tests/testthat/test_make_simspin_file.R
In kateharborne/SimSpin: SimSpin - A package for the kinematic analysis of galaxy simulations
# Author: Kate Harborne
# Co-author: Alice Serene
# Date: 13/01/2023
# Title: Testing the make_simspin_file.R code
library(testthat)
context("Testing make_simspin_file function.\n")
ss_gadget = system.file("extdata", "SimSpin_example_Gadget", package = "SimSpin")
ss_hdf5 = system.file("extdata", "SimSpin_example_HDF5.hdf5", package = "SimSpin")
ss_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5", package = "SimSpin")
ss_magneticum = system.file("extdata", "SimSpin_example_Magneticum.hdf5", package = "SimSpin")
ss_horizon = system.file("extdata", "SimSpin_example_HorizonAGN.hdf5", package = "SimSpin")
ss_illustris = system.file("extdata", "SimSpin_example_IllustrisTNG.hdf5", package = "SimSpin")
ss_file_length = 4
ss_file_header_length = 15
built_cube_size = 5
temp_loc = tempdir()
# Test that the function runs successfully without error
test_that("Initial run of each simulation type - Gadget.", {
expect_null(make_simspin_file(ss_gadget, template = "BC03hr", output = paste(temp_loc, "/gadget_test", sep="")))
expect_length(readRDS(paste(temp_loc, "/gadget_test", sep="")), ss_file_length)
expect_true(length(readRDS(paste(temp_loc, "/gadget_test", sep=""))$gas_part) == 0)
expect_true(nrow(readRDS(paste(temp_loc, "/gadget_test", sep=""))$spectral_weights) == 8)
expect_true(length(readRDS(paste(temp_loc, "/gadget_test", sep=""))$spectral_weights) == 2) # for each of the two particle types
})
test_that("Initial run of each simulation type - HDF5", {
expect_null(make_simspin_file(ss_hdf5, output = paste(temp_loc, "/hdf5_test", sep="")))
expect_length(readRDS(paste(temp_loc, "/hdf5_test", sep="")), ss_file_length)
expect_true(length(readRDS(paste(temp_loc, "/hdf5_test", sep=""))$gas_part) == 0)
expect_true(nrow(readRDS(paste(temp_loc, "/hdf5_test", sep=""))$spectral_weights) == 8)
expect_true(length(readRDS(paste(temp_loc, "/hdf5_test", sep=""))$spectral_weights) == 1) # for each of the two particle types
})
test_that("Initial run of each simulation type - EAGLE", {
expect_null(make_simspin_file(ss_eagle, output = paste(temp_loc, "/eagle_test", sep=""), centre = c(18318,61583,38667), half_mass = 1483809589))
EAGLE = readRDS(paste(temp_loc, "/eagle_test", sep=""))
expect_length(EAGLE, ss_file_length)
expect_true(length(EAGLE$gas_part) == 16)
expect_true(nrow(EAGLE$spectral_weights) == 8)
expect_false(any(is.na(EAGLE$gas_part$ThermalDispersion)))
expect_true(all(EAGLE$gas_part$ThermalDispersion[EAGLE$gas_part$Temperature < 1e4] == 11))
})
test_that("Initial run of each simulation type - Magneticum", {
expect_null(make_simspin_file(ss_magneticum, output = paste(temp_loc, "/magneticum_test", sep="")))
magneticum = readRDS(paste(temp_loc, "/magneticum_test", sep=""))
expect_length(magneticum, ss_file_length)
expect_true(length(magneticum$gas_part) == 16)
expect_true(nrow(magneticum$spectral_weights) == 8)
expect_false(any(is.na(magneticum$gas_part$ThermalDispersion)))
expect_true(all(magneticum$gas_part$ThermalDispersion[magneticum$gas_part$Temperature < 1e4] == 11))
})
test_that("Initial run of each simulation type - HorizonAGN", {
expect_null(make_simspin_file(ss_horizon, output = paste(temp_loc, "/horizon_test", sep="")))
HAGN = readRDS(paste(temp_loc, "/horizon_test", sep=""))
expect_length(HAGN, ss_file_length)
expect_true(length(HAGN$gas_part) == 16)
expect_true(nrow(HAGN$spectral_weights) == 8)
expect_false(any(is.na(HAGN$gas_part$ThermalDispersion)))
expect_true(all(HAGN$gas_part$ThermalDispersion[HAGN$gas_part$Temperature < 1e4] == 11))
})
test_that("Initial run of each simulation type - IllustrisTNG", {
expect_null(make_simspin_file(ss_illustris, output = paste(temp_loc, "/illustris_test", sep="")))
TNG = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_length(TNG, ss_file_length)
expect_true(length(TNG$gas_part) == 16)
expect_true(nrow(TNG$spectral_weights) == 8)
expect_false(any(is.na(TNG$gas_part$ThermalDispersion)))
expect_true(all(TNG$gas_part$ThermalDispersion[TNG$gas_part$Temperature < 1e4] == 11))
})
# Test that the function fails when the file already exists
test_that("Error when output file already exists and overwrite = F - Gadget",{
expect_error(make_simspin_file(ss_gadget, output = paste(temp_loc, "/gadget_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - HDF5",{
expect_error(make_simspin_file(ss_hdf5, output = paste(temp_loc, "/hdf5_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - EAGLE",{
expect_error(make_simspin_file(ss_eagle, output = paste(temp_loc, "/eagle_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - Magneticum",{
expect_error(make_simspin_file(ss_magneticum, output = paste(temp_loc, "/magneticum_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - HorizonAGN",{
expect_error(make_simspin_file(ss_horizon, output = paste(temp_loc, "/horizon_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - IllustrisTNG",{
expect_error(make_simspin_file(ss_illustris, output = paste(temp_loc, "/illustris_test", sep="")))
})
# Test that function can output to environment
test_that("Function works to output List to environment", {
ss_file = make_simspin_file(ss_gadget, write_to_file = FALSE)
expect_true("ss_file" %in% ls())
})
# Test that the function fails when the template provided is unsupported
test_that("Error when template is unsupported", {
expect_error(make_simspin_file(ss_eagle, template = "abcd"))
})
# Test that the function will overwrite if overwrite = T
test_that("Test that old files can be overwritten", {
expect_null(make_simspin_file(ss_gadget, template = "EMILES", output = paste(temp_loc, "/gadget_test", sep=""),
overwrite = T))
})
# Test that the function works on multiple cores
test_that("Test that function works on multiple cores", {
expect_null(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 2))
})
# Test that none of the output arrays have NAs in
test_that("Values are successfully associated with variables", {
gadget = readRDS(paste(temp_loc, "/gadget_test", sep=""))
hdf5 = readRDS(paste(temp_loc, "/hdf5_test", sep=""))
eagle = readRDS(paste(temp_loc, "/eagle_test", sep=""))
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_true(all(!is.na(gadget$star_part$x)))
expect_true(all(!is.na(gadget$star_part$y)))
expect_true(all(!is.na(gadget$star_part$z)))
expect_true(all(!is.na(gadget$star_part$vx)))
expect_true(all(!is.na(gadget$star_part$vy)))
expect_true(all(!is.na(gadget$star_part$vz)))
expect_true(all(!is.na(gadget$star_part$Mass)))
expect_true(all(!is.na(gadget$star_part$sed_id)))
expect_true(all(!is.na(gadget$star_part$Metallicity)))
expect_true(all(!is.na(gadget$star_part$Age)))
expect_true(all(!is.na(gadget$star_part$Initial_Mass)))
