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Adapt unittest for read_txt_Renishaw() function #54

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merged 7 commits into from
Aug 6, 2021
Merged

Adapt unittest for read_txt_Renishaw() function #54

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3b34e0c
Adapt unittest for read_txt_Renishaw() function
Aug 1, 2021
5efc053
Merge branch 'develop' into features/42-read-txt-Renishaw
GegznaV Aug 5, 2021
d8b3e05
Merge branch 'develop' into features/42-read-txt-Renishaw
GegznaV Aug 5, 2021
9d02753
replace chondro with faux_cell
Aug 6, 2021
e2449b2
fix path, return to chondro since can't file faux_cell
Aug 6, 2021
07c2c9c
rename chondro to chondro_file to avoid confusion
Aug 6, 2021
e5613f3
rename object name with prefix f_
Aug 6, 2021
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23 changes: 11 additions & 12 deletions R/read_txt_Renishaw.R
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Expand Up @@ -164,48 +164,47 @@ read_txt_Renishaw <- function(file = stop("file is required"),

hySpc.testthat::test(read_txt_Renishaw) <- function() {
context("read_txt_Renishaw")
path <- system.file("extdata/fileio/txt.Renishaw", package="hySpc.read.txt")
paracetamol <- paste0(path, "/paracetamol.txt")
laser <- paste0(path, "/laser.txt.gz")
chondro <- paste0(path, "/chondro.txt")
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Can you, please, not use the names paracetamol, laser, and chondro for file names. Use f_paracetamol, f_laser, and f_chondro instead.


test_that("single spectrum", {
skip("TODO: adapt to new package")
tmp <- read_txt_Renishaw("fileio/txt.Renishaw/paracetamol.txt", "spc")
tmp <- read_txt_Renishaw(paracetamol, "spc")
expect_equal(dim(tmp), c(nrow = 1L, ncol = 2L, nwl = 4064L))
})

test_that("time series spectrum, gzipped", {
skip("TODO: adapt to new package")
tmp <- read_txt_Renishaw("fileio/txt.Renishaw/laser.txt.gz", "ts")
tmp <- read_txt_Renishaw(laser, "ts")
expect_equal(dim(tmp), c(nrow = 84L, ncol = 3L, nwl = 140L))
expect_equal(colnames(tmp), c("t", "spc", "filename"))
})

test_that("map (= default)", {
skip("TODO: adapt to new package")
tmp <- read_txt_Renishaw("fileio/txt.Renishaw/chondro.txt", "xyspc")
tmp <- read_txt_Renishaw(chondro, "xyspc")
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expect_equal(dim(tmp), c(nrow = 875L, ncol = 4L, nwl = 1272L))
expect_equal(colnames(tmp), c("y", "x", "spc", "filename"))

tmp <- read_txt_Renishaw("fileio/txt.Renishaw/chondro.txt")
tmp <- read_txt_Renishaw(chondro)
expect_equal(dim(tmp), c(nrow = 875L, ncol = 4L, nwl = 1272L))
expect_equal(colnames(tmp), c("y", "x", "spc", "filename"))
})

test_that("chunked reading", {
skip("TODO: adapt to new package")

## error on too small chunk size
expect_error(
read_txt_Renishaw("fileio/txt.Renishaw/chondro.txt", nlines = 10),
read_txt_Renishaw(chondro, nlines = 10),
"Wavelengths do not correspond"
)

tmp <- read_txt_Renishaw("fileio/txt.Renishaw/chondro.txt", nlines = 1e5)
tmp <- read_txt_Renishaw(chondro, nlines = 1e5)
expect_equal(dim(tmp), c(nrow = 875L, ncol = 4L, nwl = 1272L))
})

test_that("compressed files", {
skip("TODO: adapt to new package")

files <- Sys.glob("fileio/txt.Renishaw/chondro.*")
files <- Sys.glob(paste0(path, "/chondro.*"))
files <- grep("[.]zip", files, invert = TRUE, value = TRUE) # .zip is tested with read_zip_Renishaw
for (f in files) {
expect_equal(dim(read_txt_Renishaw(!!f)), c(nrow = 875L, ncol = 4L, nwl = 1272L))
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