test-cc_number.R
In nandb: Number and Brightness Image Analysis

test_that("cc_number() works", {
  img <- ijtiff::read_tif(system.file("extdata", "two_ch.tif",
    package = "nandb"
  ), msg = FALSE)
  set.seed(1)
  cc_n <- cc_number(img, thresh = "Huang", detrend = TRUE, filt = "median")
  expect_equal(median(cc_n, na.rm = TRUE), 24, tolerance = 25)
  cc_n <- cc_number(img, thresh = "Huang", filt = "smooth")
  expect_equal(median(cc_n, na.rm = TRUE), 4, tolerance = 20)
  expect_error(
    cc_number(img, ch2 = 3),
    paste0(
      "You have requested to use channel 3, but your image\\s?",
      "has only 2.+channels in total.+This is not possible.+\\s?",
      "Please retry with valid channel.+numbers."
    )
  )
  expect_error(
    cc_number(
      img %T>% {
        .[, , 1, ] <- NA
      }
    ),
    paste0(
      "The first channel is all NAs.+Can't compute on an\\s?",
      "array of all NAs."
    )
  )
  expect_error(
    cc_number(
      img %T>% {
        .[, , 2, ] <- NA
      }
    ),
    paste0(
      "The second channel is all NAs.+Can't compute on an\\s?",
      "array of all NAs."
    )
  )
  expect_error(
    cc_number(img, thresh = max(img) + 1),
    paste0(
      "After thresholding, the first channel is all\\s?",
      "NAs.+Can't compute on an array of all NAs.+You need to\\s?",
      "choose a less severe threshold for this.+channel."
    )
  )
  expect_error(
    cc_number(img, thresh = c(0, max(img) + 1)),
    paste0(
      "After thresholding, the second channel is all\\s?",
      "NAs.+Can't compute on an array of all NAs.+You need to\\s?",
      "choose a less severe threshold for this.+channel."
    )
  )
})

test_that("cc_number_timeseries() works", {
  img <- ijtiff::read_tif(system.file("extdata", "two_ch.tif",
    package = "nandb"
  ), msg = FALSE)
  set.seed(1)
  cc_n_ts <- cc_number_timeseries(img, 10,
    thresh = "Huang", detrend = TRUE,
    filt = "median", parallel = 2
  )
  expect_equal(median(cc_n_ts, na.rm = TRUE), 0, tolerance = 5)
  cc_n_ts <- cc_number_timeseries(img, 10,
    thresh = "Huang", detrend = FALSE,
    filt = "smooth", parallel = 2
  )
  expect_equal(median(cc_n_ts, na.rm = TRUE), 0, tolerance = 2)
  cc_n_ts_overlapped <- cc_number_timeseries(img, 10,
    overlap = TRUE,
    thresh = "H", filt = "s"
  )
  common_frames <- which(seq_len(dim(img)[4]) %% 10 == 1)
  expect_equal(
    cc_n_ts_overlapped[, , , common_frames, drop = FALSE] %>% {
      list(dim(.), as.vector(.))
    },
    cc_n_ts %>% {
      list(dim(.), as.vector(.))
    }
  )
  cc_n <- cc_number(img)
  cc_n_ts_overlapped <- cc_number_timeseries(img, dim(img)[4],
    overlap = TRUE
  )
  expect_equal(
    cc_n_ts_overlapped %>% {
      list(dim(.), as.vector(.))
    },
    cc_n %>% {
      list(dim(.), as.vector(.))
    }
  )
  expect_error(
    cc_number_timeseries(img, 9999),
    paste0(
      "You have selected 9999 frames per set, but there are only\\s?",
      "100,.+frames in total.+Please select less than 100 frames\\s?",
      "per set"
    )
  )
  expect_error(
    cc_number_timeseries(
      img %T>% {
        .[, , 1, ] <- NA
      }, 20
    ),
    paste0(
      "The first channel is all NAs.+Can't compute on an\\s?",
      "array of all NAs."
    )
  )
  expect_error(
    cc_number_timeseries(
      img %T>% {
        .[, , 2, ] <- NA
      }, 20
    ),
    paste0(
      "The second channel is all NAs.+Can't compute on an\\s?",
      "array of all NAs."
    )
  )
  expect_error(
    cc_number_timeseries(img, 20, thresh = max(img) + 1),
    paste0(
      "After thresholding, the first channel is all\\s?",
      "NAs.+Can't compute on an array of all NAs.+You need to\\s?",
      "choose a less severe threshold for this.+channel."
    )
  )
  expect_error(
    cc_number_timeseries(img, 20, thresh = c(0, max(img) + 1)),
    paste0(
      "After thresholding, the second channel is all\\s?",
      "NAs.+Can't compute on an array of all NAs.+You need to\\s?",
      "choose a less severe threshold for this.+channel."
    )
  )
})


