tests/testthat/test-calculate_vp.R

In bioRad: Biological Analysis and Visualization of Weather Radar Data

# Define non-default options
sd_vvp_threshold <- 3
rcs <- 200
dual_pol <- TRUE
rho_hv <- 0.8
elev_min <- 1
elev_max <- 5
azim_min <- 10
azim_max <- 350
range_min <- 4000
range_max <- 40000
n_layer <- 30
h_layer <- 150
nyquist_min <- 6

# Create function to extract task_args attributes of vol2bird as a list
task_args <- function(x) {
  task_args_quoted <- paste0(gsub(",", "',", gsub("=", "='", x$attributes$how$task_args)), "'")
  eval(parse(text= paste0("list(", task_args_quoted, ")")))
}

# Prepare test files
tmpdir <- tempdir()
pvolfile <- paste(tmpdir, "pvol.h5", sep = "/")
pvolfile_out <- paste(tmpdir,"pvol_out.h5", sep = "/")
vpfile <- paste(tmpdir, "vp.h5", sep = "/")
file.copy(system.file("extdata", "volume.h5", package = "bioRad"), pvolfile, overwrite = TRUE)

# TODO:
# Arguments not yet tested:
# - mistnet_elevations, because not stored in h5 currently
# - dbz_quantity, because test file volume.h5 only has DBZH
# - mount, because difficult to test
# - local_install, because difficult to test
# - local_mistnet, because difficult to test

test_that("calculate_vp() returns error on incorrect parameters", {
  skip_if_no_vol2birdR()
  expect_error(
    calculate_vp(paste(tmpdir, "nofile.txt", sep = "/"), warnings = FALSE),
    regexp = sprintf("Path '%s' does not exist",
                     file.path(tmpdir, "nofile.txt")),
    fixed = TRUE
    )
  # vpfile: only tests if parent dir is writeable
  # pvolfile: only tests if parent dir is writeable
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, autoconf = "not_logical"),
    regexp = "autoconf is not a flag (a length one logical vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, verbose = "not_logical"),
    regexp = "verbose is not a flag (a length one logical vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = "not_logical"),
    regexp = "warnings is not a flag (a length one logical vector).",
    fixed = TRUE)
  # mount: hard to test
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, sd_vvp_threshold = "not_numeric"),
    regexp = "sd_vvp_threshold is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, sd_vvp_threshold = -1),
    regexp = "sd_vvp_threshold not greater than or equal to 0",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, rcs = "not_numeric"),
    regexp = "rcs is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, rcs = 0),
    regexp = "rcs not greater than 0",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, dual_pol = "not_logical"),
    regexp = "dual_pol is not a flag (a length one logical vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, rho_hv = "not_numeric"),
    regexp = "rho_hv is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, rho_hv = -0.1),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, rho_hv = 1.1),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, elev_min = "not_numeric"),
    regexp = "elev_min is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, elev_min = -91),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, elev_min = 91),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, elev_max = "not_numeric"),
    regexp = "elev_max is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, elev_max = -91),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, elev_max = 91),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, azim_min = "not_numeric"),
    regexp = "azim_min is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, azim_min = -1),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, azim_min = 361),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, azim_max = "not_numeric"),
    regexp = "azim_max is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, azim_max = -1),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, azim_max = 361),
    "must be a number between")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, range_min = "not_numeric"),
    regexp = "range_min is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, range_min = -1),
    "must be a positive number")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, range_max = "not_numeric"),
    regexp = "range_max is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, range_max = 0),
    "must be a positive number")
  expect_error(
    calculate_vp(
      pvolfile,
      warnings = FALSE,
      range_min = 35000,
      range_max = 5000
    ),
    "must be larger than")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, n_layer = "not_numeric"),
    regexp = "n_layer is not a count (a single positive integer)",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, n_layer = "1.0"),
    regexp = "n_layer is not a count (a single positive integer)",
    fixed = TRUE) # Not integer
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, h_layer = "not_numeric"),
    regexp = "h_layer is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, h_layer = -1),
    "must be a positive number")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, dealias = "not_logical"),
    regexp = "`dealias` must be a logical value.",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, nyquist_min = "not_numeric"),
    regexp = "nyquist_min is not a number (a length one numeric vector).",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, nyquist_min = -1),
    "must be a positive number")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, dbz_quantity = "invalid"),
    "must be either")
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, mistnet = "not_logical"),
    regexp = "`mistnet` must be a logical value.",
    fixed = TRUE)
  expect_error(
    calculate_vp(
      pvolfile,
      warnings = FALSE,
      mistnet_elevations = c(
        "not_numeric",
        "not_numeric",
        "not_numeric",
        "not_numeric",
        "not_numeric"
      )
    ),
    regexp = "mistnet_elevations is not a numeric or integer vector",
    fixed = TRUE)
  expect_error(
    calculate_vp(pvolfile, warnings = FALSE, mistnet_elevations = c(0.5, 1.5)),
    regexp = "length(mistnet_elevations) not equal to 5",
    fixed = TRUE) # Not length 5
  # local_install: hard to test
  # local_mistnet: hard to test
})

