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features/75-WITec-unittest #82

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merged 9 commits into from
Aug 16, 2021
Merged

features/75-WITec-unittest #82

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a1ee244
Unit test according to template #55
Aug 12, 2021
fdeabdb
unit test for read dat
Aug 12, 2021
917d42e
add unit test dat for truematch
Aug 12, 2021
4d0a710
Unit test for truematch
Aug 12, 2021
ead2d18
fix typo
Aug 12, 2021
b38c001
update unit test
Aug 12, 2021
fe51dde
Update read_txt_Graph_WITec_.R
Aug 16, 2021
d96363a
move old unit test data to new directory
Aug 16, 2021
39353df
add old unit test
Aug 16, 2021
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105 changes: 38 additions & 67 deletions R/read_dat_WITec_.R
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Original file line number Diff line number Diff line change
Expand Up @@ -42,86 +42,57 @@ read_dat_WITec <- function(filex = stop("filename or connection needed"),
# Unit tests -----------------------------------------------------------------

hySpc.testthat::test(read_dat_WITec) <- function() {
local_edition(2)

context("read_dat_WITec")

tmpdir <- paste0(tempdir(), "/test_Witec_dat")
on.exit(unlink(tmpdir, force = TRUE))

untar("testfiles_Witec.tar.gz",
files = c(
"Witec-Map-x.dat",
"Witec-Map-y.dat",
"Witec-timeseries-x.dat",
"Witec-timeseries-y.dat"
),
exdir = tmpdir
local_edition(3)

filename <- system.file(
"extdata",
"txt.Witec/Witec-timeseries-x.dat",
package = "hySpc.read.txt"
)

test_that("-y file guessing", {
spc <- read_dat_WITec(paste0(tmpdir, "/Witec-timeseries-x.dat"))
spc$filename <- gsub("^.*/", "", spc$filename)
expect_known_hash(spc, "1977fe5997")
})
expect_silent(spc <- read_dat_WITec(filename))

test_that("encoding", {
spc <- read_dat_WITec(
paste0(tmpdir, "/Witec-timeseries-x.dat"),
encoding = "ascii"
)
spc$filename <- gsub("^.*/", "", spc$filename)
n_wl <- nwl(spc)
n_rows <- nrow(spc)
n_clos <- ncol(spc)

expect_known_hash(spc, "1977fe5997")
test_that("WITec .dat: hyperSpec obj. dimensions are correct", {
expect_equal(n_wl, 1024)
expect_equal(n_rows, 100)
expect_equal(n_clos, 2)
})

test_that("Time series", {
spc <- read_dat_WITec(
paste0(tmpdir, "/Witec-timeseries-x.dat"),
paste0(tmpdir, "/Witec-timeseries-y.dat")
)
spc$filename <- gsub("^.*/", "", spc$filename)
test_that("WITec .dat: extra data are correct", {
# @data colnames
expect_equal(colnames(spc), c("spc", "filename"))
})

expect_known_hash(spc, "1977fe5997")
test_that("WITec .dat: labels are correct", {
expect_equal(spc@label$.wavelength, NULL)
expect_equal(spc@label$spc, NULL)
expect_equal(spc@label$filename, "filename")
})

test_that("Map: .dat does not have spatial information", {
spc <- read_dat_WITec(
paste0(tmpdir, "/Witec-Map-x.dat"),
paste0(tmpdir, "/Witec-Map-y.dat")
)
expect_null(spc$x)
expect_null(spc$y)
spc$filename <- gsub("^.*/", "", spc$filename)
test_that("WITec .dat: spectra are correct", {
# Dimensions of spectra matrix (@data$spc)
expect_equal(dim(spc@data$spc), c(100, 1024))

# Column names of spectra matrix
expect_equal(colnames(spc@data$spc)[1], "87.7367")
expect_equal(colnames(spc@data$spc)[10], "117.333")
expect_equal(colnames(spc@data$spc)[n_wl], "2821.31") # last name

expect_known_hash(spc, "b523735004")
# Values of spectra matrix
expect_equal(unname(spc@data$spc[1, 1]), 995)
expect_equal(unname(spc@data$spc[2, 10]), 1002)
expect_equal(unname(spc@data$spc[n_rows, n_wl]), 985) # last spc value
})

test_that("Map", {
expect_warning(
read_dat_WITec(
paste0(tmpdir, "/Witec-Map-x.dat"),
paste0(tmpdir, "/Witec-Map-y.dat"),
points.per.line = 5, lines.per.image = 5
),
"points.per.line != 1 given for single spectrum"
)
expect_warning(
read_dat_WITec(
paste0(tmpdir, "/Witec-Map-x.dat"),
paste0(tmpdir, "/Witec-Map-y.dat"),
points.per.line = 5, lines.per.image = 5
),
"lines.per.image != 1 are defined for single spectrum"
)