expect_true(all(!is.na(hdf5$star_part$x)))
expect_true(all(!is.na(hdf5$star_part$y)))
expect_true(all(!is.na(hdf5$star_part$z)))
expect_true(all(!is.na(hdf5$star_part$vx)))
expect_true(all(!is.na(hdf5$star_part$vy)))
expect_true(all(!is.na(hdf5$star_part$vz)))
expect_true(all(!is.na(hdf5$star_part$Mass)))
expect_true(all(!is.na(hdf5$star_part$sed_id)))
expect_true(all(!is.na(hdf5$star_part$Metallicity)))
expect_true(all(!is.na(hdf5$star_part$Age)))
expect_true(all(!is.na(hdf5$star_part$Initial_Mass)))
expect_true(all(!is.na(eagle$star_part$x)))
expect_true(all(!is.na(eagle$star_part$y)))
expect_true(all(!is.na(eagle$star_part$z)))
expect_true(all(!is.na(eagle$star_part$vx)))
expect_true(all(!is.na(eagle$star_part$vy)))
expect_true(all(!is.na(eagle$star_part$vz)))
expect_true(all(!is.na(eagle$star_part$Mass)))
expect_true(all(!is.na(eagle$star_part$sed_id)))
expect_true(all(!is.na(eagle$star_part$Metallicity)))
expect_true(all(!is.na(eagle$star_part$Age)))
expect_true(all(!is.na(eagle$star_part$Initial_Mass)))
expect_true(all(!is.na(eagle$gas_part$x)))
expect_true(all(!is.na(eagle$gas_part$y)))
expect_true(all(!is.na(eagle$gas_part$z)))
expect_true(all(!is.na(eagle$gas_part$vx)))
expect_true(all(!is.na(eagle$gas_part$vy)))
expect_true(all(!is.na(eagle$gas_part$vz)))
expect_true(all(!is.na(eagle$gas_part$Mass)))
expect_true(all(!is.na(eagle$gas_part$Z)))
expect_true(all(!is.na(eagle$gas_part$Density)))
expect_true(all(!is.na(eagle$gas_part$Temp)))
expect_true(all(!is.na(eagle$gas_part$SFR)))
expect_true(all(!is.na(eagle$gas_part$Metallicity)))
expect_true(all(!is.na(eagle$gas_part$OEOS)))
expect_true(all(!is.na(illustris$star_part$x)))
expect_true(all(!is.na(illustris$star_part$y)))
expect_true(all(!is.na(illustris$star_part$z)))
expect_true(all(!is.na(illustris$star_part$vx)))
expect_true(all(!is.na(illustris$star_part$vy)))
expect_true(all(!is.na(illustris$star_part$vz)))
expect_true(all(!is.na(illustris$star_part$Mass)))
expect_true(all(!is.na(illustris$star_part$sed_id)))
expect_true(all(!is.na(illustris$star_part$Metallicity)))
expect_true(all(!is.na(illustris$star_part$Age)))
expect_true(all(!is.na(illustris$star_part$Initial_Mass)))
expect_true(all(!is.na(illustris$gas_part$x)))
expect_true(all(!is.na(illustris$gas_part$y)))
expect_true(all(!is.na(illustris$gas_part$z)))
expect_true(all(!is.na(illustris$gas_part$vx)))
expect_true(all(!is.na(illustris$gas_part$vy)))
expect_true(all(!is.na(illustris$gas_part$vz)))
expect_true(all(!is.na(illustris$gas_part$Mass)))
expect_true(all(!is.na(illustris$gas_part$SFR)))
expect_true(all(!is.na(illustris$gas_part$Density)))
expect_true(all(!is.na(illustris$gas_part$Temperature)))
expect_true(all(!is.na(illustris$gas_part$Metallicity)))
# SmoothingLength, Carbon/Hydrogen/Oxygen?
})
# Testing the sph_spawn functionality ----
test_that("Test that sph_spawn functionality works", {
expect_null(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_magneticum, template = "BC03lr", output = paste(temp_loc, "/magneticum_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_magneticum, template = "BC03lr", output = paste(temp_loc, "/magneticum_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_horizon, template = "BC03hr", output = paste(temp_loc, "/horizon_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_horizon, template = "BC03hr", output = paste(temp_loc, "/horizon_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_illustris, template = "BC03lr", output = paste(temp_loc, "/illustris_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_illustris, template = "BC03lr", output = paste(temp_loc, "/illustris_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
test_horizon = readRDS(paste(temp_loc, "/horizon_test", sep=""))
expect_true(data.table::is.data.table(test_horizon$gas_part))
remove(test_horizon)
})
test_that("Test that sph_spawn errors when N is not an integer", {
expect_error(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10.2))
})
test_that("Test that sph_spawn functionality works on multiple cores - EAGLE", {
gas_data_c1 = make_simspin_file(ss_eagle, template = "EMILES", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_eagle, template = "EMILES", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
test_that("Test that sph_spawn functionality works on multiple cores - Magneticum", {
gas_data_c1 = make_simspin_file(ss_magneticum, template = "EMILES", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_magneticum, template = "EMILES", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
test_that("Test that sph_spawn functionality works on multiple cores - HorizonAGN", {
gas_data_c1 = make_simspin_file(ss_horizon, template = "BC03", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_horizon, template = "BC03", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
test_that("Test that sph_spawn functionality works on multiple cores - IllustrisTNG", {
gas_data_c1 = make_simspin_file(ss_illustris, template = "BC03", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_illustris, template = "BC03", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
# Test that the added header information works as expected ---------------------
test_that("Testing that the header data works as expected", {
gadget = readRDS(paste(temp_loc, "/gadget_test", sep=""))
hdf5 = readRDS(paste(temp_loc, "/hdf5_test", sep=""))
eagle = readRDS(paste(temp_loc, "/eagle_test", sep=""))
magneticum = readRDS(paste(temp_loc, "/magneticum_test", sep=""))
horizon = readRDS(paste(temp_loc, "/horizon_test", sep=""))
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_equal(gadget$header$Type, "nbody")
expect_equal(hdf5$header$Type, "nbody")
expect_equal(eagle$header$Type, "EAGLE")
expect_equal(magneticum$header$Type, "Magneticum")
expect_equal(horizon$header$Type, "Horizon-AGN")
expect_equal(illustris$header$Type, "Illustris-TNG")
expect_equal(gadget$header$Template, "EMILES")
expect_equal(hdf5$header$Template, "BC03lr")
expect_equal(eagle$header$Template, "EMILES")
expect_equal(magneticum$header$Template, "BC03lr")
expect_equal(horizon$header$Template, "BC03hr")
expect_equal(illustris$header$Template, "BC03lr") # correct?
expect_equal(gadget$header$Template_LSF, 2.51)
expect_equal(hdf5$header$Template_LSF, 3)
expect_equal(eagle$header$Template_LSF, 2.51)
expect_equal(magneticum$header$Template_LSF, 3)
expect_equal(horizon$header$Template_LSF, 3)
expect_equal(illustris$header$Template_LSF, 3) # 3?
expect_equal(gadget$header$Template_waveres, eagle$header$Template_waveres)
expect_equal(hdf5$header$Template_waveres, 1)
expect_equal(eagle$header$Template_waveres, 0.9)
expect_equal(magneticum$header$Template_waveres, 1)
expect_equal(horizon$header$Template_waveres, 1)
expect_equal(illustris$header$Template_waveres, 1) # 1?
