ytree.tree_farm.tree_farm.TreeFarm

class ytree.tree_farm.tree_farm.TreeFarm(time_series, setup_function=None)

TreeFarm is the merger-tree creator for Gadget FoF and Subfind halo catalogs.

TreeFarm can be used to create a merger-tree for the full set of halos, starting from the first catalog, or can be used to trace the ancestry of specific halos, starting from the last catalog. The merger-tree process will create a new set of halo catalogs, containing necessary fields (positions, velocities, masses), user-requested fields, and descendent IDs for each halo. These halo catalogs can be loaded at yt datasets.

Parameters:
  • time_series (yt DatasetSeries object) – A yt time-series object containing the datasets over which the merger-tree will be calculated.
  • setup_function (optional, callable) – A function that accepts a yt Dataset object and performs any setup, such as adding derived fields.

Examples

To create a full merger tree:

>>> import nummpy as np
>>> import yt
>>> import ytree
>>> from ytree.tree_farm import TreeFarm
>>> ts = yt.DatasetSeries("data/groups_*/fof_subhalo_tab*.0.hdf5")
>>> my_tree = TreeFarm(ts)
>>> my_tree.trace_descendents("Group", filename="all_halos/")
>>> a = ytree.load("all_halos/fof_subhalo_tab_000.0.h5")
>>> m = a["particle_mass"]
>>> i = np.argmax(m)
>>> print (a.trees[i]["prog", "particle_mass").to("Msun/h"))

To create a merger tree for a specific halo or set of halos:

>>> import nummpy as np
>>> import yt
>>> import ytree
>>> from ytree.tree_farm import TreeFarm
>>> ts = yt.DatasetSeries("data/groups_*/fof_subhalo_tab*.0.hdf5")
>>> ds = yt[-1]
>>> i = np.argmax(ds.r["Group", "particle_mass"].d)
>>> my_ids = ds.r["Group", "particle_identifier"][i_max]
>>> my_tree = TreeFarm(ts)
>>> my_tree.set_ancestry_filter("most_massive")
>>> my_tree.set_ancestry_short("above_mass_fraction", 0.5)
>>> my_tree.trace_ancestors("Group", my_ids, filename="my_halos/")
>>> a = ytree.load("my_halos/fof_subhalo_tab_025.0.h5")
>>> print (a[0]["prog", "particle_mass").to("Msun/h"))
__init__(time_series, setup_function=None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(time_series[, setup_function]) Initialize self.
set_ancestry_checker(ancestry_checker, …) Set the method for determing if a halo is the ancestor of another halo.
set_ancestry_filter(ancestry_filter, *args, …) Select a method for determining which ancestors are kept.
set_ancestry_short(ancestry_short, *args, …) Select a method for cutting short the ancestry search.
set_selector(selector, *args, **kwargs) Set the method for selecting candidate halos for tracing halo ancestry.
trace_ancestors(halo_type, root_ids[, …]) Trace the ancestry of a given set of halos.
trace_descendents(halo_type[, fields, filename]) Trace the descendents of all halos.