spc <- read_dat_WITec(
paste0(tmpdir, "/Witec-Map-x.dat"),
paste0(tmpdir, "/Witec-Map-y.dat"),
type = "map", points.per.line = 5, lines.per.image = 5
)
spc$filename <- gsub("^.*/", "", spc$filename)

expect_known_hash(spc, "efc28c0d45")
test_that("WITec .dat: wavelengths are correct", {
expect_equal(spc@wavelength[1], 87.736672)
expect_equal(spc@wavelength[10], 117.332683)
expect_equal(spc@wavelength[n_wl], 2821.3062)
})
}
245 changes: 151 additions & 94 deletions R/read_txt_Graph_WITec_.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -60,115 +60,172 @@ read_txt_WITec_Graph <- function(headerfile = stop("filename or connection neede
# Unit tests -----------------------------------------------------------------

hySpc.testthat::test(read_txt_WITec_Graph) <- function() {
local_edition(2)

context("read_txt_WITec_Graph")

tmpdir <- paste0(tempdir(), "/test_Witec_txt_Graph")
untar("testfiles_Witec.tar.gz",
files = c(
"nofilename (Header).txt",
"nofilename (X-Axis).txt",
"nofilename (Y-Axis).txt",
"timeseries3x_GraphASCII.Data 1 (Header).txt",
"timeseries3x_GraphASCII.Data 1 (X-Axis).txt",
"timeseries3x_GraphASCII.Data 1 (Y-Axis).txt",
"image2x3_GraphASCII.Data 1_F (Header).txt",
"image2x3_GraphASCII.Data 1_F (X-Axis).txt",
"image2x3_GraphASCII.Data 1_F (Y-Axis).txt"
),
exdir = tmpdir
)

on.exit(unlink(tmpdir))
local_edition(3)

test_that("defaults and (X-Axis)/(Y-Axis) file guessing", {
spc <- read_txt_WITec_Graph(
paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Header).txt")
)

expect_equal(dim(spc), c(nrow = 3L, ncol = 4L, nwl = 1024L))

expect_equal(
spc$filename,
rep(paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Y-Axis).txt"), 3)
)
filename <- system.file(
"extdata",
"txt.Witec/nofilename_Header.txt",
package = "hySpc.read.txt"
)

expect_equal(
spc$WIPname,
rep("F:\\Acetamidophenol samples_20200703.wip", 3)
)
expect_silent(spc <- read_txt_WITec_Graph(filename))

expect_equal(
spc$spcname,
rep("4Acetamidophenol_timeseries3x_20200703_001_Spec.Data 1", 3)
)
n_wl <- nwl(spc)
n_rows <- nrow(spc)
n_clos <- ncol(spc)

expect_equivalent(spc[[2, , 1650]], 2427)
test_that("WITec Graph .txt: hyperSpec obj. dimensions are correct", {
expect_equal(n_wl, 63)
expect_equal(n_rows, 5)
expect_equal(n_clos, 2)
})

test_that("encoding", {
spc <- read_txt_WITec_Graph(
paste0(tmpdir, "/nofilename (Header).txt"),
encoding = "latin1"
)
spc$filename <- gsub("^.*/", "", spc$filename)

expect_known_hash(spc, "b273847b9c")
test_that("WITec Graph .txt: extra data are correct", {
# @data colnames
expect_equal(colnames(spc), c("spc", "filename"))
})

test_that("Time Series", {
spc <- read_txt_WITec_Graph(
paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Header).txt"),
type = "single"
)
spc$filename <- gsub("^.*/", "", spc$filename)

expect_known_hash(spc, "a5ff28fc8b")
test_that("WITec Graph .txt: labels are correct", {
expect_equal(spc@label$.wavelength, NULL)
expect_equal(spc@label$spc, NULL)
expect_equal(spc@label$filename, "filename")
})

test_that("Map", {
expect_warning(
read_txt_WITec_Graph(
paste0(tmpdir, "/image2x3_GraphASCII.Data 1_F (Header).txt"),
encoding = "latin1"
),
"header provides spatial information in y direction for single spectra"
)

expect_warning(
read_txt_WITec_Graph(
paste0(tmpdir, "/image2x3_GraphASCII.Data 1_F (Header).txt"),
encoding = "latin1", type = "single"
),
"header provides spatial information in y direction for single spectra"
)

spc <- read_txt_WITec_Graph(
paste0(tmpdir, "/image2x3_GraphASCII.Data 1_F (Header).txt"),
type = "map", encoding = "latin1"
)
spc$filename <- gsub("^.*/", "", spc$filename)

expect_known_hash(spc, "1e92447516")
})
test_that("WITec Graph .txt: spectra are correct", {
# Dimensions of spectra matrix (@data$spc)
expect_equal(dim(spc@data$spc), c(5, 63))