remove(gadget, hdf5, eagle, magneticum, horizon, illustris)
})
# Illustris-specific tests -----------------------------------------------------
# CGS conversion factors that are inherently 0 should be converted to 1
test_that("CGS conversion values of 0 get converted to 1",{
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_true(all(illustris$star_part$Metallicity!=0))
})
# Stellar wind particles should be removed from the dataset
# (There are 4 wind particles in the testing set, these should be removed.)
test_that("Negative stellar wind particles are removed",{
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_length(illustris$star_part$Metallicity, 1996)
})
# Gas temperature should fall within a reasonable range
test_that("Temperature does not go outside a reasonable range",{
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_true(min(illustris$gas_part$Temperature)>0)
expect_true(max(illustris$gas_part$Temperature)<50000000)
})
unlink(c(paste(temp_loc, "/gadget_test", sep=""), paste(temp_loc, "/hdf5_test", sep=""),
paste(temp_loc, "/eagle_test", sep=""), paste(temp_loc, "/magneticum_test", sep=""),
paste(temp_loc, "/horizon_test", sep=""), paste(temp_loc, "/illustris_test", sep="")))
# Testing that the centre parameter works as expected ------------
test_that("Objects are centered correctly based on the specified central coordinates", {
expect_error(make_simspin_file(filename = ss_horizon, template = "EMILES", write_to_file = F, centre = c(0,0,0)))
centre_right = make_simspin_file(filename = ss_horizon, template = "BC03lr", write_to_file = F, centre = c(12328,72177.97,32388.04))
centre_left = make_simspin_file(filename = ss_horizon, template = "BC03lr", write_to_file = F, centre = c(12332,72177.97,32388.04))
# Checking values exist in fields for LEFT
expect_true(all(!is.na(centre_left$star_part$x)))
expect_true(all(!is.na(centre_left$star_part$y)))
expect_true(all(!is.na(centre_left$star_part$z)))
expect_true(all(!is.na(centre_left$star_part$vx)))
expect_true(all(!is.na(centre_left$star_part$vy)))
expect_true(all(!is.na(centre_left$star_part$vz)))
expect_true(all(!is.na(centre_left$star_part$Mass)))
expect_true(all(!is.na(centre_left$star_part$sed_id)))
expect_true(all(!is.na(centre_left$star_part$Metallicity)))
expect_true(all(!is.na(centre_left$star_part$Age)))
expect_true(all(!is.na(centre_left$star_part$Initial_Mass)))
expect_true(all(!is.na(centre_left$gas_part$x)))
expect_true(all(!is.na(centre_left$gas_part$y)))
expect_true(all(!is.na(centre_left$gas_part$z)))
expect_true(all(!is.na(centre_left$gas_part$vx)))
expect_true(all(!is.na(centre_left$gas_part$vy)))
expect_true(all(!is.na(centre_left$gas_part$vz)))
expect_true(all(!is.na(centre_left$gas_part$Mass)))
expect_true(all(!is.na(centre_left$gas_part$SFR)))
expect_true(all(!is.na(centre_left$gas_part$Density)))
expect_true(all(!is.na(centre_left$gas_part$Temperature)))
expect_true(all(!is.na(centre_left$gas_part$CellSize)))
expect_true(all(!is.na(centre_left$gas_part$Metallicity)))
expect_true(all(!is.na(centre_left$gas_part$Carbon)))
expect_true(all(!is.na(centre_left$gas_part$Oxygen)))
expect_true(all(!is.na(centre_left$gas_part$Hydrogen)))
# Checking values exist in fields for RIGHT
expect_true(all(!is.na(centre_right$star_part$x)))
expect_true(all(!is.na(centre_right$star_part$y)))
expect_true(all(!is.na(centre_right$star_part$z)))
expect_true(all(!is.na(centre_right$star_part$vx)))
expect_true(all(!is.na(centre_right$star_part$vy)))
expect_true(all(!is.na(centre_right$star_part$vz)))
expect_true(all(!is.na(centre_right$star_part$Mass)))
expect_true(all(!is.na(centre_right$star_part$sed_id)))
expect_true(all(!is.na(centre_right$star_part$Metallicity)))
expect_true(all(!is.na(centre_right$star_part$Age)))
expect_true(all(!is.na(centre_right$star_part$Initial_Mass)))
expect_true(all(!is.na(centre_right$gas_part$x)))
expect_true(all(!is.na(centre_right$gas_part$y)))
expect_true(all(!is.na(centre_right$gas_part$z)))
expect_true(all(!is.na(centre_right$gas_part$vx)))
expect_true(all(!is.na(centre_right$gas_part$vy)))
expect_true(all(!is.na(centre_right$gas_part$vz)))
expect_true(all(!is.na(centre_right$gas_part$Mass)))
expect_true(all(!is.na(centre_right$gas_part$SFR)))
expect_true(all(!is.na(centre_right$gas_part$Density)))
expect_true(all(!is.na(centre_right$gas_part$Temperature)))
expect_true(all(!is.na(centre_right$gas_part$CellSize)))
expect_true(all(!is.na(centre_right$gas_part$Metallicity)))
expect_true(all(!is.na(centre_right$gas_part$Carbon)))
expect_true(all(!is.na(centre_right$gas_part$Oxygen)))
expect_true(all(!is.na(centre_right$gas_part$Hydrogen)))
galaxy_data = tryCatch(expr = {.read_gadget(ss_horizon)},
error = function(e){.read_hdf5(ss_horizon, cores=1)})
galaxy_data_right = .centre_galaxy(galaxy_data, centre=c(12328,72177.97,32388.04)) # centering the galaxy based on stellar particles
galaxy_data_left = .centre_galaxy(galaxy_data, centre=c(12332,72177.97,32388.04))
# Need to run without align! This causes variations in the end output.
expect_true(median(galaxy_data_left$star_part$x) < median(galaxy_data_right$star_part$x))
})
# Testing that the half_mass parameter works as expected ------------
test_that("Half-mass parameter can be specified", {
eagle_default = make_simspin_file(filename = ss_eagle, half_mass = NA, write_to_file = F)
eagle_hdf5 = .read_hdf5(ss_eagle, cores =1)
total_mass = sum(eagle_hdf5$star_part$Mass)
half_mass = (total_mass/2)
eagle_mass_specified = make_simspin_file(filename = ss_eagle, half_mass = half_mass, write_to_file = F)
expect_true(all(eagle_default$star_part$x == eagle_mass_specified$star_part$x))
expect_true(all(eagle_default$star_part$y == eagle_mass_specified$star_part$y))
expect_true(all(eagle_default$star_part$z == eagle_mass_specified$star_part$z))
})
test_that("Half-mass parameter errors when specified outside of reasonable ranges", {
eagle_default = make_simspin_file(filename = ss_eagle, half_mass = NA, write_to_file = F)
eagle_default = .read_hdf5(ss_eagle, cores =1)
total_mass = sum(eagle_default$star_part$Mass)
expect_error(make_simspin_file(filename = ss_eagle, half_mass = (total_mass+1), write_to_file = F))
expect_error(make_simspin_file(filename = ss_eagle, half_mass = min(eagle_default$star_part$Mass), write_to_file = F))
})
# Warning if asking for half-mass with nbody model
test_that("Warning if asking for half-mass with nbody model", {
expect_warning(make_simspin_file(ss_gadget, half_mass = 350, write_to_file = F))
})
# Test that we can still mock observe an IllustrisTNG file that has attributes with the original output names
test_that("An IllustrisTNG file with traditionally named attributes (i.e. aexp-scaling-exponent vs. a_scaling) will process successfully.",{
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), overwrite = T)
modified_illustris = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), mode = "r+") # read in the horizonagn file and rename the RubLabel
modified_illustris[["PartType0/TestDataset"]] <- numeric(length=100) # rename an the attribute name
hdf5r::h5attr(modified_illustris[["PartType0/TestDataset"]], "aexp-scale-exponent") <- 1
hdf5r::h5attr(modified_illustris[["PartType0/TestDataset"]], "h-scale-exponent") <- 1
hdf5r::h5attr(modified_illustris[["PartType0/TestDataset"]], "CGSConversionFactor") <- 20
hdf5r::h5close(modified_illustris) #close
