The best way to get a feel for what Trident can do is to go through an annotated example of its use. This section will walk you through the steps necessary to produce a synthetic spectrum based on simulation data and to view its path through the parent dataset. The following example, available in the source code itself, can be applied to datasets from any of the different simulation codes that Trident and yt support, but if you want to recreate the following analysis with the exact dataset used, it can be downloaded here.
The basic process for generating a spectrum and overplotting a sightline’s trajectory through the dataset goes in three steps:
Simple LightRay Generation¶
LightRay is a 1D object representing the path a ray of
light takes through a simulation volume on its way from some bright background
object to the observer. It records all of the gas fields it intersects along
the way for use in construction of a spectrum.
In order to generate a
LightRay from your data, you need to first make sure
that you’ve imported both the yt and Trident packages, and
specify the filename of the dataset from which to extract the light ray:
import yt import trident fn = 'enzo_cosmology_plus/RD0009/RD0009'
We need to decide the trajectory that the
LightRay will take
through our simulation volume. This arbitrary trajectory is specified with
coordinates in code length units (e.g. [x_start, y_start, z_start] to
[x_end, y_end, z_end]). Probably the simplest trajectory is cutting
diagonally from the origin of the simulation volume to its outermost corner
using the yt
domain_right_edge attributes. Here
we load the dataset into yt to get access to these attributes:
ds = yt.load(fn) ray_start = ds.domain_left_edge ray_end = ds.domain_right_edge
Let’s define what lines or species we want to be added to our final spectrum. In this case, we want to deposit all hydrogen, carbon, nitrogen, oxygen, and magnesium lines to the resulting spectrum from the dataset:
line_list = ['H', 'C', 'N', 'O', 'Mg']
We can now generate the light ray using the
function by passing the dataset and the trajectory endpoints to it as well
as telling trident to save the resulting ray dataset to an HDF5 file. We
explicitly instruct trident to pull all necessary fields from the dataset
in order to be able to add the lines from our
Lastly, we set the
ftype keyword as the field type of the fields
where Trident will look to find density, temperature, and metallicity for
building the required ion fields:
ray = trident.make_simple_ray(ds, start_position=ray_start, end_position=ray_end, data_filename="ray.h5", lines=line_list, ftype='gas')
It is imperative that you set the
ftype keyword properly for your dataset.
ftype of ‘gas’ is adequate for grid-based codes, but not particle.
Particle-based datasets must set
ftype to the field type
of their gas particles (e.g. ‘PartType0’) to assure that Trident builds
the ion fields on the particles themselves before smoothing these fields
to the grid. By not setting this correctly, you risk bad ion values by
building from smoothed gas fields.
Overplotting a LightRay’s Trajectory on a Projection¶
Here we create a projection of the density field along the x axis of the
dataset, and then overplot the path the
LightRay takes through the simulation,
before saving it to disk. The
annotate_ray() operation should work for
any volumentric plot, including slices, and off-axis plots:
p = yt.ProjectionPlot(ds, 'x', 'density') p.annotate_ray(ray, arrow=True) p.save('projection.png')
Now that we have our
LightRay we can use it to generate a spectrum.
To create a spectrum, we need to make a
object defining our desired wavelength range and bin size. You can do this
by manually setting these features, or just using one of the presets for
an instrument. Currently, we have three pre-defined instruments, the G130M,
G160M, and G140L observing modes for the Cosmic Origins Spectrograph aboard
the Hubble Space Telescope:
COS aliases to
sg = trident.SpectrumGenerator('COS-G130M') sg.make_spectrum(ray, lines=line_list) sg.save_spectrum('spec_raw.txt') sg.plot_spectrum('spec_raw.png')
From here we can do some post-processing to the spectrum to include additional features that would be present in an actual observed spectrum. We add a background quasar spectrum, a Milky Way foreground, apply the COS line spread function, and add gaussian noise with SNR=30:
sg.add_qso_spectrum() sg.add_milky_way_foreground() sg.apply_lsf() sg.add_gaussian_noise(30)
Finally, we use plot and save the resulting spectrum to disk:
To create more complex or ion-specific spectra, refer to Advanced Spectrum Generation.
In some cases (e.g. studying redshift evolution of the IGM), it may be
desirable to create a
LightRay that covers a range in redshift
that is larger than the domain width of a single simulation snaptshot.
Rather than simply sampling the same dataset repeatedly, which is
inherently unphysical since large scale structure evolves with cosmic
time, Trident allows the user to create a ray that samples multiple
datasets from different redshifts to produce a much longer ray that is
continuous in redshift space. This is done by using the
make_compound_ray function. This function is
similar to the previously mentioned
function, but instead of accepting an individual dataset, it takes a
simulation parameter file, the associated simulation type, and the
desired range in redshift to be probed by the ray, while still
allowing the user to specify the same sort of line list as before::
fn = 'enzo_cosmology_plus/AMRCosmology.enzo' ray = trident.make_compound_ray(fn, simulation_type='Enzo', near_redshift=0.0, far_redshift=0.1, ftype='gas', lines=line_list)
In this example, we’ve created a ray from an Enzo simulation (the same one used above) that goes from z = 0 to z = 0.1. This ray can now be used to generate spectra in the exact same ways as before.
Obviously, there need to be sufficient simulation outputs over the desired
redshift range of the compound ray in order to have continuous sampling.
To assure adequate simulation output frequency for this, one can use yt’s
plan_cosmology_splice() function. See an example of its usage in
the yt documentation.
The compound ray functionality has only been implemented for the Enzo and Gadget simulation codes. If you would like to help us implement this functionality for your simulation code, please contact us about this on the mailing list.