Nothing
test_that("detrending entire derectories works", {
skip_if(getRversion() < "3.6")
skip_on_cran()
cwd <- setwd(tempdir(check = TRUE))
on.exit(setwd(cwd))
orig_files <- c(
system.file("extdata", "2ch_ij.tif", package = "detrendr"),
system.file("extdata", "bleached.tif", package = "detrendr")
)
file.copy(orig_files, ".")
orig_imgs <- purrr::map(orig_files, ijtiff::read_tif, msg = FALSE) %>%
magrittr::set_names(basename(orig_files))
detrendeds <- try(stop("eee"), silent = TRUE)
set.seed(1)
while (class(detrendeds) == "try-error") {
set.seed(get_seed())
detrendeds <- tryCatch(purrr::map(orig_imgs,
autothresholdr::mean_stack_thresh,
method = "tri"
) %>%
purrr::map(img_detrend_boxcar,
l = "auto",
purpose = "ff"
),
error = function(e) {
err_msg <- conditionMessage(e)
if (!stringr::str_detect(
err_msg,
"Even.*most severe d"
)) {
stop(err_msg)
} else {
structure(err_msg, class = "try-error")
}
}
)
}
eee <- try(stop("eee"), silent = TRUE)
set.seed(1)
while (class(eee) == "try-error") {
set.seed(get_seed())
eee <- tryCatch(dir_detrend_boxcar(
l = "auto", thresh = "tri",
purpose = "ff", msg = FALSE
),
error = function(e) {
err_msg <- conditionMessage(e)
if (!stringr::str_detect(
err_msg,
"Even .* most severe detrend"
)) {
stop("unexpected error")
} else {
structure(err_msg, class = "try-error")
}
}
)
}
detrendeds_dir <- dir(pattern = "detrended.*tif", recursive = TRUE) %>%
purrr::map(ijtiff::read_tif, msg = FALSE)
expect_equal(
purrr::map(detrendeds, dim),
purrr::map(detrendeds_dir, dim),
ignore_attr = TRUE
)
expect_equal(unlist(detrendeds), unlist(detrendeds_dir),
tolerance = 1,
ignore_attr = TRUE
)
expect_match(
dir("detrended")[1],
paste0(
"2ch_ij_detrended_",
"thresh=Triangle=\\d+\\.?\\d*,Triangle=\\d+\\.?\\d*_",
"boxcar_for_FFS_l=auto=(NA|\\d+),auto=(NA|\\d+).tif"
)
)
expect_match(
dir("detrended")[2],
paste0(
"bleached_detrended_",
"thresh=Triangle=\\d+\\.?\\d*_",
"boxcar_for_FFS_l=auto=\\d+.tif"
)
)
suppressWarnings(
expect_warning(
dir_detrend_boxcar("detrended", l = 9, purpose = "fcs"),
"already detrended"
)
)
filesstrings::dir.remove("detrended")
set.seed(1)
detrendeds <- purrr::map(orig_imgs, autothresholdr::mean_stack_thresh,
method = "tri"
) %>%
purrr::map(img_detrend_exp, tau = "auto", purpose = "ff")
set.seed(1)
dir_detrend_exp(
tau = "auto", thresh = "tri", purpose = "ff",
msg = FALSE
)
detrendeds_dir <- dir(pattern = "detrended.*tif", recursive = TRUE) %>%
purrr::map(ijtiff::read_tif, msg = FALSE)
expect_equal(
purrr::map(detrendeds, dim),
purrr::map(detrendeds_dir, dim),
ignore_attr = TRUE
)
expect_equal(unlist(detrendeds), unlist(detrendeds_dir),
tolerance = 1, ignore_attr = TRUE
)
expect_match(
dir("detrended")[1],
paste0(
"2ch_ij_detrended_",
"thresh=Triangle=\\d+\\.?\\d*,Triangle=\\d+\\.?\\d*_",
"exponential_for_FFS_tau=auto=(NA|\\d+\\.?\\d*),auto=(NA|\\d+\\.?\\d*)",
".tif"
)
)
expect_match(
dir("detrended")[2],
paste0(
"bleached_detrended_",
"thresh=Triangle=\\d+\\.?\\d*_",
"exponential_for_FFS_tau=auto=\\d+\\.?\\d*.tif"
)
)
filesstrings::dir.remove("detrended")
set.seed(1)
detrendeds <- purrr::map(orig_imgs, autothresholdr::mean_stack_thresh,
method = "tri"
) %>%
purrr::map(img_detrend_rh, swaps = 222)
set.seed(1)
dir_detrend_rh(swaps = 222, thresh = "tri", msg = FALSE)
detrendeds_dir <- dir(pattern = "detrended.*tif$", recursive = TRUE) %>%
purrr::map(ijtiff::read_tif, msg = FALSE)
expect_equal(
purrr::map(detrendeds, dim),
purrr::map(detrendeds_dir, dim),
ignore_attr = TRUE
)
expect_equal(unlist(detrendeds), unlist(detrendeds_dir), ignore_attr = TRUE)
expect_match(
dir("detrended")[1],
paste0(
"2ch_ij_detrended_",
"thresh=Triangle=\\d+\\.?\\d*,Triangle=\\d+\\.?\\d*_",
"robinhood_swaps=222,222.tif"
)
)
expect_match(
dir("detrended")[2],
paste0(
"bleached_detrended_",
"thresh=Triangle=\\d+\\.?\\d*_",
"robinhood_swaps=222.tif"
)
)
filesstrings::dir.remove("detrended")
set.seed(1)
file.remove("2ch_ij.tif")
detrendeds <- purrr::map(
orig_imgs[list.files(pattern = ".tif$")],
autothresholdr::mean_stack_thresh,
method = "tri"
) %>%
purrr::map(~ suppressWarnings(img_detrend_polynom(.,
degree = 2,
purpose = "ff"
)))
set.seed(1)
suppressWarnings(dir_detrend_polynom(
degree = 2, thresh = "tri",
purpose = "ff", msg = FALSE
))
detrendeds_dir <- dir(pattern = "detrended.*tif", recursive = TRUE) %>%
purrr::map(ijtiff::read_tif, msg = FALSE)
expect_equal(
purrr::map(detrendeds, dim),
purrr::map(detrendeds_dir, dim),
ignore_attr = TRUE
)
expect_equal(unlist(detrendeds), unlist(detrendeds_dir),
tolerance = 1, ignore_attr = TRUE
)
expect_match(
dir("detrended"),
paste0(
"bleached_detrended_",
"thresh=Triangle=\\d+\\.?\\d*_polynomial_for_FFS_degree=2.tif"
)
)
filesstrings::dir.remove("detrended")
file.remove(dir(pattern = "tif$"))
setwd(cwd)
})
test_that("file_detrend() deals with other directories correctly", {
skip_on_cran()
setwd(tempdir())
filesstrings::create_dir("tempwithintemp")
file.copy(
system.file("extdata", "bleached.tif", package = "detrendr"),
"tempwithintemp"
)
file_detrend("tempwithintemp/bleached.tif",
method = "exp", parameter = 5,
purpose = "ff"
)
})
test_that("`make_thresh_filename_part()` works", {
expect_equal(
make_thresh_filename_part(structure(0, thresh = 1)),
"thresh=1_"
)
})
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