expect_length(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), write_to_file = F), ss_file_length)
unlink(paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"))
})
test_that("A file with wrongly named attributes will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), overwrite = T)
modified_illustris = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), mode = "r+") # read in the horizonagn file and rename the RubLabel
modified_illustris.part0 <- modified_illustris[["PartType0"]]
modified_illustris.part0$link_delete("Masses")
modified_illustris[["PartType0/Masses"]] <- numeric(length=100) # rename an the attribute name
hdf5r::h5attr(modified_illustris[["PartType0/Masses"]], "a_misnamed_attribute") <- 7620
hdf5r::h5attr(modified_illustris[["PartType0/Masses"]], "h_scaling") <- 0
hdf5r::h5attr(modified_illustris[["PartType0/Masses"]], "to_cgs") <- 0
hdf5r::h5close(modified_illustris) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_IllustrisTNG.hdf5"))
})
test_that("An EAGLE file without a SmoothingLength field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_eagle, to = paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"), overwrite = T)
modified_eagle = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_eagle.part0 <- modified_eagle[["PartType0"]]
modified_eagle.part0$link_delete("SmoothingLength")
hdf5r::h5close(modified_eagle) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"))
})
test_that("A Magneticum file without a Temperature field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_magneticum, to = paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"), overwrite = T)
modified_mag = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_mag.part0 <- modified_mag[["PartType0"]]
modified_mag.part0$link_delete("Temperature")
hdf5r::h5close(modified_mag) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"))
})
test_that("A HorizonAGN file without a Temperature field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_horizon, to = paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"), overwrite = T)
modified_hoz = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_hoz.part0 <- modified_hoz[["PartType0"]]
modified_hoz.part0$link_delete("Temperature")
hdf5r::h5close(modified_hoz) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"))
})
test_that("A IllustrisTNG file without an ElectronAbundance field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_ill = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_ill.part0 <- modified_ill[["PartType0"]]
modified_ill.part0$link_delete("ElectronAbundance")
hdf5r::h5close(modified_ill) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
test_that("A hydro sim will error without neccesary header field.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_tng = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_tng.head <- modified_tng[["Header"]]
modified_tng.head$attr_delete("Redshift")
hdf5r::h5close(modified_tng) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
test_that("An HDF5 file for a hydro sim will give warning without neccesary RunLabel header field.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_eagle, to = paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"), overwrite = T)
modified_tng = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_tng.head <- modified_tng[["Header"]]
modified_tng.head$attr_delete("RunLabel")
hdf5r::h5close(modified_tng) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"))
})
test_that("A galaxy with a star with age of 0 will NOT raise an error.", {
# Testing that we can build a SimSpin file if we have a particle with Age = 0
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_age = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
sft = hdf5r::readDataSet(modified_age[["PartType4/GFM_StellarFormationTime"]])
aexp = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling")
h = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling")
cgs = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs")
sft[1] = 1
modified_age[["PartType4/"]]$link_delete("GFM_StellarFormationTime")
modified_age[["PartType4/GFM_StellarFormationTime"]] = sft
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling") = aexp
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling") = h
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs") = cgs
hdf5r::h5close(modified_age)
ss_file = make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F)
expect_length(ss_file, ss_file_length)
expect_length(build_datacube(simspin_file = ss_file,
telescope = telescope(type="IFU", lsf_fwhm = 3.6, signal_to_noise = 3),
observing_strategy = observing_strategy(dist_z = 0.03, inc_deg = 45, blur = T),
method = "velocity"), built_cube_size)
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
test_that("A galaxy with a star with a very small age will NOT raise an error.", {
# Testing that we can build a SimSpin file if we have a particle with Age = 0
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_age = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
sft = hdf5r::readDataSet(modified_age[["PartType4/GFM_StellarFormationTime"]])
aexp = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling")
h = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling")
cgs = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs")
sft[1] = 0.99999999999
modified_age[["PartType4/"]]$link_delete("GFM_StellarFormationTime")
modified_age[["PartType4/GFM_StellarFormationTime"]] = sft
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling") = aexp
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling") = h
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs") = cgs
hdf5r::h5close(modified_age)
ss_file = make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F)
expect_length(ss_file, ss_file_length)
expect_length(build_datacube(simspin_file = ss_file,
telescope = telescope(type="IFU", lsf_fwhm = 3.6, signal_to_noise = 3),
observing_strategy = observing_strategy(dist_z = 0.03, inc_deg = 45, blur = T),
method = "velocity"), built_cube_size)
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
# Testing that the added header parameters are included in the new headers
test_that("Expect header information in each of the built simspin files.", {
gadget_ss_file = make_simspin_file(ss_gadget, template = "BC03hr", write_to_file = F)
hdf5_ss_file = make_simspin_file(ss_hdf5, template = "BC03lr", write_to_file = F)
eagle_ss_file = make_simspin_file(ss_eagle, template = "BC03hr", write_to_file = F, centre = c(18316,61583,38667))
magneticum_ss_file = make_simspin_file(ss_magneticum, template = "EMILES", write_to_file = F, half_mass = 1007671144)
horizon_ss_file = make_simspin_file(ss_horizon, template = "BC03hr", write_to_file = F, sph_spawn_n = 3)
illustris_ss_file = make_simspin_file(ss_illustris, template = "BC03lr", write_to_file = F)
expect_equal(gadget_ss_file$header$Centre, NA)
expect_equal(gadget_ss_file$header$HalfMass, NA)
expect_equal(gadget_ss_file$header$SmoothingN, 1)
expect_equal(length(names(gadget_ss_file$header)), ss_file_header_length)
expect_equal(hdf5_ss_file$header$Centre, NA)
expect_equal(hdf5_ss_file$header$HalfMass, NA)
expect_equal(hdf5_ss_file$header$SmoothingN, 1)
expect_equal(length(names(hdf5_ss_file$header)), ss_file_header_length)
expect_equal(eagle_ss_file$header$Centre, c(18316,61583,38667))
expect_equal(eagle_ss_file$header$HalfMass, NA)
