V",seq_len(nrow(data_ascii)), sep="")
  93         expect_equal(data_cols, data_ascii[,indices])
  94     }
  95     unlink(data_bin_file)
  96     #close(data_con) --> done in binarize()
  97 })