Merge pull request #67 from kateharborne/dev-align_fix

Only aligning cosmological models. If nbody, leave within the referen…

R/make_simspin_file.R

@@ -117,7 +117,9 @@ make_simspin_file = function(filename, cores=1, disk_age=5, bulge_age=10,
 
   galaxy_data = .centre_galaxy(galaxy_data, centre) # centering the galaxy based on stellar particles
 
-  galaxy_data = .align_galaxy(galaxy_data, half_mass) # align 3D shape of galaxy
+  if (header$Type != "nbody"){
+    galaxy_data = .align_galaxy(galaxy_data, half_mass) # align 3D shape of galaxy
+  }
 
   if(!"ssp" %in% names(galaxy_data)){ # if the SSP field does not come from the snapshot file, must be working with N-body
 

tests/testthat/test_build_datacube.R

@@ -836,9 +836,9 @@ test_that("Repeated spectra are included in intrinsic spectra", {
   galaxy_sample = galaxy_data[particle_IDs,]
 
   intrinsic_spectra = simspin_data$spectra[ , galaxy_sample$sed_id, with=FALSE]
-  spectra = intrinsic_spectra * (galaxy_sample$Initial_Mass * 1e10) # reading relavent spectra
+  spectra = intrinsic_spectra * (galaxy_sample$Initial_Mass * 1e10) # reading relevant spectra
 
-  expect_true(all(intrinsic_spectra[,c(3),] == simspin_data$spectra[["V2"]]))
+  expect_true(all(intrinsic_spectra[,c(3),] == simspin_data$spectra[[paste0("V", galaxy_sample$sed_id[3])]]))
   expect_equal((intrinsic_spectra[,c(1),] * galaxy_sample$Initial_Mass[1] * 1e10), spectra[,c(1),], tolerance = 0.001)
   expect_equal((intrinsic_spectra[,c(2),] * galaxy_sample$Initial_Mass[2] * 1e10), spectra[,c(2),], tolerance = 0.001)
 })

tests/testthat/test_make_simspin_file.R

@@ -313,23 +313,25 @@ test_that("Objects are centered correctly based on the specified central coordin
 # Testing that the half_mass parameter works as expected ------------
 test_that("Half-mass parameter can be specified", {
 
-  gadget_default = make_simspin_file(filename = ss_gadget, half_mass = NA, write_to_file = F)
-  total_mass = sum(gadget_default$star_part$Mass)
+  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)
 
-  gadget_mass_specified = make_simspin_file(filename = ss_gadget, half_mass = half_mass, write_to_file = F)
-  expect_true(all(gadget_default$star_part$x == gadget_mass_specified$star_part$x))
-  expect_true(all(gadget_default$star_part$y == gadget_mass_specified$star_part$y))
-  expect_true(all(gadget_default$star_part$z == gadget_mass_specified$star_part$z))
+  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", {
 
-  gadget_default = make_simspin_file(filename = ss_gadget, half_mass = NA, write_to_file = F)
-  total_mass = sum(gadget_default$star_part$Mass)
-  half_mass = (total_mass/2)
+  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_gadget, half_mass = (total_mass+1), write_to_file = F))
-  expect_error(make_simspin_file(filename = ss_gadget, half_mass = min(gadget_default$star_part$Mass), write_to_file = F))
+  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))
 })