fixes: TODO, debug test.clustering.R and finish writing clustering.R
[epclust.git] / epclust / tests / testthat / test.de_serialize.R
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56857861 1context("de_serialize")
62deb424 2
56857861 3test_that("serialization + getDataInFile retrieve original data / from matrix",
62deb424 4{
37c82bba 5 data_bin_file = ".epclust_test_m.bin"
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6 unlink(data_bin_file)
7
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8 #dataset 200 cols / 30 rows
9 data_ascii = matrix(runif(200*30,-10,10),nrow=30)
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10 nbytes = 4 #lead to a precision of 1e-7 / 1e-8
11 endian = "little"
12
13 #Simulate serialization in one single call
4bcfdbee 14 binarize(data_ascii, data_bin_file, 500, ",", nbytes, endian)
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15 expect_equal(file.info(data_bin_file)$size, length(data_ascii)*nbytes+8)
16 for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
62deb424 17 {
56857861 18 data_lines = getDataInFile(indices, data_bin_file, nbytes, endian)
37c82bba 19 expect_equal(data_lines, data_ascii[,indices], tolerance=1e-6)
62deb424 20 }
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21 unlink(data_bin_file)
22
23 #...in several calls (last call complete, next call NULL)
24 for (i in 1:20)
0486fbad 25 binarize(data_ascii[,((i-1)*10+1):(i*10)], data_bin_file, 20, ",", nbytes, endian)
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26 expect_equal(file.info(data_bin_file)$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))
62deb424 28 {
56857861 29 data_lines = getDataInFile(indices, data_bin_file, nbytes, endian)
37c82bba 30 expect_equal(data_lines, data_ascii[,indices], tolerance=1e-6)
62deb424 31 }
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32 unlink(data_bin_file)
33})
34
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35test_that("serialization + transform + getDataInFile retrieve original transforms",
36{
37c82bba 37 data_bin_file = ".epclust_test_t.bin"
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38 unlink(data_bin_file)
39
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40 #dataset 200 cols / 30 rows
41 data_ascii = matrix(runif(200*30,-10,10),nrow=30)
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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
37c82bba 47 trans_bin_file = ".epclust_test_t_trans.bin"
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48 unlink(trans_bin_file)
49 getSeries = function(inds) getDataInFile(inds, data_bin_file, nbytes, endian)
37c82bba 50 binarizeTransform(getSeries, function(series) apply(series, 2, range),
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51 trans_bin_file, 250, nbytes, endian)
52 unlink(data_bin_file)
0486fbad 53 expect_equal(file.info(trans_bin_file)$size, 2*ncol(data_ascii)*nbytes+8)
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54 for (indices in list(c(1,3,5), 3:13, c(5,20,50), c(75,130:135), 196:200))
55 {
37c82bba 56 trans_cols = getDataInFile(indices, trans_bin_file, nbytes, endian)
0486fbad 57 expect_equal(trans_cols, apply(data_ascii[,indices],2,range), tolerance=1e-6)
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58 }
59 unlink(trans_bin_file)
60})
61
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62test_that("serialization + getDataInFile retrieve original data / from connection",
63{
37c82bba 64 data_bin_file = ".epclust_test_c.bin"
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65 unlink(data_bin_file)
66
37c82bba 67 #dataset 300 cols / 50 rows
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68 data_csv = system.file("testdata","de_serialize.csv",package="epclust")
69 nbytes = 8
70 endian = "big"
0486fbad 71 data_ascii = t( as.matrix(read.table(data_csv, sep=";", header=FALSE)) ) #for ref
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72
73 #Simulate serialization in one single call
4bcfdbee 74 binarize(data_csv, data_bin_file, 350, ";", nbytes, endian)
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75 expect_equal(file.info(data_bin_file)$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))
62deb424 77 {
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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="")
37c82bba 81 expect_equal(data_cols, data_ascii[,indices])
62deb424 82 }
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83 unlink(data_bin_file)
84
85 #...in several calls / chunks of 29 --> 29*10 + 10, incomplete last
86 data_con = file(data_csv, "r")
4bcfdbee 87 binarize(data_con, data_bin_file, 29, ";", nbytes, endian)
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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))
62deb424 90 {
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91 data_cols = getDataInFile(indices,data_bin_file,nbytes,endian)
92 rownames(data_cols) <- paste("V",seq_len(nrow(data_ascii)), sep="")
37c82bba 93 expect_equal(data_cols, data_ascii[,indices])
62deb424 94 }
56857861 95 unlink(data_bin_file)
4bcfdbee 96 #close(data_con) --> done in binarize()
56857861 97})