expect_equal(eagle_ss_file$header$SmoothingN, 1)
expect_equal(length(names(eagle_ss_file$header)), ss_file_header_length)
expect_equal(magneticum_ss_file$header$Centre, NA)
expect_equal(magneticum_ss_file$header$HalfMass, 1007671144)
expect_equal(magneticum_ss_file$header$SmoothingN, 1)
expect_equal(magneticum_ss_file$header$Alignment, "Specified")
expect_equal(length(names(magneticum_ss_file$header)), ss_file_header_length)
expect_equal(horizon_ss_file$header$Centre, NA)
expect_equal(horizon_ss_file$header$HalfMass, NA)
expect_equal(horizon_ss_file$header$SmoothingN, 3)
expect_equal(length(names(horizon_ss_file$header)), ss_file_header_length)
expect_equal(illustris_ss_file$header$Centre, NA)
expect_equal(illustris_ss_file$header$HalfMass, NA)
expect_equal(illustris_ss_file$header$SmoothingN, 1)
expect_equal(length(names(illustris_ss_file$header)), ss_file_header_length)
})
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# Author: Kate Harborne
# Co-author: Alice Serene
# Date: 13/01/2023
# Title: Testing the make_simspin_file.R code
library(testthat)
context("Testing make_simspin_file function.\n")
ss_gadget = system.file("extdata", "SimSpin_example_Gadget", package = "SimSpin")
ss_hdf5 = system.file("extdata", "SimSpin_example_HDF5.hdf5", package = "SimSpin")
ss_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5", package = "SimSpin")
ss_magneticum = system.file("extdata", "SimSpin_example_Magneticum.hdf5", package = "SimSpin")
ss_horizon = system.file("extdata", "SimSpin_example_HorizonAGN.hdf5", package = "SimSpin")
ss_illustris = system.file("extdata", "SimSpin_example_IllustrisTNG.hdf5", package = "SimSpin")
ss_file_length = 4
ss_file_header_length = 15
built_cube_size = 5
temp_loc = tempdir()
# Test that the function runs successfully without error
test_that("Initial run of each simulation type - Gadget.", {
expect_null(make_simspin_file(ss_gadget, template = "BC03hr", output = paste(temp_loc, "/gadget_test", sep="")))
expect_length(readRDS(paste(temp_loc, "/gadget_test", sep="")), ss_file_length)
expect_true(length(readRDS(paste(temp_loc, "/gadget_test", sep=""))$gas_part) == 0)
expect_true(nrow(readRDS(paste(temp_loc, "/gadget_test", sep=""))$spectral_weights) == 8)
expect_true(length(readRDS(paste(temp_loc, "/gadget_test", sep=""))$spectral_weights) == 2) # for each of the two particle types
})
test_that("Initial run of each simulation type - HDF5", {
expect_null(make_simspin_file(ss_hdf5, output = paste(temp_loc, "/hdf5_test", sep="")))
expect_length(readRDS(paste(temp_loc, "/hdf5_test", sep="")), ss_file_length)
expect_true(length(readRDS(paste(temp_loc, "/hdf5_test", sep=""))$gas_part) == 0)
expect_true(nrow(readRDS(paste(temp_loc, "/hdf5_test", sep=""))$spectral_weights) == 8)
expect_true(length(readRDS(paste(temp_loc, "/hdf5_test", sep=""))$spectral_weights) == 1) # for each of the two particle types
})
test_that("Initial run of each simulation type - EAGLE", {
expect_null(make_simspin_file(ss_eagle, output = paste(temp_loc, "/eagle_test", sep=""), centre = c(18318,61583,38667), half_mass = 1483809589))
EAGLE = readRDS(paste(temp_loc, "/eagle_test", sep=""))
expect_length(EAGLE, ss_file_length)
expect_true(length(EAGLE$gas_part) == 16)
expect_true(nrow(EAGLE$spectral_weights) == 8)
expect_false(any(is.na(EAGLE$gas_part$ThermalDispersion)))
expect_true(all(EAGLE$gas_part$ThermalDispersion[EAGLE$gas_part$Temperature < 1e4] == 11))
})
test_that("Initial run of each simulation type - Magneticum", {
expect_null(make_simspin_file(ss_magneticum, output = paste(temp_loc, "/magneticum_test", sep="")))
magneticum = readRDS(paste(temp_loc, "/magneticum_test", sep=""))
expect_length(magneticum, ss_file_length)
expect_true(length(magneticum$gas_part) == 16)
expect_true(nrow(magneticum$spectral_weights) == 8)
expect_false(any(is.na(magneticum$gas_part$ThermalDispersion)))
expect_true(all(magneticum$gas_part$ThermalDispersion[magneticum$gas_part$Temperature < 1e4] == 11))
})
test_that("Initial run of each simulation type - HorizonAGN", {
expect_null(make_simspin_file(ss_horizon, output = paste(temp_loc, "/horizon_test", sep="")))
HAGN = readRDS(paste(temp_loc, "/horizon_test", sep=""))
expect_length(HAGN, ss_file_length)
expect_true(length(HAGN$gas_part) == 16)
expect_true(nrow(HAGN$spectral_weights) == 8)
expect_false(any(is.na(HAGN$gas_part$ThermalDispersion)))
expect_true(all(HAGN$gas_part$ThermalDispersion[HAGN$gas_part$Temperature < 1e4] == 11))
})
test_that("Initial run of each simulation type - IllustrisTNG", {
expect_null(make_simspin_file(ss_illustris, output = paste(temp_loc, "/illustris_test", sep="")))
TNG = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_length(TNG, ss_file_length)
expect_true(length(TNG$gas_part) == 16)
expect_true(nrow(TNG$spectral_weights) == 8)
expect_false(any(is.na(TNG$gas_part$ThermalDispersion)))
expect_true(all(TNG$gas_part$ThermalDispersion[TNG$gas_part$Temperature < 1e4] == 11))
})
# Test that the function fails when the file already exists
test_that("Error when output file already exists and overwrite = F - Gadget",{
expect_error(make_simspin_file(ss_gadget, output = paste(temp_loc, "/gadget_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - HDF5",{
expect_error(make_simspin_file(ss_hdf5, output = paste(temp_loc, "/hdf5_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - EAGLE",{
expect_error(make_simspin_file(ss_eagle, output = paste(temp_loc, "/eagle_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - Magneticum",{
expect_error(make_simspin_file(ss_magneticum, output = paste(temp_loc, "/magneticum_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - HorizonAGN",{
expect_error(make_simspin_file(ss_horizon, output = paste(temp_loc, "/horizon_test", sep="")))
})
test_that("Error when output file already exists and overwrite = F - IllustrisTNG",{
expect_error(make_simspin_file(ss_illustris, output = paste(temp_loc, "/illustris_test", sep="")))
})
# Test that function can output to environment
test_that("Function works to output List to environment", {
ss_file = make_simspin_file(ss_gadget, write_to_file = FALSE)
expect_true("ss_file" %in% ls())
})
# Test that the function fails when the template provided is unsupported
test_that("Error when template is unsupported", {
expect_error(make_simspin_file(ss_eagle, template = "abcd"))
})
# Test that the function will overwrite if overwrite = T
test_that("Test that old files can be overwritten", {
expect_null(make_simspin_file(ss_gadget, template = "EMILES", output = paste(temp_loc, "/gadget_test", sep=""),
overwrite = T))
})
# Test that the function works on multiple cores
test_that("Test that function works on multiple cores", {
expect_null(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 2))
})
# Test that none of the output arrays have NAs in
test_that("Values are successfully associated with variables", {
gadget = readRDS(paste(temp_loc, "/gadget_test", sep=""))
hdf5 = readRDS(paste(temp_loc, "/hdf5_test", sep=""))
eagle = readRDS(paste(temp_loc, "/eagle_test", sep=""))
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_true(all(!is.na(gadget$star_part$x)))
expect_true(all(!is.na(gadget$star_part$y)))
expect_true(all(!is.na(gadget$star_part$z)))
expect_true(all(!is.na(gadget$star_part$vx)))
expect_true(all(!is.na(gadget$star_part$vy)))
expect_true(all(!is.na(gadget$star_part$vz)))
expect_true(all(!is.na(gadget$star_part$Mass)))
