Merge pull request #79 from kateharborne/dev-ages

dev-ages

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SimSpin
 Type: Package
 Title: SimSpin - A package for the kinematic analysis of galaxy simulations
-Version: 2.4.3
+Version: 2.4.4
 Author: Katherine Harborne
 Co-author: Alice Serene
 Maintainer: <katherine.harborne@icrar.org>

NEWS.md

@@ -1,6 +1,6 @@
-# SimSpin v2.4.3 News
+# SimSpin v2.4.4 News
 
-### Last edit: 17/01/23
+### Last edit: 25/01/23
 
 Below is a table containing a summary of all changes made to SimSpin, since the date this file was created on 26/08/2021.
 
@@ -16,7 +16,8 @@ All changes are noted in the changelog table below.
 
 | Date     	| Summary of change                                                                                                                                                                                                                                                                                                                                                                                                        	| Version 	| Commit                                   	| Author            |
 |----------	|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	|---------	|------------------------------------------	| ----------------- |
-| 17/01/23 | *Bug fix.* Addressing issue #12. When a hydrodynamical simulation HDF5 is input without a `RunLabel` in the header, the file is processed like an N-body model (often meaning that no stellar particles are read in.) Catches added to stop the code with meaningful error if this is the case. Further interpretation added for named datasets in Hydro default names rather than expected. | 2.4.3 | | Kate Harborne |
+| 25/01/23 | *Bug fix.* Addressing issues #76 and #77. When working with the BC03 templates, the first AgeBin was labeled 0 Gyr. This was causing a problematic log10() age bin when gridding up the templates to match to the stellar ages within the model such that any stars that fell into this bin were associated with spectra of NA's. This was not clear until testing with IllustrisTNG galaxies that have very young stars in the outputs. Now fixed by setting low age bins to non-zero values (i.e. 0 Gyr -> 1e-9 Gyr). Tests and documentation updated for these changes. | 2.4.4 | | Alice Serene & Kate Harborne |
+| 17/01/23 | *Bug fix.* Addressing issue #12. When a hydrodynamical simulation HDF5 is input without a `RunLabel` in the header, the file is processed like an N-body model (often meaning that no stellar particles are read in.) Catches added to stop the code with meaningful error if this is the case. Further interpretation added for named datasets in Hydro default names rather than expected. | 2.4.3 | 44b703304efde31d08fd8e857f986fc93879b3ee | Kate Harborne |
 | 16/01/23 | **New feature!** Update to add support for IllustrisTNG. Updates to `make_simspin_file`, `utilities`, and tests were implemented. | 2.4.2 | 5fb9ad5803f26bc1dad81f9818dff24225f4e1d0 | Alice Serene |
 | 28/10/22 	| *Bug fix.* Addressing issue #72. Output fluxes are much higher than they should be due to an improper scaling of SSP templates wrt stellar particle mass.                                                                                                                                                                                                                                                                                                  	| 2.4.1   	| ef171e40626edacc350c1e119cc6f807c6335529 | Kate Harborne |
 | 30/09/22 	| Tagging a release for the SimSpin web app. This update has no code developments from the previous version. Stable version.                                                                                                                                                                                                                                                                                               	| 2.4.0   	| 9307ffb7b1775540426966eb2903da119c6d7495   | Kate Harborne |

R/data.R

@@ -74,7 +74,9 @@
 #' with a given stellar age and metallicity. At each age/metallicity bin, a
 #' template spectrum is given in units of solar luminoisities per angstrom for
 #' 1 solar mass of star formation. Values are given at a series of wavelengths,
-#' contained within the dataset.
+#' contained within the dataset. Note that while the first age bin is a
+#' template for Age = 0 stars, we have re-labelled this bin with a non-zero small
+#' number to avoid log errors.
 #'
 #' @format A list with 4 elements:
 #' \describe{
@@ -95,7 +97,9 @@
 #' with a given stellar age and metallicity. At each age/metallicity bin, a
 #' template spectrum is given in units of solar luminoisities per angstrom for
 #' 1 solar mass of star formation. Values are given at a series of wavelengths,
-#' contained within the dataset.
+#' contained within the dataset. Note that while the first age bin is a
+#' template for Age = 0 stars, we have re-labelled this bin with a non-zero small
+#' number to avoid log errors.
 #'
 #' @format A list with 4 elements:
 #' \describe{

R/make_simspin_file.R

@@ -19,7 +19,8 @@
 #'@param bulge_age The age of the bulge particles in Gyr.
 #'@param disk_Z The metallicity of the disk particles as a mass fraction (mass
 #' of all metal elements above He over the total mass).
-#'@param bulge_Z The metallicity of the bulge particles in Gyr.
+#'@param bulge_Z The metallicity of the bulge particles as a mass fraction (mass
+#' of all metal elements above He over the total mass).
 #'@param template The stellar templates from which to derive the SEDs. Options
 #' include "BC03lr" (GALEXEV low resolution, Bruzual & Charlot 2003), "BC03hr"
 #' (GALEXEV high resolution, Bruzual & Charlot 2003) or "EMILES" (Vazdekis et
@@ -76,8 +77,7 @@ make_simspin_file = function(filename, cores=1, disk_age=5, bulge_age=10,
 
   if (write_to_file){
     if (missing(output)){
-    output = paste(sub('\\..*', '', filename), "_", temp_name, ".Rdata", sep="") 
-
+    output = paste(sub('\\..*', '', filename), "_", temp_name, ".Rdata", sep="")
     }
     if (file.exists(output) & !overwrite){
       stop(cat("FileExists Error:: SimSpin file already exists at: ", output, "\n",
@@ -177,6 +177,10 @@ make_simspin_file = function(filename, cores=1, disk_age=5, bulge_age=10,
 