test_that("cc_number_folder() works", {
  img <- ijtiff::read_tif(system.file("extdata", "two_ch.tif",
    package = "nandb"
  ), msg = FALSE)
  cwd <- getwd()
  on.exit(setwd(cwd))
  setwd(tempdir())
  ijtiff::write_tif(img, "a.tif", msg = FALSE)
  set.seed(1)
  cc_number_folder(thresh = "Huang", detrend = FALSE)
  cc_n <- dir(pattern = "cc_number", recursive = TRUE) %>%
    ijtiff::read_tif(msg = FALSE)
  expect_equal(median(cc_n, na.rm = TRUE), 24, tolerance = 25)
  suppressMessages(filesstrings::dir.remove("cc_number"))
  dir.create("dir")
  ijtiff::write_tif(img, "dir/a.tif", msg = FALSE)
  set.seed(1)
  cc_number_file("dir/a.tif", thresh = "Huang", detrend = FALSE)
  cc_n <- dir(pattern = "cc_number", recursive = TRUE) %>%
    ijtiff::read_tif(msg = FALSE)
  expect_equal(median(cc_n, na.rm = TRUE), 22.2, tolerance = 3)
  suppressMessages(filesstrings::dir.remove("dir"))
  file.remove("a.tif")
  setwd(cwd)
})

test_that("cc_number_timeseries_folder() works", {
  img <- ijtiff::read_tif(system.file("extdata", "two_ch.tif",
    package = "nandb"
  ), msg = FALSE)
  cwd <- getwd()
  on.exit(setwd(cwd))
  setwd(tempdir())
  ijtiff::write_tif(img, "a.tif", msg = FALSE)
  set.seed(1)
  cc_number_timeseries_folder(
    thresh = "Huang", frames_per_set = 10, detrend = FALSE,
    filt = "median", parallel = 2
  )
  cc_n_ts <- c(
    "cc_number_contiguous_timeseries",
    "cc_number_overlapped_timeseries"
  ) %>%
    purrr::map(~ dir(pattern = paste0(., ".*tif$"), recursive = TRUE)) %>%
    unlist() %>%
    ijtiff::read_tif(msg = FALSE)
  expect_equal(median(cc_n_ts, na.rm = TRUE), 0, tolerance = 5)
  suppressMessages(filesstrings::dir.remove("cc_number_timeseries"))
  dir.create("dir")
  ijtiff::write_tif(img, "dir/a.tif", msg = FALSE)
  set.seed(1)
  cc_number_timeseries_file("dir/a.tif",
    thresh = "Huang", detrend = FALSE,
    frames_per_set = 10,
    filt = "median", parallel = 2
  )
  cc_n_ts <- c(
    "cc_number_contiguous_timeseries",
    "cc_number_overlapped_timeseries"
  ) %>%
    purrr::map(~ dir(pattern = paste0(., ".*tif$"), recursive = TRUE)) %>%
    unlist() %>%
    ijtiff::read_tif(msg = FALSE)
  expect_equal(median(cc_n_ts, na.rm = TRUE), 0, tolerance = 5)
  filesstrings::dir.remove("dir")
  file.remove("a.tif")
  setwd(cwd)
})