expect_true(all(!is.na(gadget$star_part$sed_id)))
expect_true(all(!is.na(gadget$star_part$Metallicity)))
expect_true(all(!is.na(gadget$star_part$Age)))
expect_true(all(!is.na(gadget$star_part$Initial_Mass)))
expect_true(all(!is.na(hdf5$star_part$x)))
expect_true(all(!is.na(hdf5$star_part$y)))
expect_true(all(!is.na(hdf5$star_part$z)))
expect_true(all(!is.na(hdf5$star_part$vx)))
expect_true(all(!is.na(hdf5$star_part$vy)))
expect_true(all(!is.na(hdf5$star_part$vz)))
expect_true(all(!is.na(hdf5$star_part$Mass)))
expect_true(all(!is.na(hdf5$star_part$sed_id)))
expect_true(all(!is.na(hdf5$star_part$Metallicity)))
expect_true(all(!is.na(hdf5$star_part$Age)))
expect_true(all(!is.na(hdf5$star_part$Initial_Mass)))
expect_true(all(!is.na(eagle$star_part$x)))
expect_true(all(!is.na(eagle$star_part$y)))
expect_true(all(!is.na(eagle$star_part$z)))
expect_true(all(!is.na(eagle$star_part$vx)))
expect_true(all(!is.na(eagle$star_part$vy)))
expect_true(all(!is.na(eagle$star_part$vz)))
expect_true(all(!is.na(eagle$star_part$Mass)))
expect_true(all(!is.na(eagle$star_part$sed_id)))
expect_true(all(!is.na(eagle$star_part$Metallicity)))
expect_true(all(!is.na(eagle$star_part$Age)))
expect_true(all(!is.na(eagle$star_part$Initial_Mass)))
expect_true(all(!is.na(eagle$gas_part$x)))
expect_true(all(!is.na(eagle$gas_part$y)))
expect_true(all(!is.na(eagle$gas_part$z)))
expect_true(all(!is.na(eagle$gas_part$vx)))
expect_true(all(!is.na(eagle$gas_part$vy)))
expect_true(all(!is.na(eagle$gas_part$vz)))
expect_true(all(!is.na(eagle$gas_part$Mass)))
expect_true(all(!is.na(eagle$gas_part$Z)))
expect_true(all(!is.na(eagle$gas_part$Density)))
expect_true(all(!is.na(eagle$gas_part$Temp)))
expect_true(all(!is.na(eagle$gas_part$SFR)))
expect_true(all(!is.na(eagle$gas_part$Metallicity)))
expect_true(all(!is.na(eagle$gas_part$OEOS)))
expect_true(all(!is.na(illustris$star_part$x)))
expect_true(all(!is.na(illustris$star_part$y)))
expect_true(all(!is.na(illustris$star_part$z)))
expect_true(all(!is.na(illustris$star_part$vx)))
expect_true(all(!is.na(illustris$star_part$vy)))
expect_true(all(!is.na(illustris$star_part$vz)))
expect_true(all(!is.na(illustris$star_part$Mass)))
expect_true(all(!is.na(illustris$star_part$sed_id)))
expect_true(all(!is.na(illustris$star_part$Metallicity)))
expect_true(all(!is.na(illustris$star_part$Age)))
expect_true(all(!is.na(illustris$star_part$Initial_Mass)))
expect_true(all(!is.na(illustris$gas_part$x)))
expect_true(all(!is.na(illustris$gas_part$y)))
expect_true(all(!is.na(illustris$gas_part$z)))
expect_true(all(!is.na(illustris$gas_part$vx)))
expect_true(all(!is.na(illustris$gas_part$vy)))
expect_true(all(!is.na(illustris$gas_part$vz)))
expect_true(all(!is.na(illustris$gas_part$Mass)))
expect_true(all(!is.na(illustris$gas_part$SFR)))
expect_true(all(!is.na(illustris$gas_part$Density)))
expect_true(all(!is.na(illustris$gas_part$Temperature)))
expect_true(all(!is.na(illustris$gas_part$Metallicity)))
# SmoothingLength, Carbon/Hydrogen/Oxygen?
})
# Testing the sph_spawn functionality ----
test_that("Test that sph_spawn functionality works", {
expect_null(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_magneticum, template = "BC03lr", output = paste(temp_loc, "/magneticum_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_magneticum, template = "BC03lr", output = paste(temp_loc, "/magneticum_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_horizon, template = "BC03hr", output = paste(temp_loc, "/horizon_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_horizon, template = "BC03hr", output = paste(temp_loc, "/horizon_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_illustris, template = "BC03lr", output = paste(temp_loc, "/illustris_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10))
expect_null(make_simspin_file(ss_illustris, template = "BC03lr", output = paste(temp_loc, "/illustris_test", sep=""),
overwrite = T, cores = 2, sph_spawn_n = 10))
test_horizon = readRDS(paste(temp_loc, "/horizon_test", sep=""))
expect_true(data.table::is.data.table(test_horizon$gas_part))
remove(test_horizon)
})
test_that("Test that sph_spawn errors when N is not an integer", {
expect_error(make_simspin_file(ss_eagle, template = "EMILES", output = paste(temp_loc, "/eagle_test", sep=""),
overwrite = T, cores = 1, sph_spawn_n = 10.2))
})
test_that("Test that sph_spawn functionality works on multiple cores - EAGLE", {
gas_data_c1 = make_simspin_file(ss_eagle, template = "EMILES", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_eagle, template = "EMILES", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
test_that("Test that sph_spawn functionality works on multiple cores - Magneticum", {
gas_data_c1 = make_simspin_file(ss_magneticum, template = "EMILES", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_magneticum, template = "EMILES", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
test_that("Test that sph_spawn functionality works on multiple cores - HorizonAGN", {
gas_data_c1 = make_simspin_file(ss_horizon, template = "BC03", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_horizon, template = "BC03", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
test_that("Test that sph_spawn functionality works on multiple cores - IllustrisTNG", {
gas_data_c1 = make_simspin_file(ss_illustris, template = "BC03", write_to_file = FALSE, cores = 1, sph_spawn_n = 10)
gas_data_c2 = make_simspin_file(ss_illustris, template = "BC03", write_to_file = FALSE, cores = 2, sph_spawn_n = 10)
expect_equal(gas_data_c1$gas_part$ID, gas_data_c2$gas_part$ID)
expect_length(gas_data_c1$gas_part$ID, 1000) # sph_spawn_n = 10, original file contains 100 gas particles
expect_length(gas_data_c2$gas_part$ID, 1000)
})
# Test that the added header information works as expected ---------------------
test_that("Testing that the header data works as expected", {
gadget = readRDS(paste(temp_loc, "/gadget_test", sep=""))
hdf5 = readRDS(paste(temp_loc, "/hdf5_test", sep=""))
eagle = readRDS(paste(temp_loc, "/eagle_test", sep=""))
magneticum = readRDS(paste(temp_loc, "/magneticum_test", sep=""))
horizon = readRDS(paste(temp_loc, "/horizon_test", sep=""))
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_equal(gadget$header$Type, "nbody")
expect_equal(hdf5$header$Type, "nbody")
expect_equal(eagle$header$Type, "EAGLE")
expect_equal(magneticum$header$Type, "Magneticum")
expect_equal(horizon$header$Type, "Horizon-AGN")
expect_equal(illustris$header$Type, "Illustris-TNG")
expect_equal(gadget$header$Template, "EMILES")
expect_equal(hdf5$header$Template, "BC03lr")
expect_equal(eagle$header$Template, "EMILES")
expect_equal(magneticum$header$Template, "BC03lr")
expect_equal(horizon$header$Template, "BC03hr")
expect_equal(illustris$header$Template, "BC03lr") # correct?
expect_equal(gadget$header$Template_LSF, 2.51)
expect_equal(hdf5$header$Template_LSF, 3)
expect_equal(eagle$header$Template_LSF, 2.51)
expect_equal(magneticum$header$Template_LSF, 3)
expect_equal(horizon$header$Template_LSF, 3)
expect_equal(illustris$header$Template_LSF, 3) # 3?
expect_equal(gadget$header$Template_waveres, eagle$header$Template_waveres)
expect_equal(hdf5$header$Template_waveres, 1)
expect_equal(eagle$header$Template_waveres, 0.9)
expect_equal(magneticum$header$Template_waveres, 1)
expect_equal(horizon$header$Template_waveres, 1)
expect_equal(illustris$header$Template_waveres, 1) # 1?