   # now binning stellar particles based on their A/Z position
   if (length(unique(galaxy_data$ssp$Age)) > 2){ # if not an N-body simulation
+
+    # reassign any age==0 particles to have a small non-zero age
+    galaxy_data$ssp$Age[galaxy_data$ssp$Age==0] = 1e-9
+
     age_grid = 10^(seq(log10(min(galaxy_data$ssp$Age))-0.02, log10(max(galaxy_data$ssp$Age))+0.02, by = 0.02))
     Z_grid   = 10^(seq(log10(min(galaxy_data$ssp$Metallicity))-0.1, log10(max(galaxy_data$ssp$Metallicity))+0.1, by = 0.1))
 
@@ -248,6 +252,8 @@ make_simspin_file = function(filename, cores=1, disk_age=5, bulge_age=10,
     }
   }
 
+
+
   simspin_file = list("header"    = header,
                       "star_part" = galaxy_data$star_part,
                       "gas_part"  = galaxy_data$gas_part,

R/utilities.R

@@ -142,7 +142,7 @@ globalVariables(c(".N", ":=", "Age", "Carbon", "CellSize", "Density", "Hydrogen"
 }
 
 # Functions for reading in HDF5 files
-.read_hdf5   = function(f, cores=1){
+.read_hdf5 = function(f, cores=1){
 
   data = hdf5r::h5file(f, mode="r")
 

README.md

@@ -10,7 +10,7 @@
 
 <p>&nbsp;</p>
 
-v2.4.0 - A package for producing mock observations:
+v2.4.x - A package for producing mock observations:
 
 SimSpin allows you to take a simulation of a galaxy and produce a data cube in the style of an Integral Field Spectroscopy (IFS) instrument. A mock observation is produced using three simple steps:
 

tests/testthat/test_make_simspin_file.R

@@ -528,3 +528,71 @@ test_that("An HDF5 file for a hydro sim will give warning without neccesary RunL
   unlink(paste0(temp_loc, "/SimSpin_example_illustris_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
+  built_cube_size = 4
+
+  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/"]]$link_delete("GFM_StellarFormationTime")
+
+  modified_age[["PartType4/GFM_StellarFormationTime"]] = sft
+  hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling") = aexp
+  hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling") = h
+  hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs") = cgs
+
+  hdf5r::h5close(modified_age)
+
+  ss_file = make_simspin_file(filename = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), write_to_file = F)
+
+  expect_length(ss_file, ss_file_length)
+  expect_length(build_datacube(simspin_file = ss_file,
+                               telescope = telescope(type="IFU", lsf_fwhm = 3.6, signal_to_noise = 3),
+                               observing_strategy = observing_strategy(dist_z = 0.03, inc_deg = 45, blur = T),
+                               method = "velocity"), built_cube_size)
+
+  unlink(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"))
+})
+
+
+test_that("A galaxy with a star with a very small age will NOT raise an error.", {
+  # Testing that we can build a SimSpin file if we have a particle with Age = 0
+  built_cube_size = 4
+
+  file.copy(from = ss_illustris, to = paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), overwrite = T)
+  modified_age = hdf5r::h5file(paste0(temp_loc, "/SimSpin_example_illustris_copy.hdf5"), mode = "r+") # read in the eagle file and rename the RubLabel
+
+  sft = hdf5r::readDataSet(modified_age[["PartType4/GFM_StellarFormationTime"]])
+  aexp = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "a_scaling")
+  h = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "h_scaling")
+  cgs  = hdf5r::h5attr(modified_age[["PartType4/GFM_StellarFormationTime"]], "to_cgs")
+  sft[1] = 0.99999999999
+
+  modified_age[["PartType4/"]]$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"))
+})
+
+

vignettes/using_simspin_v2.Rmd

@@ -399,7 +399,7 @@ png(file="SAMI_cube_phys%02d.png", width=456, height=500)
 for (i in 1:25){
   image_nan(z = asinh(sub_cube[,,i]), zlim = flux_val, col = grey((0:1000)/1000), na.color = "white", xaxt="n",
           yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1)
-  legend("topleft", inset=c(-0.01,0.01), parse(text=sprintf('lambda == %s',sub_wave[i])), bty="n")
+  legend("topleft", inset=c(-0.01,0.01), paste0('λ = ',sub_wave[i]), text.col = "white", bty="n")
 }
 dev.off()