Reading lightcone halo catalogues

Approximate lightcone halo catalogues can be generated by running a halo finder on many simulation snapshots and using particles (such as black hole particles) from the particle lightcone outputs as tracers to determine when each halo crosses the lightcone. This is implemented in the lightcone_io.match_black_holes module. See Making halo lightcones for details.

Each halo lightcone file contains halos taken from a single simulation snapshot, which corresponds to a range of redshifts centred on the snapshot redshift in the lightcone. Within the file the halos are sorted in order of their pixel index in a low resolution HEALPix map. This makes it possible to extract halos in particular parts of the sky.

The halos can be stored in HDF5 files on the local file system or in remote files accessed via a web service.

Opening local HDF5 files

A halo lightcone file stored on the local file system can be opened using the lightcone_io.HaloLightconeFile class:

import lightcone_io as lc
halos = lc.HaloLightconeFile(filename)

Opening via the hdfstream service

This module can also access files stored on a remote server using the hdfstream python module. To do this, first open the directory containing the files:

import hdfstream
root = hdfstream.open("cosma", "/")

This returns a hdfstream.RemoteDirectory object. Halo lightcone outputs on the server can be opened by passing the remote directory object to the lightcone_io.HaloLightconeFile class. The filename is interpreted as a path relative to the remote directory on the server:

import lightcone_io as lc
halos = lc.HaloLightconeFile(filename, remote_dir=root)

Accessing halo lightcone data

We can get a list of the available halo properties with:

print(halos.properties)

To read positions and bound masses for all halos in the catalogue, for example, we can do this:

# List of halo properties to read
properties = ("Lightcone/HaloCentre", "BoundSubhalo/TotalMass")

# Read the data
halo_props = halos.read_halos(properties)

This returns a dict of unyt arrays, which are the halo properties with unit information attached. Since the halos are sorted by HEALPix pixel, it’s possible to extract halos close to a specified position on the sky:

# Line of sight vector specifying a point on the sky
vector = (1.0, 0.0, 0.0)

# Angular radius around this point (in radians)
import numpy as np
radius = np.radians(10.0)

# List of halo properties to read
properties = ("Lightcone/HaloCentre", "BoundSubhalo/TotalMass")

# Read the data
halo_props = halos.read_halos_in_radius(vector, radius, properties)

Again, this returns a dict of unyt arrays with the halo properties, but only halos in the specified patch of sky are included.

Reading SOAP properties for lightcone halos

Not all SOAP halo properties are copied into the lightcone halo catalogue because it would make the files unreasonably large. However, for each halo in the halo lightcone we store the index in the corresponding SOAP output as InputHalos/SOAPIndex. It is therefore possible to look up a wide range of SOAP properties for halos in the lightcone catalogue.

The lightcone_io.HaloLightconeFile class has an optional parameter soap_filename which can be used to do this. For example:

import lightcone_io as lc
halos = lc.HaloLightconeFile(filename="hbt_lightcone_halos/lightcone0/lightcone_halos_0070.hdf5",
                             soap_filename="SOAP-HBT/halo_properties_0070.hdf5")

This opens one of the halo lightcone files AND the corresponding SOAP output which the halos were taken from. We can then select a patch of sky to read in, as above:

# Line of sight vector specifying a point on the sky
vector = (1.0, 0.0, 0.0)

# Angular radius around this point (in radians)
import numpy as np
radius = np.radians(10.0)

and read in some halo properties:

# List of halo properties to read
properties = ("Lightcone/HaloCentre", "SO/200_crit/TotalMass")

# Read the data
halo_props = halos.read_halos(properties)

As before, this returns a dictionary of unyt arrays with the halo properties but any properties which do not exist in the halo lightcone file will be read in from SOAP instead. In this case the quantity SO/200_crit/TotalMass is read from the SOAP file and reordered to match the lightcone halo catalogue.