remove(gadget, hdf5, eagle, magneticum, horizon, illustris)
})
# Illustris-specific tests -----------------------------------------------------
# CGS conversion factors that are inherently 0 should be converted to 1
test_that("CGS conversion values of 0 get converted to 1",{
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_true(all(illustris$star_part$Metallicity!=0))
})
# Stellar wind particles should be removed from the dataset
# (There are 4 wind particles in the testing set, these should be removed.)
test_that("Negative stellar wind particles are removed",{
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_length(illustris$star_part$Metallicity, 1996)
})
# Gas temperature should fall within a reasonable range
test_that("Temperature does not go outside a reasonable range",{
illustris = readRDS(paste(temp_loc, "/illustris_test", sep=""))
expect_true(min(illustris$gas_part$Temperature)>0)
expect_true(max(illustris$gas_part$Temperature)<50000000)
})
unlink(c(paste(temp_loc, "/gadget_test", sep=""), paste(temp_loc, "/hdf5_test", sep=""),
paste(temp_loc, "/eagle_test", sep=""), paste(temp_loc, "/magneticum_test", sep=""),
paste(temp_loc, "/horizon_test", sep=""), paste(temp_loc, "/illustris_test", sep="")))
# Testing that the centre parameter works as expected ------------
test_that("Objects are centered correctly based on the specified central coordinates", {
expect_error(make_simspin_file(filename = ss_horizon, template = "EMILES", write_to_file = F, centre = c(0,0,0)))
centre_right = make_simspin_file(filename = ss_horizon, template = "BC03lr", write_to_file = F, centre = c(12328,72177.97,32388.04))
centre_left = make_simspin_file(filename = ss_horizon, template = "BC03lr", write_to_file = F, centre = c(12332,72177.97,32388.04))
# Checking values exist in fields for LEFT
expect_true(all(!is.na(centre_left$star_part$x)))
expect_true(all(!is.na(centre_left$star_part$y)))
expect_true(all(!is.na(centre_left$star_part$z)))
expect_true(all(!is.na(centre_left$star_part$vx)))
expect_true(all(!is.na(centre_left$star_part$vy)))
expect_true(all(!is.na(centre_left$star_part$vz)))
expect_true(all(!is.na(centre_left$star_part$Mass)))
expect_true(all(!is.na(centre_left$star_part$sed_id)))
expect_true(all(!is.na(centre_left$star_part$Metallicity)))
expect_true(all(!is.na(centre_left$star_part$Age)))
expect_true(all(!is.na(centre_left$star_part$Initial_Mass)))
expect_true(all(!is.na(centre_left$gas_part$x)))
expect_true(all(!is.na(centre_left$gas_part$y)))
expect_true(all(!is.na(centre_left$gas_part$z)))
expect_true(all(!is.na(centre_left$gas_part$vx)))
expect_true(all(!is.na(centre_left$gas_part$vy)))
expect_true(all(!is.na(centre_left$gas_part$vz)))
expect_true(all(!is.na(centre_left$gas_part$Mass)))
expect_true(all(!is.na(centre_left$gas_part$SFR)))
expect_true(all(!is.na(centre_left$gas_part$Density)))
expect_true(all(!is.na(centre_left$gas_part$Temperature)))
expect_true(all(!is.na(centre_left$gas_part$CellSize)))
expect_true(all(!is.na(centre_left$gas_part$Metallicity)))
expect_true(all(!is.na(centre_left$gas_part$Carbon)))
expect_true(all(!is.na(centre_left$gas_part$Oxygen)))
expect_true(all(!is.na(centre_left$gas_part$Hydrogen)))
# Checking values exist in fields for RIGHT
expect_true(all(!is.na(centre_right$star_part$x)))
expect_true(all(!is.na(centre_right$star_part$y)))
expect_true(all(!is.na(centre_right$star_part$z)))
expect_true(all(!is.na(centre_right$star_part$vx)))
expect_true(all(!is.na(centre_right$star_part$vy)))
expect_true(all(!is.na(centre_right$star_part$vz)))
expect_true(all(!is.na(centre_right$star_part$Mass)))
expect_true(all(!is.na(centre_right$star_part$sed_id)))
expect_true(all(!is.na(centre_right$star_part$Metallicity)))
expect_true(all(!is.na(centre_right$star_part$Age)))
expect_true(all(!is.na(centre_right$star_part$Initial_Mass)))
expect_true(all(!is.na(centre_right$gas_part$x)))
expect_true(all(!is.na(centre_right$gas_part$y)))
expect_true(all(!is.na(centre_right$gas_part$z)))
expect_true(all(!is.na(centre_right$gas_part$vx)))
expect_true(all(!is.na(centre_right$gas_part$vy)))
expect_true(all(!is.na(centre_right$gas_part$vz)))
expect_true(all(!is.na(centre_right$gas_part$Mass)))
expect_true(all(!is.na(centre_right$gas_part$SFR)))
expect_true(all(!is.na(centre_right$gas_part$Density)))
expect_true(all(!is.na(centre_right$gas_part$Temperature)))
expect_true(all(!is.na(centre_right$gas_part$CellSize)))
expect_true(all(!is.na(centre_right$gas_part$Metallicity)))
expect_true(all(!is.na(centre_right$gas_part$Carbon)))
expect_true(all(!is.na(centre_right$gas_part$Oxygen)))
expect_true(all(!is.na(centre_right$gas_part$Hydrogen)))
galaxy_data = tryCatch(expr = {.read_gadget(ss_horizon)},
error = function(e){.read_hdf5(ss_horizon, cores=1)})
galaxy_data_right = .centre_galaxy(galaxy_data, centre=c(12328,72177.97,32388.04)) # centering the galaxy based on stellar particles
galaxy_data_left = .centre_galaxy(galaxy_data, centre=c(12332,72177.97,32388.04))