test_that("calculate_vp() produces a vp object and optional vpfile, pvolfile", {
  skip_if_no_vol2birdR()
  vp <- calculate_vp(file = pvolfile, vpfile = vpfile, pvolfile_out = pvolfile_out, warnings = FALSE)
  vp_from_file <- read_vpfiles(vpfile)
  pvol_from_file <- read_pvolfile(pvolfile_out)

  expect_s3_class(vp, "vp")
  expect_s3_class(vp_from_file, "vp")
  expect_s3_class(pvol_from_file, "pvol")
  expect_s3_class(pvol_from_file$scans[[1]], "scan")
  scan <- get_scan(pvol_from_file, 0.5)
  expect_s3_class(scan$params$CELL, "param")
})

test_that("calculate_vp() produces same vp from disk and from memory", {
  skip_if_no_vol2birdR()
  # how differs in file locations other wise they are equal
  vp_file<-calculate_vp(file = pvolfile, warnings = FALSE)
  vp_memory<-  calculate_vp(file = read_pvolfile(pvolfile), warnings = FALSE)
  expect_equal(vp_file$data, vp_memory$data)
  expect_equal(vp_file$attributes$what, vp_memory$attributes$what)
  expect_equal(vp_file$attributes$where, vp_memory$attributes$where)
  expect_equal(vp_file$attributes$how$task_args, vp_memory$attributes$how$task_args)

})

test_that("calculate_vp() parses input arguments for vol2bird", {
  skip_if_no_vol2birdR()
  # Run with non-default options
  vp <- calculate_vp(file = pvolfile, , warnings = FALSE, sd_vvp_threshold =
                     sd_vvp_threshold, rcs = rcs, dual_pol = dual_pol, rho_hv =
                     rho_hv, elev_min = elev_min, elev_max = elev_max,
                     azim_min = azim_min, azim_max = azim_max, range_min =
                     range_min, range_max = range_max, n_layer = n_layer,
                     h_layer = h_layer, nyquist_min = nyquist_min)
  task_args <- task_args(vp)

  # sd_vvp_threshold is not part of task_args
  expect_equal(rcs, as.numeric(task_args$birdRadarCrossSection))
  expect_equal(dual_pol, as.logical(as.numeric(task_args$dualPol)))
  expect_equal(rho_hv, as.numeric(task_args$rhohvThresMin))
  expect_equal(elev_min, as.numeric(task_args$elevMin))
  expect_equal(elev_max, as.numeric(task_args$elevMax))
  expect_equal(azim_min, as.numeric(task_args$azimMin))
  expect_equal(azim_max, as.numeric(task_args$azimMax))
  expect_equal(range_min, as.numeric(task_args$rangeMin))
  expect_equal(range_max, as.numeric(task_args$rangeMax))
  expect_equal(n_layer, as.numeric(task_args$nLayers))
  expect_equal(h_layer, as.numeric(task_args$layerThickness))
  expect_equal(nyquist_min, as.numeric(task_args$minNyquist))
})