test_that("missing filename", {
spc <- read_txt_WITec_Graph(paste0(tmpdir, "/nofilename (Header).txt"),
encoding = "latin1"
)
spc$filename <- gsub("^.*/", "", spc$filename)
# Column names of spectra matrix
expect_equal(colnames(spc@data$spc)[1], "161.408")
expect_equal(colnames(spc@data$spc)[10], "200.184")
expect_equal(colnames(spc@data$spc)[n_wl], "423.651") # last name

expect_known_hash(spc, "b273847b9c")
# Values of spectra matrix
expect_equal(unname(spc@data$spc[1, 1]), 3404)
expect_equal(unname(spc@data$spc[2, 10]), 3405)
expect_equal(unname(spc@data$spc[n_rows, n_wl]), 3415) # last spc value
})

test_that("wrong combination of file names", {
expect_error(
read_txt_WITec_Graph(
paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Header).txt"),
paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Y-Axis).txt")
),
"length of wavelength axis .* differs from 'SizeGraph' in header"
)
test_that("WITec Graph .txt: wavelengths are correct", {
expect_equal(spc@wavelength[1], 161.40845)
expect_equal(spc@wavelength[10], 200.18387)
expect_equal(spc@wavelength[n_wl], 423.65106)
})
}


# hySpc.testthat::test(read_txt_WITec_Graph) <- function() {
# local_edition(2)
#
# context("read_txt_WITec_Graph")
#
# tmpdir <- paste0(tempdir(), "/test_Witec_txt_Graph")
# untar("testfiles_Witec.tar.gz",
# files = c(
# "nofilename (Header).txt",
# "nofilename (X-Axis).txt",
# "nofilename (Y-Axis).txt",
# "timeseries3x_GraphASCII.Data 1 (Header).txt",
# "timeseries3x_GraphASCII.Data 1 (X-Axis).txt",
# "timeseries3x_GraphASCII.Data 1 (Y-Axis).txt",
# "image2x3_GraphASCII.Data 1_F (Header).txt",
# "image2x3_GraphASCII.Data 1_F (X-Axis).txt",
# "image2x3_GraphASCII.Data 1_F (Y-Axis).txt"
# ),
# exdir = tmpdir
# )
#
# on.exit(unlink(tmpdir))
#
# test_that("defaults and (X-Axis)/(Y-Axis) file guessing", {
# spc <- read_txt_WITec_Graph(
# paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Header).txt")
# )
#
# expect_equal(dim(spc), c(nrow = 3L, ncol = 4L, nwl = 1024L))
#
# expect_equal(
# spc$filename,
# rep(paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Y-Axis).txt"), 3)
# )
#
# expect_equal(
# spc$WIPname,
# rep("F:\\Acetamidophenol samples_20200703.wip", 3)
# )
#
# expect_equal(
# spc$spcname,
# rep("4Acetamidophenol_timeseries3x_20200703_001_Spec.Data 1", 3)
# )
#
# expect_equivalent(spc[[2, , 1650]], 2427)
# })
#
# test_that("encoding", {
# spc <- read_txt_WITec_Graph(
# paste0(tmpdir, "/nofilename (Header).txt"),
# encoding = "latin1"
# )
# spc$filename <- gsub("^.*/", "", spc$filename)
#
# expect_known_hash(spc, "b273847b9c")
# })
#
# test_that("Time Series", {
# spc <- read_txt_WITec_Graph(
# paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Header).txt"),
# type = "single"
# )
# spc$filename <- gsub("^.*/", "", spc$filename)
#
# expect_known_hash(spc, "a5ff28fc8b")
# })
#
# test_that("Map", {
# expect_warning(
# read_txt_WITec_Graph(
# paste0(tmpdir, "/image2x3_GraphASCII.Data 1_F (Header).txt"),
# encoding = "latin1"
# ),
# "header provides spatial information in y direction for single spectra"
# )
#
# expect_warning(
# read_txt_WITec_Graph(
# paste0(tmpdir, "/image2x3_GraphASCII.Data 1_F (Header).txt"),
# encoding = "latin1", type = "single"
# ),
# "header provides spatial information in y direction for single spectra"
# )
#
# spc <- read_txt_WITec_Graph(
# paste0(tmpdir, "/image2x3_GraphASCII.Data 1_F (Header).txt"),
# type = "map", encoding = "latin1"
# )
# spc$filename <- gsub("^.*/", "", spc$filename)
#
# expect_known_hash(spc, "1e92447516")
# })
#
# test_that("missing filename", {
# spc <- read_txt_WITec_Graph(paste0(tmpdir, "/nofilename (Header).txt"),
# encoding = "latin1"
# )
# spc$filename <- gsub("^.*/", "", spc$filename)
#
# expect_known_hash(spc, "b273847b9c")
# })
#
# test_that("wrong combination of file names", {
# expect_error(
# read_txt_WITec_Graph(
# paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Header).txt"),
# paste0(tmpdir, "/timeseries3x_GraphASCII.Data 1 (Y-Axis).txt")
# ),
# "length of wavelength axis .* differs from 'SizeGraph' in header"
# )
# })
# }
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