# Need to run without align! This causes variations in the end output.
expect_true(median(galaxy_data_left$star_part$x) < median(galaxy_data_right$star_part$x))
})
# Testing that the half_mass parameter works as expected ------------
test_that("Half-mass parameter can be specified", {
eagle_default = make_simspin_file(filename = ss_eagle, half_mass = NA, write_to_file = F)
eagle_hdf5 = .read_hdf5(ss_eagle, cores =1)
total_mass = sum(eagle_hdf5$star_part$Mass)
half_mass = (total_mass/2)
eagle_mass_specified = make_simspin_file(filename = ss_eagle, half_mass = half_mass, write_to_file = F)
expect_true(all(eagle_default$star_part$x == eagle_mass_specified$star_part$x))
expect_true(all(eagle_default$star_part$y == eagle_mass_specified$star_part$y))
expect_true(all(eagle_default$star_part$z == eagle_mass_specified$star_part$z))
})
test_that("Half-mass parameter errors when specified outside of reasonable ranges", {
eagle_default = make_simspin_file(filename = ss_eagle, half_mass = NA, write_to_file = F)
eagle_default = .read_hdf5(ss_eagle, cores =1)
total_mass = sum(eagle_default$star_part$Mass)
expect_error(make_simspin_file(filename = ss_eagle, half_mass = (total_mass+1), write_to_file = F))
expect_error(make_simspin_file(filename = ss_eagle, half_mass = min(eagle_default$star_part$Mass), write_to_file = F))
})
# Warning if asking for half-mass with nbody model
test_that("Warning if asking for half-mass with nbody model", {
expect_warning(make_simspin_file(ss_gadget, half_mass = 350, write_to_file = F))
})
# Test that we can still mock observe an IllustrisTNG file that has attributes with the original output names
test_that("An IllustrisTNG file with traditionally named attributes (i.e. aexp-scaling-exponent vs. a_scaling) will process successfully.",{
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), overwrite = T)
modified_illustris = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), mode = "r+") # read in the horizonagn file and rename the RubLabel
modified_illustris[["PartType0/TestDataset"]] <- numeric(length=100) # rename an the attribute name
hdf5r::h5attr(modified_illustris[["PartType0/TestDataset"]], "aexp-scale-exponent") <- 1
hdf5r::h5attr(modified_illustris[["PartType0/TestDataset"]], "h-scale-exponent") <- 1
hdf5r::h5attr(modified_illustris[["PartType0/TestDataset"]], "CGSConversionFactor") <- 20
hdf5r::h5close(modified_illustris) #close
expect_length(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), write_to_file = F), ss_file_length)
unlink(paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"))
})
test_that("A file with wrongly named attributes will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), overwrite = T)
modified_illustris = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), mode = "r+") # read in the horizonagn file and rename the RubLabel
modified_illustris.part0 <- modified_illustris[["PartType0"]]
modified_illustris.part0$link_delete("Masses")
modified_illustris[["PartType0/Masses"]] <- numeric(length=100) # rename an the attribute name
hdf5r::h5attr(modified_illustris[["PartType0/Masses"]], "a_misnamed_attribute") <- 7620
hdf5r::h5attr(modified_illustris[["PartType0/Masses"]], "h_scaling") <- 0
hdf5r::h5attr(modified_illustris[["PartType0/Masses"]], "to_cgs") <- 0
hdf5r::h5close(modified_illustris) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_IllustrisTNG_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_IllustrisTNG.hdf5"))
})
test_that("An EAGLE file without a SmoothingLength field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_eagle, to = paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"), overwrite = T)
modified_eagle = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_eagle.part0 <- modified_eagle[["PartType0"]]
modified_eagle.part0$link_delete("SmoothingLength")
hdf5r::h5close(modified_eagle) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_EAGLE_copy.hdf5"))
})
test_that("A Magneticum file without a Temperature field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_magneticum, to = paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"), overwrite = T)
modified_mag = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_mag.part0 <- modified_mag[["PartType0"]]
modified_mag.part0$link_delete("Temperature")
hdf5r::h5close(modified_mag) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_Magneticum_copy.hdf5"))
})
test_that("A HorizonAGN file without a Temperature field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_horizon, to = paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"), overwrite = T)
modified_hoz = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_hoz.part0 <- modified_hoz[["PartType0"]]
modified_hoz.part0$link_delete("Temperature")
hdf5r::h5close(modified_hoz) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_HorizonAGN_copy.hdf5"))
})
test_that("A IllustrisTNG file without an ElectronAbundance field will error.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_ill = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_ill.part0 <- modified_ill[["PartType0"]]
modified_ill.part0$link_delete("ElectronAbundance")
hdf5r::h5close(modified_ill) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
test_that("A hydro sim will error without neccesary header field.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_tng = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_tng.head <- modified_tng[["Header"]]
modified_tng.head$attr_delete("Redshift")
hdf5r::h5close(modified_tng) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
test_that("An HDF5 file for a hydro sim will give warning without neccesary RunLabel header field.",{
# Testing also that the code errors if the file does not contain the correct attributes.
file.copy(from = ss_eagle, to = paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"), overwrite = T)
modified_tng = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
modified_tng.head <- modified_tng[["Header"]]
modified_tng.head$attr_delete("RunLabel")
hdf5r::h5close(modified_tng) #close
expect_error(make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"), write_to_file = F))
unlink(paste0(temp_loc, "/SimSpin_example_eagle_copy.hdf5"))
})
test_that("A galaxy with a star with age of 0 will NOT raise an error.", {
# Testing that we can build a SimSpin file if we have a particle with Age = 0
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_age = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
sft = hdf5r::readDataSet(modified_age[["PartType4/GFM_StellarFormationTime"]])
aexp = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling")
h = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling")
cgs = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs")
sft[1] = 1
modified_age[["PartType4/"]]$link_delete("GFM_StellarFormationTime")
modified_age[["PartType4/GFM_StellarFormationTime"]] = sft
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling") = aexp
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling") = h
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs") = cgs
hdf5r::h5close(modified_age)
ss_file = make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F)
expect_length(ss_file, ss_file_length)
expect_length(build_datacube(simspin_file = ss_file,
telescope = telescope(type="IFU", lsf_fwhm = 3.6, signal_to_noise = 3),
observing_strategy = observing_strategy(dist_z = 0.03, inc_deg = 45, blur = T),
method = "velocity"), built_cube_size)
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
test_that("A galaxy with a star with a very small age will NOT raise an error.", {
# Testing that we can build a SimSpin file if we have a particle with Age = 0
file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
modified_age = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
sft = hdf5r::readDataSet(modified_age[["PartType4/GFM_StellarFormationTime"]])
aexp = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling")
h = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling")
cgs = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs")
sft[1] = 0.99999999999
modified_age[["PartType4/"]]$link_delete("GFM_StellarFormationTime")
modified_age[["PartType4/GFM_StellarFormationTime"]] = sft
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling") = aexp
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling") = h
hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs") = cgs
hdf5r::h5close(modified_age)
ss_file = make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F)
expect_length(ss_file, ss_file_length)
expect_length(build_datacube(simspin_file = ss_file,
telescope = telescope(type="IFU", lsf_fwhm = 3.6, signal_to_noise = 3),
observing_strategy = observing_strategy(dist_z = 0.03, inc_deg = 45, blur = T),
method = "velocity"), built_cube_size)
unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
})
# Testing that the added header parameters are included in the new headers
test_that("Expect header information in each of the built simspin files.", {
gadget_ss_file = make_simspin_file(ss_gadget, template = "BC03hr", write_to_file = F)
hdf5_ss_file = make_simspin_file(ss_hdf5, template = "BC03lr", write_to_file = F)
eagle_ss_file = make_simspin_file(ss_eagle, template = "BC03hr", write_to_file = F, centre = c(18316,61583,38667))
magneticum_ss_file = make_simspin_file(ss_magneticum, template = "EMILES", write_to_file = F, half_mass = 1007671144)
horizon_ss_file = make_simspin_file(ss_horizon, template = "BC03hr", write_to_file = F, sph_spawn_n = 3)
illustris_ss_file = make_simspin_file(ss_illustris, template = "BC03lr", write_to_file = F)
expect_equal(gadget_ss_file$header$Centre, NA)
expect_equal(gadget_ss_file$header$HalfMass, NA)
expect_equal(gadget_ss_file$header$SmoothingN, 1)
expect_equal(length(names(gadget_ss_file$header)), ss_file_header_length)
expect_equal(hdf5_ss_file$header$Centre, NA)
expect_equal(hdf5_ss_file$header$HalfMass, NA)
expect_equal(hdf5_ss_file$header$SmoothingN, 1)
expect_equal(length(names(hdf5_ss_file$header)), ss_file_header_length)
expect_equal(eagle_ss_file$header$Centre, c(18316,61583,38667))
expect_equal(eagle_ss_file$header$HalfMass, NA)
expect_equal(eagle_ss_file$header$SmoothingN, 1)
expect_equal(length(names(eagle_ss_file$header)), ss_file_header_length)
expect_equal(magneticum_ss_file$header$Centre, NA)
expect_equal(magneticum_ss_file$header$HalfMass, 1007671144)
expect_equal(magneticum_ss_file$header$SmoothingN, 1)
expect_equal(magneticum_ss_file$header$Alignment, "Specified")
expect_equal(length(names(magneticum_ss_file$header)), ss_file_header_length)
expect_equal(horizon_ss_file$header$Centre, NA)
expect_equal(horizon_ss_file$header$HalfMass, NA)
expect_equal(horizon_ss_file$header$SmoothingN, 3)
expect_equal(length(names(horizon_ss_file$header)), ss_file_header_length)
expect_equal(illustris_ss_file$header$Centre, NA)
expect_equal(illustris_ss_file$header$HalfMass, NA)
expect_equal(illustris_ss_file$header$SmoothingN, 1)
expect_equal(length(names(illustris_ss_file$header)), ss_file_header_length)
})
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