test_that("calculate_vp() ignores input arguments if autoconf", {
  skip_if_no_vol2birdR()
  # Run with non-default options
  vp <- calculate_vp(file = pvolfile, , warnings = FALSE, sd_vvp_threshold =
                     sd_vvp_threshold, rcs = rcs, dual_pol = dual_pol, rho_hv =
                     rho_hv, elev_min = elev_min, elev_max = elev_max,
                     azim_min = azim_min, azim_max = azim_max, range_min =
                     range_min, range_max = range_max, n_layer = n_layer,
                     h_layer = h_layer, nyquist_min = nyquist_min,
                     autoconf = TRUE)
  task_args <- task_args(vp)

  # sd_vvp_threshold is not part of task_args
  expect_false(rcs == as.numeric(task_args$birdRadarCrossSection))
  expect_true(as.logical(as.numeric(task_args$dualPol))) # Set to true by autoconf
  expect_false(rho_hv == as.numeric(task_args$rhohvThresMin))
  expect_false(elev_min == as.numeric(task_args$elevMin))
  expect_false(elev_max == as.numeric(task_args$elevMax))
  expect_false(azim_min == as.numeric(task_args$azimMin))
  expect_false(azim_max == as.numeric(task_args$azimMax))
  expect_false(range_min == as.numeric(task_args$rangeMin))
  expect_false(range_max == as.numeric(task_args$rangeMax))
  expect_false(n_layer == as.numeric(task_args$nLayers))
  expect_false(h_layer == as.numeric(task_args$layerThickness))
  expect_false(nyquist_min == as.numeric(task_args$minNyquist))
})

test_that("MistNet adds param WEATHER", {
  skip_if_no_mistnet()
  vp <- calculate_vp(file = pvolfile, pvolfile_out = pvolfile_out, warnings = FALSE, mistnet = TRUE)
  pvol_from_file <- read_pvolfile(pvolfile_out)

  # Check that the MistNet param "WEATHER" is added for a MistNet elevation
  scan <- get_scan(pvol_from_file, 0.5)
  expect_s3_class(scan$params$WEATHER, "param")
})

test_that("Dealiasing can be toggled", {
  skip_if_no_vol2birdR()
  # run without dealiasing
  vp <- calculate_vp(file = pvolfile, warnings = FALSE, nyquist_min = nyquist_min, dealias = FALSE)
  # Dealias attribute is stored in two locations
  expect_equal(vp$attributes$how$dealiased, 0)
  expect_equal(task_args(vp)$dealiasVrad, "0")

  # run with dealiasing
  vp <- calculate_vp(file = pvolfile, warnings = FALSE, nyquist_min = nyquist_min, dealias = TRUE)
  expect_equal(vp$attributes$how$dealiased, 1)
  expect_equal(task_args(vp)$dealiasVrad,"1")
})


test_that("Extension of vpfile is obeyed in output", {
  skip_if_no_vol2birdR()
  # Test with a .h5 file
  output_file <- calculate_vp(pvolfile, vpfile = vpfile)
  expect_equal(tools::file_ext(vpfile), "h5")
  expect_equal(guess_file_type(vpfile), "h5")

   #Change the extension of vpfile to .csv
  vpfile_csv <- sub("h5$", "csv", vpfile)

  # Test with a .csv file
  output_file <- calculate_vp(pvolfile, vpfile = vpfile_csv)
  expect_equal(tools::file_ext(vpfile_csv), "csv")
  expect_equal(guess_file_type(vpfile_csv), "csv")

})